[{"article_processing_charge":"Yes (via OA deal)","date_created":"2020-12-09T14:48:28Z","related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"10083"}]},"quality_controlled":"1","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351"}],"publication_status":"published","volume":303,"language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"Bio"}],"month":"02","type":"journal_article","doi":"10.1016/j.plantsci.2020.110750","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","oa":1,"publication_identifier":{"issn":["0168-9452"]},"pmid":1,"article_number":"110750","scopus_import":"1","corr_author":"1","author":[{"full_name":"Gelová, Zuzana","last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"full_name":"Gallei, Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","orcid":"0000-0003-1286-7368"},{"last_name":"Pernisová","full_name":"Pernisová, Markéta","first_name":"Markéta"},{"first_name":"Géraldine","last_name":"Brunoud","full_name":"Brunoud, Géraldine"},{"orcid":"0000-0001-7048-4627","first_name":"Xixi","full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang"},{"orcid":"0000-0003-0619-7783","first_name":"Matous","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc"},{"orcid":"0000-0002-5607-272X","first_name":"Lanxin","full_name":"Li, Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko","full_name":"Michalko, Jaroslav","first_name":"Jaroslav"},{"full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova","first_name":"Zlata"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328"},{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert"},{"last_name":"Čovanová","full_name":"Čovanová, Milada","first_name":"Milada"},{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","first_name":"Lukas"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas","orcid":"0000-0002-9767-8699"},{"first_name":"Tongda","last_name":"Xu","full_name":"Xu, Tongda"},{"first_name":"Teva","full_name":"Vernoux, Teva","last_name":"Vernoux"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"publication":"Plant Science","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"intvolume":"       303","file":[{"checksum":"a7f2562bdca62d67dfa88e271b62a629","access_level":"open_access","relation":"main_file","date_updated":"2021-02-04T07:49:25Z","content_type":"application/pdf","creator":"dernst","success":1,"file_id":"9083","file_name":"2021_PlantScience_Gelova.pdf","date_created":"2021-02-04T07:49:25Z","file_size":12563728}],"external_id":{"pmid":["33487339"],"isi":["000614154500001"]},"oa_version":"Published Version","status":"public","_id":"8931","publisher":"Elsevier","year":"2021","acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","citation":{"apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>."},"isi":1,"day":"01","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.1016/j.plantsci.2020.110750","date_published":"2021-02-01T00:00:00Z","has_accepted_license":"1","ddc":["580"],"date_updated":"2026-10-26T23:30:34Z","abstract":[{"text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.","lang":"eng"}],"ec_funded":1,"file_date_updated":"2021-02-04T07:49:25Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"scopus_import":"1","publication":"eLife","author":[{"first_name":"Simone","full_name":"Bersini, Simone","last_name":"Bersini"},{"first_name":"Roberta","full_name":"Schulte, Roberta","last_name":"Schulte"},{"first_name":"Ling","full_name":"Huang, Ling","last_name":"Huang"},{"first_name":"Hannah","last_name":"Tsai","full_name":"Tsai, Hannah"},{"orcid":"0000-0002-2111-992X","first_name":"Martin W","full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER"}],"oa":1,"title":"Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome","publication_identifier":{"issn":["2050-084X"]},"pmid":1,"type":"journal_article","doi":"10.7554/elife.54383","article_number":"e54383","extern":"1","publication_status":"published","language":[{"iso":"eng"}],"volume":9,"month":"09","article_processing_charge":"No","date_created":"2022-04-07T07:43:48Z","quality_controlled":"1","date_updated":"2024-10-14T11:17:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2022-04-08T06:53:10Z","abstract":[{"lang":"eng","text":"Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro."}],"date_published":"2020-09-08T00:00:00Z","has_accepted_license":"1","ddc":["570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"fulldoi":"https://doi.org/10.7554/elife.54383","article_type":"original","status":"public","_id":"11055","oa_version":"Published Version","day":"08","publisher":"eLife Sciences Publications","citation":{"chicago":"Bersini, Simone, Roberta Schulte, Ling Huang, Hannah Tsai, and Martin Hetzer. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>.","short":"S. Bersini, R. Schulte, L. Huang, H. Tsai, M. Hetzer, ELife 9 (2020).","mla":"Bersini, Simone, et al. “Direct Reprogramming of Human Smooth Muscle and Vascular Endothelial Cells Reveals Defects Associated with Aging and Hutchinson-Gilford Progeria Syndrome.” <i>ELife</i>, vol. 9, e54383, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>.","ista":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. 2020. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife. 9, e54383.","ama":"Bersini S, Schulte R, Huang L, Tsai H, Hetzer M. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.54383\">10.7554/elife.54383</a>","apa":"Bersini, S., Schulte, R., Huang, L., Tsai, H., &#38; Hetzer, M. (2020). Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.54383\">https://doi.org/10.7554/elife.54383</a>","ieee":"S. Bersini, R. Schulte, L. Huang, H. Tsai, and M. Hetzer, “Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020."},"year":"2020","external_id":{"pmid":["32896271"]},"intvolume":"         9","file":[{"file_id":"11132","success":1,"file_size":4399825,"date_created":"2022-04-08T06:53:10Z","file_name":"2020_eLife_Bersini.pdf","relation":"main_file","access_level":"open_access","checksum":"f8b3821349a194050be02570d8fe7d4b","creator":"dernst","content_type":"application/pdf","date_updated":"2022-04-08T06:53:10Z"}]},{"_id":"11056","status":"public","oa_version":"Published Version","day":"01","publisher":"Wiley","citation":{"short":"S. Bersini, R. Arrojo e Drigo, L. Huang, M.N. Shokhirev, M. Hetzer, Advanced Biosystems 4 (2020).","mla":"Bersini, Simone, et al. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” <i>Advanced Biosystems</i>, vol. 4, no. 5, 2000044, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/adbi.202000044\">10.1002/adbi.202000044</a>.","chicago":"Bersini, Simone, Rafael Arrojo e Drigo, Ling Huang, Maxim N. Shokhirev, and Martin Hetzer. “Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease.” <i>Advanced Biosystems</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/adbi.202000044\">https://doi.org/10.1002/adbi.202000044</a>.","apa":"Bersini, S., Arrojo e Drigo, R., Huang, L., Shokhirev, M. N., &#38; Hetzer, M. (2020). Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. <i>Advanced Biosystems</i>. Wiley. <a href=\"https://doi.org/10.1002/adbi.202000044\">https://doi.org/10.1002/adbi.202000044</a>","ieee":"S. Bersini, R. Arrojo e Drigo, L. Huang, M. N. Shokhirev, and M. Hetzer, “Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease,” <i>Advanced Biosystems</i>, vol. 4, no. 5. Wiley, 2020.","ama":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. <i>Advanced Biosystems</i>. 2020;4(5). doi:<a href=\"https://doi.org/10.1002/adbi.202000044\">10.1002/adbi.202000044</a>","ista":"Bersini S, Arrojo e Drigo R, Huang L, Shokhirev MN, Hetzer M. 2020. Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease. Advanced Biosystems. 4(5), 2000044."},"year":"2020","issue":"5","external_id":{"pmid":["32402127"]},"intvolume":"         4","file":[{"success":1,"file_id":"11134","date_created":"2022-04-08T07:06:05Z","file_size":2490829,"file_name":"2020_AdvancedBiosystems_Bersini.pdf","checksum":"5584d9a1609812dc75c02ce1e35d2ec0","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2022-04-08T07:06:05Z"}],"date_updated":"2024-10-14T11:18:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2022-04-08T07:06:05Z","abstract":[{"text":"Aging of the circulatory system correlates with the pathogenesis of a large spectrum of diseases. However, it is largely unknown which factors drive the age-dependent or pathological decline of the vasculature and how vascular defects relate to tissue aging. The goal of the study is to design a multianalytical approach to identify how the cellular microenvironment (i.e., fibroblasts) and serum from healthy donors of different ages or Alzheimer disease (AD) patients can modulate the functionality of organ-specific vascular endothelial cells (VECs). Long-living human microvascular networks embedding VECs and fibroblasts from skin biopsies are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate that fibroblasts from young donors restore the functionality of aged endothelial cells, an effect also achieved by serum from young donors. New biomarkers of vascular aging are validated in human biopsies and it is shown that young serum induces angiopoietin-like-4, which can restore compromised vascular barriers. This strategy is then employed to characterize transcriptional/functional changes induced on the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in the regulation of permeability. Features of vascular degeneration during aging and AD are recapitulated, and a tool to identify novel biomarkers that can be exploited to develop future therapeutics modulating vascular function is established.","lang":"eng"}],"has_accepted_license":"1","date_published":"2020-05-01T00:00:00Z","ddc":["570"],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"keyword":["General Biochemistry","Genetics and Molecular Biology","Biomedical Engineering","Biomaterials"],"article_type":"original","fulldoi":"https://doi.org/10.1002/adbi.202000044","publication_status":"published","language":[{"iso":"eng"}],"volume":4,"month":"05","article_processing_charge":"No","date_created":"2022-04-07T07:43:57Z","quality_controlled":"1","scopus_import":"1","publication":"Advanced Biosystems","author":[{"first_name":"Simone","last_name":"Bersini","full_name":"Bersini, Simone"},{"first_name":"Rafael","last_name":"Arrojo e Drigo","full_name":"Arrojo e Drigo, Rafael"},{"last_name":"Huang","full_name":"Huang, Ling","first_name":"Ling"},{"first_name":"Maxim N.","full_name":"Shokhirev, Maxim N.","last_name":"Shokhirev"},{"full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X","first_name":"Martin W"}],"title":"Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease","oa":1,"pmid":1,"publication_identifier":{"issn":["2366-7478","2366-7478"]},"type":"journal_article","doi":"10.1002/adbi.202000044","article_number":"2000044","extern":"1"},{"date_updated":"2024-10-14T11:18:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division."}],"file_date_updated":"2022-04-08T07:12:33Z","ddc":["570"],"date_published":"2020-04-28T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.1101/gad.335794.119","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["Developmental Biology","Genetics"],"status":"public","_id":"11057","oa_version":"Published Version","day":"28","year":"2020","citation":{"chicago":"Kang, Hyeseon, Maxim N. Shokhirev, Zhichao Xu, Sahaana Chandran, Jesse R. Dixon, and Martin Hetzer. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory Press, 2020. <a href=\"https://doi.org/10.1101/gad.335794.119\">https://doi.org/10.1101/gad.335794.119</a>.","short":"H. Kang, M.N. Shokhirev, Z. Xu, S. Chandran, J.R. Dixon, M. Hetzer, Genes &#38; Development 34 (2020) 913–930.","mla":"Kang, Hyeseon, et al. “Dynamic Regulation of Histone Modifications and Long-Range Chromosomal Interactions during Postmitotic Transcriptional Reactivation.” <i>Genes &#38; Development</i>, vol. 34, no. 13–14, Cold Spring Harbor Laboratory Press, 2020, pp. 913–30, doi:<a href=\"https://doi.org/10.1101/gad.335794.119\">10.1101/gad.335794.119</a>.","ama":"Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. <i>Genes &#38; Development</i>. 2020;34(13-14):913-930. doi:<a href=\"https://doi.org/10.1101/gad.335794.119\">10.1101/gad.335794.119</a>","ista":"Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer M. 2020. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes &#38; Development. 34(13–14), 913–930.","apa":"Kang, H., Shokhirev, M. N., Xu, Z., Chandran, S., Dixon, J. R., &#38; Hetzer, M. (2020). Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. <i>Genes &#38; Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.335794.119\">https://doi.org/10.1101/gad.335794.119</a>","ieee":"H. Kang, M. N. Shokhirev, Z. Xu, S. Chandran, J. R. Dixon, and M. Hetzer, “Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation,” <i>Genes &#38; Development</i>, vol. 34, no. 13–14. Cold Spring Harbor Laboratory Press, pp. 913–930, 2020."},"publisher":"Cold Spring Harbor Laboratory Press","external_id":{"pmid":["32499403"]},"issue":"13-14","file":[{"access_level":"open_access","checksum":"84e92d40e67936c739628315c238daf9","relation":"main_file","content_type":"application/pdf","date_updated":"2022-04-08T07:12:33Z","creator":"dernst","success":1,"file_id":"11136","file_name":"2020_GenesDevelopment_Kang.pdf","file_size":4406772,"date_created":"2022-04-08T07:12:33Z"}],"intvolume":"        34","scopus_import":"1","publication":"Genes & Development","author":[{"full_name":"Kang, Hyeseon","last_name":"Kang","first_name":"Hyeseon"},{"first_name":"Maxim N.","last_name":"Shokhirev","full_name":"Shokhirev, Maxim N."},{"full_name":"Xu, Zhichao","last_name":"Xu","first_name":"Zhichao"},{"first_name":"Sahaana","last_name":"Chandran","full_name":"Chandran, Sahaana"},{"last_name":"Dixon","full_name":"Dixon, Jesse R.","first_name":"Jesse R."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","full_name":"HETZER, Martin W","first_name":"Martin W","orcid":"0000-0002-2111-992X"}],"pmid":1,"publication_identifier":{"issn":["0890-9369","1549-5477"]},"oa":1,"title":"Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation","doi":"10.1101/gad.335794.119","type":"journal_article","extern":"1","page":"913-930","volume":34,"language":[{"iso":"eng"}],"publication_status":"published","month":"04","date_created":"2022-04-07T07:44:09Z","article_processing_charge":"No","quality_controlled":"1"},{"intvolume":"         3","file":[{"date_updated":"2022-04-08T07:33:01Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","checksum":"3bf33e7e93bef7823287807206b69b38","relation":"main_file","file_name":"2020_LifeScienceAlliance_Bersini.pdf","file_size":2653960,"date_created":"2022-04-08T07:33:01Z","success":1,"file_id":"11137"}],"issue":"1","external_id":{"pmid":["31959624"]},"publisher":"Life Science Alliance","citation":{"short":"S. Bersini, N.K. Lytle, R. Schulte, L. Huang, G.M. Wahl, M. Hetzer, Life Science Alliance 3 (2020).","mla":"Bersini, Simone, et al. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” <i>Life Science Alliance</i>, vol. 3, no. 1, e201900623, Life Science Alliance, 2020, doi:<a href=\"https://doi.org/10.26508/lsa.201900623\">10.26508/lsa.201900623</a>.","chicago":"Bersini, Simone, Nikki K Lytle, Roberta Schulte, Ling Huang, Geoffrey M Wahl, and Martin Hetzer. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” <i>Life Science Alliance</i>. Life Science Alliance, 2020. <a href=\"https://doi.org/10.26508/lsa.201900623\">https://doi.org/10.26508/lsa.201900623</a>.","apa":"Bersini, S., Lytle, N. K., Schulte, R., Huang, L., Wahl, G. M., &#38; Hetzer, M. (2020). Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.201900623\">https://doi.org/10.26508/lsa.201900623</a>","ieee":"S. Bersini, N. K. Lytle, R. Schulte, L. Huang, G. M. Wahl, and M. Hetzer, “Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling,” <i>Life Science Alliance</i>, vol. 3, no. 1. Life Science Alliance, 2020.","ista":"Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. 2020. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. 3(1), e201900623.","ama":"Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. <i>Life Science Alliance</i>. 2020;3(1). doi:<a href=\"https://doi.org/10.26508/lsa.201900623\">10.26508/lsa.201900623</a>"},"year":"2020","day":"01","oa_version":"Published Version","status":"public","_id":"11058","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"fulldoi":"https://doi.org/10.26508/lsa.201900623","article_type":"original","has_accepted_license":"1","date_published":"2020-01-01T00:00:00Z","ddc":["570"],"file_date_updated":"2022-04-08T07:33:01Z","abstract":[{"text":"Nucleoporin 93 (Nup93) expression inversely correlates with the survival of triple-negative breast cancer patients. However, our knowledge of Nup93 function in breast cancer besides its role as structural component of the nuclear pore complex is not understood. Combination of functional assays and genetic analyses suggested that chromatin interaction of Nup93 partially modulates the expression of genes associated with actin cytoskeleton remodeling and epithelial to mesenchymal transition, resulting in impaired invasion of triple-negative, claudin-low breast cancer cells. Nup93 depletion induced stress fiber formation associated with reduced cell migration/proliferation and impaired expression of mesenchymal-like genes. Silencing LIMCH1, a gene responsible for actin cytoskeleton remodeling and up-regulated upon Nup93 depletion, partially restored the invasive phenotype of cancer cells. Loss of Nup93 led to significant defects in tumor establishment/propagation in vivo, whereas patient samples revealed that high Nup93 and low LIMCH1 expression correlate with late tumor stage. Our approach identified Nup93 as contributor of triple-negative, claudin-low breast cancer cell invasion and paves the way to study the role of nuclear envelope proteins during breast cancer tumorigenesis.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-14T11:18:41Z","quality_controlled":"1","article_processing_charge":"No","date_created":"2022-04-07T07:44:18Z","month":"01","publication_status":"published","volume":3,"language":[{"iso":"eng"}],"extern":"1","article_number":"e201900623","type":"journal_article","doi":"10.26508/lsa.201900623","title":"Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling","oa":1,"pmid":1,"publication_identifier":{"issn":["2575-1077"]},"author":[{"last_name":"Bersini","full_name":"Bersini, Simone","first_name":"Simone"},{"last_name":"Lytle","full_name":"Lytle, Nikki K","first_name":"Nikki K"},{"first_name":"Roberta","last_name":"Schulte","full_name":"Schulte, Roberta"},{"first_name":"Ling","full_name":"Huang, Ling","last_name":"Huang"},{"first_name":"Geoffrey M","full_name":"Wahl, Geoffrey M","last_name":"Wahl"},{"full_name":"HETZER, Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","orcid":"0000-0002-2111-992X"}],"publication":"Life Science Alliance","scopus_import":"1"},{"status":"public","_id":"12189","oa_version":"Published Version","day":"29","acknowledgement":"The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.","year":"2020","citation":{"short":"N. Christophorou, W. She, J. Long, A. Hurel, S. Beaubiat, Y. Idir, M. Tagliaro-Jahns, A. Chambon, V. Solier, D. Vezon, M. Grelon, X. Feng, N. Bouché, C. Mézard, PLOS Genetics 16 (2020).","mla":"Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” <i>PLOS Genetics</i>, vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008894\">10.1371/journal.pgen.1008894</a>.","chicago":"Christophorou, Nicolas, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” <i>PLOS Genetics</i>. Public Library of Science (PLoS), 2020. <a href=\"https://doi.org/10.1371/journal.pgen.1008894\">https://doi.org/10.1371/journal.pgen.1008894</a>.","apa":"Christophorou, N., She, W., Long, J., Hurel, A., Beaubiat, S., Idir, Y., … Mézard, C. (2020). AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. <i>PLOS Genetics</i>. Public Library of Science (PLoS). <a href=\"https://doi.org/10.1371/journal.pgen.1008894\">https://doi.org/10.1371/journal.pgen.1008894</a>","ieee":"N. Christophorou <i>et al.</i>, “AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization,” <i>PLOS Genetics</i>, vol. 16, no. 6. Public Library of Science (PLoS), 2020.","ista":"Christophorou N, She W, Long J, Hurel A, Beaubiat S, Idir Y, Tagliaro-Jahns M, Chambon A, Solier V, Vezon D, Grelon M, Feng X, Bouché N, Mézard C. 2020. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 16(6), e1008894.","ama":"Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. <i>PLOS Genetics</i>. 2020;16(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008894\">10.1371/journal.pgen.1008894</a>"},"publisher":"Public Library of Science (PLoS)","external_id":{"pmid":["32598340"]},"issue":"6","intvolume":"        16","date_updated":"2023-05-08T10:54:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells."}],"date_published":"2020-06-29T00:00:00Z","fulldoi":"https://doi.org/10.1371/journal.pgen.1008894","article_type":"original","keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"volume":16,"language":[{"iso":"eng"}],"department":[{"_id":"XiFe"}],"publication_status":"published","month":"06","date_created":"2023-01-16T09:16:10Z","article_processing_charge":"No","quality_controlled":"1","scopus_import":"1","publication":"PLOS Genetics","author":[{"first_name":"Nicolas","full_name":"Christophorou, Nicolas","last_name":"Christophorou"},{"first_name":"Wenjing","last_name":"She","full_name":"She, Wenjing"},{"first_name":"Jincheng","last_name":"Long","full_name":"Long, Jincheng"},{"full_name":"Hurel, Aurélie","last_name":"Hurel","first_name":"Aurélie"},{"first_name":"Sébastien","last_name":"Beaubiat","full_name":"Beaubiat, Sébastien"},{"first_name":"Yassir","full_name":"Idir, Yassir","last_name":"Idir"},{"first_name":"Marina","full_name":"Tagliaro-Jahns, Marina","last_name":"Tagliaro-Jahns"},{"last_name":"Chambon","full_name":"Chambon, Aurélie","first_name":"Aurélie"},{"first_name":"Victor","last_name":"Solier","full_name":"Solier, Victor"},{"full_name":"Vezon, Daniel","last_name":"Vezon","first_name":"Daniel"},{"full_name":"Grelon, Mathilde","last_name":"Grelon","first_name":"Mathilde"},{"full_name":"Feng, Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"full_name":"Bouché, Nicolas","last_name":"Bouché","first_name":"Nicolas"},{"last_name":"Mézard","full_name":"Mézard, Christine","first_name":"Christine"}],"pmid":1,"publication_identifier":{"issn":["1553-7404"]},"title":"AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization","oa":1,"doi":"10.1371/journal.pgen.1008894","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/","open_access":"1"}],"type":"journal_article","article_number":"e1008894","extern":"1"},{"date_updated":"2024-06-04T05:52:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Bacteria and archaea employ CRISPR (clustered, regularly, interspaced, short palindromic repeats)-Cas (CRISPR-associated) systems as a type of adaptive immunity to target and degrade foreign nucleic acids. While a myriad of CRISPR-Cas systems have been identified to date, type I-C is one of the most commonly found subtypes in nature. Interestingly, the type I-C system employs a minimal Cascade effector complex, which encodes only three unique subunits in its operon. Here, we present a 3.1 Å resolution cryo-EM structure of the <jats:italic>Desulfovibrio vulgaris</jats:italic> type I-C Cascade, revealing the molecular mechanisms that underlie RNA-directed complex assembly. We demonstrate how this minimal Cascade utilizes previously overlooked, non-canonical small subunits to stabilize R-loop formation. Furthermore, we describe putative PAM and Cas3 binding sites. These findings provide the structural basis for harnessing the type I-C Cascade as a genome-engineering tool."}],"date_published":"2020-11-23T00:00:00Z","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"fulldoi":"https://doi.org/10.1038/s41467-020-19785-8","article_type":"original","status":"public","_id":"15142","oa_version":"Published Version","day":"23","publisher":"Springer Nature","year":"2020","citation":{"ieee":"R. E. O’Brien <i>et al.</i>, “Structural basis for assembly of non-canonical small subunits into type I-C Cascade,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","apa":"O’Brien, R. E., Santos, I. C., Wrapp, D., Bravo, J. P. K., Schwartz, E. A., Brodbelt, J. S., &#38; Taylor, D. W. (2020). Structural basis for assembly of non-canonical small subunits into type I-C Cascade. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-19785-8\">https://doi.org/10.1038/s41467-020-19785-8</a>","ista":"O’Brien RE, Santos IC, Wrapp D, Bravo JPK, Schwartz EA, Brodbelt JS, Taylor DW. 2020. Structural basis for assembly of non-canonical small subunits into type I-C Cascade. Nature Communications. 11, 5931.","ama":"O’Brien RE, Santos IC, Wrapp D, et al. Structural basis for assembly of non-canonical small subunits into type I-C Cascade. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-19785-8\">10.1038/s41467-020-19785-8</a>","mla":"O’Brien, Roisin E., et al. “Structural Basis for Assembly of Non-Canonical Small Subunits into Type I-C Cascade.” <i>Nature Communications</i>, vol. 11, 5931, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-19785-8\">10.1038/s41467-020-19785-8</a>.","short":"R.E. O’Brien, I.C. Santos, D. Wrapp, J.P.K. Bravo, E.A. Schwartz, J.S. Brodbelt, D.W. Taylor, Nature Communications 11 (2020).","chicago":"O’Brien, Roisin E., Inês C. Santos, Daniel Wrapp, Jack Peter Kelly Bravo, Evan A. Schwartz, Jennifer S. Brodbelt, and David W. Taylor. “Structural Basis for Assembly of Non-Canonical Small Subunits into Type I-C Cascade.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-19785-8\">https://doi.org/10.1038/s41467-020-19785-8</a>."},"external_id":{"pmid":["33230133"]},"intvolume":"        11","scopus_import":"1","publication":"Nature Communications","author":[{"first_name":"Roisin E.","last_name":"O’Brien","full_name":"O’Brien, Roisin E."},{"first_name":"Inês C.","last_name":"Santos","full_name":"Santos, Inês C."},{"first_name":"Daniel","full_name":"Wrapp, Daniel","last_name":"Wrapp"},{"last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","first_name":"Jack Peter Kelly","orcid":"0000-0003-0456-0753"},{"full_name":"Schwartz, Evan A.","last_name":"Schwartz","first_name":"Evan A."},{"first_name":"Jennifer S.","last_name":"Brodbelt","full_name":"Brodbelt, Jennifer S."},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"title":"Structural basis for assembly of non-canonical small subunits into type I-C Cascade","oa":1,"pmid":1,"publication_identifier":{"issn":["2041-1723"]},"type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1038/s41467-020-19785-8","open_access":"1"}],"doi":"10.1038/s41467-020-19785-8","article_number":"5931","extern":"1","publication_status":"published","language":[{"iso":"eng"}],"volume":11,"month":"11","article_processing_charge":"Yes","date_created":"2024-03-20T10:43:07Z","quality_controlled":"1"},{"scopus_import":"1","publication":"eLife","author":[{"last_name":"Fribourgh","full_name":"Fribourgh, Jennifer L","first_name":"Jennifer L"},{"last_name":"Srivastava","full_name":"Srivastava, Ashutosh","first_name":"Ashutosh"},{"last_name":"Sandate","full_name":"Sandate, Colby R","first_name":"Colby R"},{"first_name":"Alicia Kathleen","full_name":"Michael, Alicia Kathleen","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"full_name":"Hsu, Peter L","last_name":"Hsu","first_name":"Peter L"},{"first_name":"Christin","last_name":"Rakers","full_name":"Rakers, Christin"},{"last_name":"Nguyen","full_name":"Nguyen, Leslee T","first_name":"Leslee T"},{"first_name":"Megan R","full_name":"Torgrimson, Megan R","last_name":"Torgrimson"},{"first_name":"Gian Carlo G","full_name":"Parico, Gian Carlo G","last_name":"Parico"},{"last_name":"Tripathi","full_name":"Tripathi, Sarvind","first_name":"Sarvind"},{"last_name":"Zheng","full_name":"Zheng, Ning","first_name":"Ning"},{"last_name":"Lander","full_name":"Lander, Gabriel C","first_name":"Gabriel C"},{"last_name":"Hirota","full_name":"Hirota, Tsuyoshi","first_name":"Tsuyoshi"},{"full_name":"Tama, Florence","last_name":"Tama","first_name":"Florence"},{"full_name":"Partch, Carrie L","last_name":"Partch","first_name":"Carrie L"}],"publication_identifier":{"issn":["2050-084X"]},"title":"Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing","oa":1,"doi":"10.7554/elife.55275","main_file_link":[{"url":"https://doi.org/10.7554/eLife.55275","open_access":"1"}],"type":"journal_article","article_number":"55275","extern":"1","volume":9,"language":[{"iso":"eng"}],"publication_status":"published","month":"02","date_created":"2024-03-21T07:55:12Z","article_processing_charge":"No","quality_controlled":"1","date_updated":"2024-03-25T12:25:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1."}],"date_published":"2020-02-26T00:00:00Z","article_type":"original","fulldoi":"https://doi.org/10.7554/elife.55275","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"status":"public","_id":"15153","oa_version":"Published Version","day":"26","citation":{"apa":"Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L., Rakers, C., … Partch, C. L. (2020). Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.55275\">https://doi.org/10.7554/elife.55275</a>","ieee":"J. L. Fribourgh <i>et al.</i>, “Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","ama":"Fribourgh JL, Srivastava A, Sandate CR, et al. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.55275\">10.7554/elife.55275</a>","ista":"Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL. 2020. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 9, 55275.","short":"J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers, L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander, T. Hirota, F. Tama, C.L. Partch, ELife 9 (2020).","mla":"Fribourgh, Jennifer L., et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” <i>ELife</i>, vol. 9, 55275, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.55275\">10.7554/elife.55275</a>.","chicago":"Fribourgh, Jennifer L, Ashutosh Srivastava, Colby R Sandate, Alicia K. Michael, Peter L Hsu, Christin Rakers, Leslee T Nguyen, et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.55275\">https://doi.org/10.7554/elife.55275</a>."},"year":"2020","publisher":"eLife Sciences Publications","intvolume":"         9"},{"publisher":"Elsevier","acknowledgement":"The authors thank Nicolas Chiaruttini, Jean Gruenberg, and Lena Harker-Kirschneck for careful correction of this manuscript and helpful discussions. The authors want to thank the NCCR Chemical Biology for constant support during this project. A.R. acknowledges funding from the Swiss National Fund for Research (31003A_130520, 31003A_149975, and 31003A_173087) and the European Research Council Consolidator (311536). A.Š. acknowledges the European Research Council (802960). B.B. thanks the BBSRC (BB/K009001/1) and Wellcome Trust (203276/Z/16/Z) for support. J.M.v.F. acknowledges funding through an EMBO Long-Term Fellowship (ALTF 1065-2015), the European Commission FP7 (Marie Curie Actions, LTFCOFUND2013, and GA-2013-609409), and a Transitional Postdoc fellowship (2015/345) from the Swiss SystemsX.ch initiative, evaluated by the Swiss National Science Foundation and Swiss National Science Foundation Research (SNSF SINERGIA 160728/1 [leader, Sophie Martin]).","year":"2020","citation":{"ieee":"A.-K. Pfitzner <i>et al.</i>, “An ESCRT-III polymerization sequence drives membrane deformation and fission,” <i>Cell</i>, vol. 182, no. 5. Elsevier, p. 1140–1155.e18, 2020.","apa":"Pfitzner, A.-K., Mercier, V., Jiang, X., Moser von Filseck, J., Baum, B., Šarić, A., &#38; Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane deformation and fission. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">https://doi.org/10.1016/j.cell.2020.07.021</a>","ama":"Pfitzner A-K, Mercier V, Jiang X, et al. An ESCRT-III polymerization sequence drives membrane deformation and fission. <i>Cell</i>. 2020;182(5):1140-1155.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">10.1016/j.cell.2020.07.021</a>","ista":"Pfitzner A-K, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. 2020. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 182(5), 1140–1155.e18.","short":"A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić, A. Roux, Cell 182 (2020) 1140–1155.e18.","mla":"Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” <i>Cell</i>, vol. 182, no. 5, Elsevier, 2020, p. 1140–1155.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">10.1016/j.cell.2020.07.021</a>.","chicago":"Pfitzner, Anna-Katharina, Vincent Mercier, Xiuyun Jiang, Joachim Moser von Filseck, Buzz Baum, Anđela Šarić, and Aurélien Roux. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” <i>Cell</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">https://doi.org/10.1016/j.cell.2020.07.021</a>."},"day":"18","oa_version":"Published Version","status":"public","_id":"10348","intvolume":"       182","issue":"5","external_id":{"pmid":["32814015"]},"abstract":[{"lang":"eng","text":"The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-11-26T08:58:37Z","keyword":["general biochemistry","genetics and molecular biology"],"article_type":"original","fulldoi":"https://doi.org/10.1016/j.cell.2020.07.021","date_published":"2020-08-18T00:00:00Z","month":"08","publication_status":"published","volume":182,"language":[{"iso":"eng"}],"page":"1140-1155.e18","quality_controlled":"1","article_processing_charge":"No","date_created":"2021-11-26T08:02:27Z","author":[{"first_name":"Anna-Katharina","full_name":"Pfitzner, Anna-Katharina","last_name":"Pfitzner"},{"first_name":"Vincent","last_name":"Mercier","full_name":"Mercier, Vincent"},{"full_name":"Jiang, Xiuyun","last_name":"Jiang","first_name":"Xiuyun"},{"first_name":"Joachim","last_name":"Moser von Filseck","full_name":"Moser von Filseck, Joachim"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Aurélien","full_name":"Roux, Aurélien","last_name":"Roux"}],"publication":"Cell","scopus_import":"1","extern":"1","type":"journal_article","main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S0092867420309296","open_access":"1"}],"doi":"10.1016/j.cell.2020.07.021","title":"An ESCRT-III polymerization sequence drives membrane deformation and fission","oa":1,"pmid":1,"publication_identifier":{"issn":["0092-8674"]}},{"citation":{"apa":"Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C., … Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. <i>BMC Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12915-019-0733-6\">https://doi.org/10.1186/s12915-019-0733-6</a>","ieee":"H. Rampelt <i>et al.</i>, “The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments,” <i>BMC Biology</i>, vol. 18. Springer Nature, 2020.","ista":"Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 18, 2.","ama":"Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. <i>BMC Biology</i>. 2020;18. doi:<a href=\"https://doi.org/10.1186/s12915-019-0733-6\">10.1186/s12915-019-0733-6</a>","short":"H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou, M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).","mla":"Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” <i>BMC Biology</i>, vol. 18, 2, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1186/s12915-019-0733-6\">10.1186/s12915-019-0733-6</a>.","chicago":"Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil, Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” <i>BMC Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1186/s12915-019-0733-6\">https://doi.org/10.1186/s12915-019-0733-6</a>."},"year":"2020","publisher":"Springer Nature","day":"06","oa_version":"Published Version","_id":"8402","status":"public","intvolume":"        18","external_id":{"pmid":["31907035"]},"abstract":[{"text":"Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins.","lang":"eng"}],"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","date_updated":"2024-10-15T13:23:11Z","OA_place":"publisher","DOAJ_listed":"1","article_type":"original","fulldoi":"https://doi.org/10.1186/s12915-019-0733-6","keyword":["Biotechnology","Plant Science","General Biochemistry","Genetics and Molecular Biology","Developmental Biology","Cell Biology","Physiology","Ecology","Evolution","Behavior and Systematics","Structural Biology","General Agricultural and Biological Sciences"],"date_published":"2020-01-06T00:00:00Z","OA_type":"gold","month":"01","volume":18,"language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","date_created":"2020-09-17T10:26:53Z","article_processing_charge":"No","author":[{"first_name":"Heike","full_name":"Rampelt, Heike","last_name":"Rampelt"},{"last_name":"Sucec","full_name":"Sucec, Iva","first_name":"Iva"},{"first_name":"Beate","full_name":"Bersch, Beate","last_name":"Bersch"},{"last_name":"Horten","full_name":"Horten, Patrick","first_name":"Patrick"},{"full_name":"Perschil, Inge","last_name":"Perschil","first_name":"Inge"},{"first_name":"Jean-Claude","full_name":"Martinou, Jean-Claude","last_name":"Martinou"},{"last_name":"van der Laan","full_name":"van der Laan, Martin","first_name":"Martin"},{"first_name":"Nils","full_name":"Wiedemann, Nils","last_name":"Wiedemann"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul"},{"first_name":"Nikolaus","last_name":"Pfanner","full_name":"Pfanner, Nikolaus"}],"publication":"BMC Biology","extern":"1","article_number":"2","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12915-019-0733-6"}],"doi":"10.1186/s12915-019-0733-6","type":"journal_article","publication_identifier":{"issn":["1741-7007"]},"pmid":1,"oa":1,"title":"The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments"},{"article_number":"4838","doi":"10.1038/s41467-020-18610-6","type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"pmid":1,"title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","oa":1,"author":[{"first_name":"Christian","full_name":"Prehal, Christian","last_name":"Prehal"},{"last_name":"Fitzek","full_name":"Fitzek, Harald","first_name":"Harald"},{"full_name":"Kothleitner, Gerald","last_name":"Kothleitner","first_name":"Gerald"},{"first_name":"Volker","full_name":"Presser, Volker","last_name":"Presser"},{"first_name":"Bernhard","full_name":"Gollas, Bernhard","last_name":"Gollas"},{"first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"},{"last_name":"Abbas","full_name":"Abbas, Qamar","first_name":"Qamar"}],"publication":"Nature Communications","scopus_import":"1","corr_author":"1","quality_controlled":"1","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-19720-x","relation":"erratum"}]},"date_created":"2020-09-25T07:23:13Z","article_processing_charge":"No","month":"09","department":[{"_id":"StFr"}],"language":[{"iso":"eng"}],"volume":11,"publication_status":"published","fulldoi":"https://doi.org/10.1038/s41467-020-18610-6","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"date_published":"2020-09-24T00:00:00Z","has_accepted_license":"1","file_date_updated":"2020-09-28T13:16:15Z","abstract":[{"lang":"eng","text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-12T06:58:51Z","file":[{"success":1,"file_id":"8585","file_size":1822469,"date_created":"2020-09-28T13:16:15Z","file_name":"2020_NatureComm_Prehal.pdf","access_level":"open_access","checksum":"eada7bc8dd16a49390137cff882ef328","relation":"main_file","creator":"dernst","date_updated":"2020-09-28T13:16:15Z","content_type":"application/pdf"}],"intvolume":"        11","external_id":{"isi":["000573756600004"],"pmid":["32973214"]},"year":"2020","citation":{"apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., &#38; Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>","ieee":"C. Prehal <i>et al.</i>, “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>, vol. 11, 4838, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>.","chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>."},"publisher":"Springer Nature","day":"24","isi":1,"oa_version":"Published Version","_id":"8568","status":"public"},{"oa_version":"Published Version","_id":"8592","status":"public","publisher":"Wiley","acknowledgement":"The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.","year":"2020","citation":{"chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” <i>Advanced Science</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/advs.202001724\">https://doi.org/10.1002/advs.202001724</a>.","short":"A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020).","mla":"Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” <i>Advanced Science</i>, vol. 7, no. 21, 2001724, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/advs.202001724\">10.1002/advs.202001724</a>.","ama":"Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. <i>Advanced Science</i>. 2020;7(21). doi:<a href=\"https://doi.org/10.1002/advs.202001724\">10.1002/advs.202001724</a>","ista":"Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724.","ieee":"A. Tian <i>et al.</i>, “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” <i>Advanced Science</i>, vol. 7, no. 21. Wiley, 2020.","apa":"Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. <i>Advanced Science</i>. Wiley. <a href=\"https://doi.org/10.1002/advs.202001724\">https://doi.org/10.1002/advs.202001724</a>"},"isi":1,"day":"04","intvolume":"         7","file":[{"file_id":"8938","success":1,"file_name":"2020_AdvScience_Tian.pdf","date_created":"2020-12-10T14:07:24Z","file_size":7835833,"relation":"main_file","checksum":"92818c23ecc70e35acfa671f3cfb9909","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-12-10T14:07:24Z","creator":"dernst"}],"issue":"21","external_id":{"pmid":["33173731"],"isi":["000573860700001"]},"date_updated":"2025-06-12T06:59:38Z","abstract":[{"lang":"eng","text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma."}],"ec_funded":1,"file_date_updated":"2020-12-10T14:07:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"fulldoi":"https://doi.org/10.1002/advs.202001724","article_type":"original","date_published":"2020-11-04T00:00:00Z","has_accepted_license":"1","ddc":["570"],"publication_status":"published","volume":7,"department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"month":"11","article_processing_charge":"No","date_created":"2020-10-01T09:44:13Z","quality_controlled":"1","project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"scopus_import":"1","author":[{"last_name":"Tian","full_name":"Tian, Anhao","first_name":"Anhao"},{"full_name":"Kang, Bo","last_name":"Kang","first_name":"Bo"},{"first_name":"Baizhou","full_name":"Li, Baizhou","last_name":"Li"},{"full_name":"Qiu, Biying","last_name":"Qiu","first_name":"Biying"},{"last_name":"Jiang","full_name":"Jiang, Wenhong","first_name":"Wenhong"},{"first_name":"Fangjie","last_name":"Shao","full_name":"Shao, Fangjie"},{"first_name":"Qingqing","last_name":"Gao","full_name":"Gao, Qingqing"},{"last_name":"Liu","full_name":"Liu, Rui","first_name":"Rui"},{"last_name":"Cai","full_name":"Cai, Chengwei","first_name":"Chengwei"},{"full_name":"Jing, Rui","last_name":"Jing","first_name":"Rui"},{"full_name":"Wang, Wei","last_name":"Wang","first_name":"Wei"},{"first_name":"Pengxiang","last_name":"Chen","full_name":"Chen, Pengxiang"},{"first_name":"Qinghui","last_name":"Liang","full_name":"Liang, Qinghui"},{"full_name":"Bao, Lili","last_name":"Bao","first_name":"Lili"},{"first_name":"Jianghong","full_name":"Man, Jianghong","last_name":"Man"},{"last_name":"Wang","full_name":"Wang, Yan","first_name":"Yan"},{"full_name":"Shi, Yu","last_name":"Shi","first_name":"Yu"},{"first_name":"Jin","full_name":"Li, Jin","last_name":"Li"},{"full_name":"Yang, Minmin","last_name":"Yang","first_name":"Minmin"},{"first_name":"Lisha","full_name":"Wang, Lisha","last_name":"Wang"},{"first_name":"Jianmin","last_name":"Zhang","full_name":"Zhang, Jianmin"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"full_name":"Zhu, Junming","last_name":"Zhu","first_name":"Junming"},{"first_name":"Xiuwu","last_name":"Bian","full_name":"Bian, Xiuwu"},{"last_name":"Wang","full_name":"Wang, Ying‐Jie","first_name":"Ying‐Jie"},{"last_name":"Liu","full_name":"Liu, Chong","first_name":"Chong"}],"publication":"Advanced Science","type":"journal_article","doi":"10.1002/advs.202001724","oa":1,"title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","publication_identifier":{"issn":["2198-3844"]},"pmid":1,"article_number":"2001724"},{"file":[{"file_name":"2020_NatureComm_Schulte.pdf","date_created":"2020-11-09T07:56:24Z","file_size":1670898,"success":1,"file_id":"8745","date_updated":"2020-11-09T07:56:24Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","checksum":"b2688f0347e69e6629bba582077278c5","relation":"main_file"}],"intvolume":"        11","external_id":{"pmid":["33149120"],"isi":["000592028600001"]},"oa_version":"Published Version","_id":"8744","status":"public","acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.","citation":{"short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>, vol. 11, 5569, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>.","chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>.","ieee":"L. Schulte <i>et al.</i>, “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>","ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569."},"year":"2020","publisher":"Springer Nature","day":"04","isi":1,"fulldoi":"https://doi.org/10.1038/s41467-020-19372-x","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"ddc":["570"],"date_published":"2020-11-04T00:00:00Z","has_accepted_license":"1","date_updated":"2025-06-12T07:01:22Z","abstract":[{"text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.","lang":"eng"}],"file_date_updated":"2020-11-09T07:56:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-11-09T07:49:36Z","article_processing_charge":"No","quality_controlled":"1","department":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"volume":11,"publication_status":"published","month":"11","doi":"10.1038/s41467-020-19372-x","type":"journal_article","pmid":1,"publication_identifier":{"issn":["2041-1723"]},"oa":1,"title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","article_number":"5569","scopus_import":"1","author":[{"full_name":"Schulte, Linda","last_name":"Schulte","first_name":"Linda"},{"last_name":"Mao","full_name":"Mao, Jiafei","first_name":"Jiafei"},{"first_name":"Julian","full_name":"Reitz, Julian","last_name":"Reitz"},{"full_name":"Sreeramulu, Sridhar","last_name":"Sreeramulu","first_name":"Sridhar"},{"full_name":"Kudlinzki, Denis","last_name":"Kudlinzki","first_name":"Denis"},{"last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin"},{"first_name":"Jakob","last_name":"Meier-Credo","full_name":"Meier-Credo, Jakob"},{"full_name":"Saxena, Krishna","last_name":"Saxena","first_name":"Krishna"},{"full_name":"Buhr, Florian","last_name":"Buhr","first_name":"Florian"},{"first_name":"Julian D.","full_name":"Langer, Julian D.","last_name":"Langer"},{"first_name":"Martin","full_name":"Blackledge, Martin","last_name":"Blackledge"},{"last_name":"Frangakis","full_name":"Frangakis, Achilleas S.","first_name":"Achilleas S."},{"full_name":"Glaubitz, Clemens","last_name":"Glaubitz","first_name":"Clemens"},{"full_name":"Schwalbe, Harald","last_name":"Schwalbe","first_name":"Harald"}],"publication":"Nature Communications"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"fulldoi":"https://doi.org/10.1371/journal.pcbi.1008402","article_type":"original","date_published":"2020-11-05T00:00:00Z","has_accepted_license":"1","ddc":["000"],"file_date_updated":"2020-11-18T07:26:10Z","abstract":[{"lang":"eng","text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-12T07:02:01Z","intvolume":"        16","file":[{"relation":"main_file","access_level":"open_access","checksum":"555456dd0e47bcf9e0994bcb95577e88","creator":"dernst","date_updated":"2020-11-18T07:26:10Z","content_type":"application/pdf","file_id":"8768","success":1,"date_created":"2020-11-18T07:26:10Z","file_size":2498594,"file_name":"2020_PlosCompBio_Kaveh.pdf"}],"issue":"11","external_id":{"pmid":["33151935"],"isi":["000591317200004"]},"publisher":"Public Library of Science","acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","citation":{"ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. 2020;16(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., &#38; Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>","ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” <i>PLOS Computational Biology</i>, vol. 16, no. 11. Public Library of Science, 2020.","chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>.","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020)."},"year":"2020","isi":1,"day":"05","oa_version":"Published Version","_id":"8767","status":"public","article_number":"e1008402","type":"journal_article","doi":"10.1371/journal.pcbi.1008402","oa":1,"title":"The Moran process on 2-chromatic graphs","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"pmid":1,"author":[{"full_name":"Kaveh, Kamran","last_name":"Kaveh","first_name":"Kamran"},{"full_name":"McAvoy, Alex","last_name":"McAvoy","first_name":"Alex"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"publication":"PLOS Computational Biology","scopus_import":"1","quality_controlled":"1","article_processing_charge":"No","date_created":"2020-11-18T07:20:23Z","month":"11","publication_status":"published","department":[{"_id":"KrCh"}],"volume":16,"language":[{"iso":"eng"}]},{"article_number":"6437","type":"journal_article","doi":"10.1038/s41467-020-20286-x","oa":1,"title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","publication_identifier":{"issn":["2041-1723"]},"author":[{"last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","first_name":"Florian","orcid":"0000-0001-7149-769X"},{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","orcid":"0000-0001-8370-6161"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X"},{"first_name":"William","last_name":"Wan","full_name":"Wan, William"},{"full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"publication":"Nature Communications","scopus_import":"1","corr_author":"1","quality_controlled":"1","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/"}]},"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"grant_number":"M02495","name":"Protein structure and function in filopodia across scales","_id":"2674F658-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_processing_charge":"No","date_created":"2020-12-23T08:25:45Z","month":"12","publication_status":"published","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"volume":11,"language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.1038/s41467-020-20286-x","date_published":"2020-12-22T00:00:00Z","has_accepted_license":"1","ddc":["570"],"file_date_updated":"2020-12-28T08:16:10Z","abstract":[{"text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2025-04-15T07:52:12Z","intvolume":"        11","file":[{"file_id":"8975","success":1,"date_created":"2020-12-28T08:16:10Z","file_size":3958727,"file_name":"2020_NatureComm_Faessler.pdf","relation":"main_file","access_level":"open_access","checksum":"55d43ea0061cc4027ba45e966e1db8cc","creator":"dernst","content_type":"application/pdf","date_updated":"2020-12-28T08:16:10Z"}],"external_id":{"isi":["000603078000003"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publisher":"Springer Nature","year":"2020","citation":{"ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>."},"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","isi":1,"day":"22","oa_version":"Published Version","status":"public","_id":"8971"},{"external_id":{"pmid":["32901014"],"isi":["000577280200001"]},"intvolume":"        11","file":[{"date_updated":"2020-09-18T13:02:37Z","content_type":"application/pdf","creator":"dernst","checksum":"88f92544889eb18bb38e25629a422a86","access_level":"open_access","relation":"main_file","file_name":"2020_NatureComm_Arnold.pdf","file_size":1002818,"date_created":"2020-09-18T13:02:37Z","success":1,"file_id":"8530"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"isi":1,"day":"08","publisher":"Springer Nature","citation":{"apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>","ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>","mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>, vol. 11, 4460, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>."},"acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","year":"2020","_id":"8529","status":"public","oa_version":"Published Version","has_accepted_license":"1","date_published":"2020-09-08T00:00:00Z","ddc":["530"],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.1038/s41467-020-18269-z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-09-18T13:02:37Z","abstract":[{"text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a <jats:italic>V</jats:italic><jats:sub><jats:italic>π</jats:italic></jats:sub> as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.","lang":"eng"}],"ec_funded":1,"date_updated":"2026-10-26T23:30:27Z","project":[{"grant_number":"732894","name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"grant_number":"862644","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-18912-9"},{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/"}],"record":[{"relation":"research_data","id":"13056","status":"public"},{"relation":"dissertation_contains","id":"18871","status":"public"}]},"quality_controlled":"1","article_processing_charge":"No","date_created":"2020-09-18T10:56:20Z","month":"09","publication_status":"published","department":[{"_id":"JoFi"}],"volume":11,"language":[{"iso":"eng"}],"article_number":"4460","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","oa":1,"publication_identifier":{"issn":["2041-1723"]},"pmid":1,"type":"journal_article","doi":"10.1038/s41467-020-18269-z","publication":"Nature Communications","author":[{"last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","first_name":"Georg M","orcid":"0000-0003-1397-7876"},{"orcid":"0000-0001-6613-1378","first_name":"Matthias","full_name":"Wulf, Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","first_name":"Shabir"},{"first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","full_name":"Redchenko, Elena"},{"first_name":"Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","first_name":"William J","orcid":"0000-0001-9868-2166"},{"first_name":"Farid","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"corr_author":"1","scopus_import":"1"},{"date_published":"2019-01-01T00:00:00Z","fulldoi":"https://doi.org/10.1038/s41576-018-0063-5","article_type":"review","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"date_updated":"2024-10-14T11:18:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation. These genome regulatory roles of proteins of the nuclear periphery have important influences on development, disease and ageing.","lang":"eng"}],"external_id":{"pmid":["30356165"]},"issue":"1","intvolume":"        20","_id":"11059","status":"public","oa_version":"None","day":"01","year":"2019","citation":{"ieee":"A. Buchwalter, J. M. Kaneshiro, and M. Hetzer, “Coaching from the sidelines: The nuclear periphery in genome regulation,” <i>Nature Reviews Genetics</i>, vol. 20, no. 1. Springer Nature, pp. 39–50, 2019.","apa":"Buchwalter, A., Kaneshiro, J. M., &#38; Hetzer, M. (2019). Coaching from the sidelines: The nuclear periphery in genome regulation. <i>Nature Reviews Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41576-018-0063-5\">https://doi.org/10.1038/s41576-018-0063-5</a>","ama":"Buchwalter A, Kaneshiro JM, Hetzer M. Coaching from the sidelines: The nuclear periphery in genome regulation. <i>Nature Reviews Genetics</i>. 2019;20(1):39-50. doi:<a href=\"https://doi.org/10.1038/s41576-018-0063-5\">10.1038/s41576-018-0063-5</a>","ista":"Buchwalter A, Kaneshiro JM, Hetzer M. 2019. Coaching from the sidelines: The nuclear periphery in genome regulation. Nature Reviews Genetics. 20(1), 39–50.","short":"A. Buchwalter, J.M. Kaneshiro, M. Hetzer, Nature Reviews Genetics 20 (2019) 39–50.","mla":"Buchwalter, Abigail, et al. “Coaching from the Sidelines: The Nuclear Periphery in Genome Regulation.” <i>Nature Reviews Genetics</i>, vol. 20, no. 1, Springer Nature, 2019, pp. 39–50, doi:<a href=\"https://doi.org/10.1038/s41576-018-0063-5\">10.1038/s41576-018-0063-5</a>.","chicago":"Buchwalter, Abigail, Jeanae M. Kaneshiro, and Martin Hetzer. “Coaching from the Sidelines: The Nuclear Periphery in Genome Regulation.” <i>Nature Reviews Genetics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41576-018-0063-5\">https://doi.org/10.1038/s41576-018-0063-5</a>."},"publisher":"Springer Nature","pmid":1,"publication_identifier":{"issn":["1471-0056"],"eissn":["1471-0064"]},"title":"Coaching from the sidelines: The nuclear periphery in genome regulation","doi":"10.1038/s41576-018-0063-5","type":"journal_article","extern":"1","scopus_import":"1","publication":"Nature Reviews Genetics","author":[{"last_name":"Buchwalter","full_name":"Buchwalter, Abigail","first_name":"Abigail"},{"first_name":"Jeanae M.","full_name":"Kaneshiro, Jeanae M.","last_name":"Kaneshiro"},{"last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","first_name":"Martin W","orcid":"0000-0002-2111-992X"}],"date_created":"2022-04-07T07:44:45Z","article_processing_charge":"No","quality_controlled":"1","page":"39-50","volume":20,"language":[{"iso":"eng"}],"publication_status":"published","month":"01"},{"article_processing_charge":"No","date_created":"2022-04-07T07:45:02Z","quality_controlled":"1","related_material":{"record":[{"id":"13079","relation":"research_data","status":"public"}]},"publication_status":"published","language":[{"iso":"eng"}],"volume":8,"month":"10","type":"journal_article","doi":"10.7554/elife.49796","title":"Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress","oa":1,"pmid":1,"publication_identifier":{"issn":["2050-084X"]},"extern":"1","article_number":"e49796","scopus_import":"1","author":[{"full_name":"Buchwalter, Abigail","last_name":"Buchwalter","first_name":"Abigail"},{"last_name":"Schulte","full_name":"Schulte, Roberta","first_name":"Roberta"},{"first_name":"Hsiao","last_name":"Tsai","full_name":"Tsai, Hsiao"},{"full_name":"Capitanio, Juliana","last_name":"Capitanio","first_name":"Juliana"},{"orcid":"0000-0002-2111-992X","first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W"}],"publication":"eLife","intvolume":"         8","file":[{"success":1,"file_id":"11138","date_created":"2022-04-08T08:18:01Z","file_size":6984654,"file_name":"2019_eLife_Buchwalter.pdf","checksum":"1e8672a1e9c3dc0a2d3d0dad89673616","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2022-04-08T08:18:01Z"}],"external_id":{"pmid":["31599721"]},"oa_version":"Published Version","status":"public","_id":"11060","publisher":"eLife Sciences Publications","year":"2019","citation":{"chicago":"Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.49796\">https://doi.org/10.7554/elife.49796</a>.","mla":"Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” <i>ELife</i>, vol. 8, e49796, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.49796\">10.7554/elife.49796</a>.","short":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019).","ama":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.49796\">10.7554/elife.49796</a>","ista":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 8, e49796.","ieee":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","apa":"Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., &#38; Hetzer, M. (2019). Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.49796\">https://doi.org/10.7554/elife.49796</a>"},"day":"10","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"fulldoi":"https://doi.org/10.7554/elife.49796","article_type":"original","has_accepted_license":"1","date_published":"2019-10-10T00:00:00Z","ddc":["570"],"date_updated":"2024-10-14T12:08:36Z","file_date_updated":"2022-04-08T08:18:01Z","abstract":[{"text":"The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"extern":"1","pmid":1,"publication_identifier":{"issn":["0960-9822"]},"title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","doi":"10.1016/j.cub.2019.06.084","type":"journal_article","publication":"Current Biology","author":[{"first_name":"Emma J.","last_name":"Lawrence","full_name":"Lawrence, Emma J."},{"last_name":"Gao","full_name":"Gao, Hongbo","first_name":"Hongbo"},{"full_name":"Tock, Andrew J.","last_name":"Tock","first_name":"Andrew J."},{"last_name":"Lambing","full_name":"Lambing, Christophe","first_name":"Christophe"},{"first_name":"Alexander R.","last_name":"Blackwell","full_name":"Blackwell, Alexander R."},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"full_name":"Henderson, Ian R.","last_name":"Henderson","first_name":"Ian R."}],"scopus_import":"1","quality_controlled":"1","date_created":"2023-01-16T09:16:33Z","article_processing_charge":"No","month":"08","page":"2676-2686.e3","department":[{"_id":"XiFe"}],"language":[{"iso":"eng"}],"volume":29,"publication_status":"published","date_published":"2019-08-19T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.cub.2019.06.084","article_type":"original","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor."}],"date_updated":"2025-01-14T14:31:02Z","external_id":{"pmid":["31378616"]},"issue":"16","intvolume":"        29","day":"19","year":"2019","acknowledgement":"We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.).","citation":{"mla":"Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” <i>Current Biology</i>, vol. 29, no. 16, Elsevier, 2019, p. 2676–2686.e3, doi:<a href=\"https://doi.org/10.1016/j.cub.2019.06.084\">10.1016/j.cub.2019.06.084</a>.","short":"E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3.","chicago":"Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” <i>Current Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cub.2019.06.084\">https://doi.org/10.1016/j.cub.2019.06.084</a>.","apa":"Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., &#38; Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2019.06.084\">https://doi.org/10.1016/j.cub.2019.06.084</a>","ieee":"E. J. Lawrence <i>et al.</i>, “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” <i>Current Biology</i>, vol. 29, no. 16. Elsevier, p. 2676–2686.e3, 2019.","ama":"Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. <i>Current Biology</i>. 2019;29(16):2676-2686.e3. doi:<a href=\"https://doi.org/10.1016/j.cub.2019.06.084\">10.1016/j.cub.2019.06.084</a>","ista":"Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3."},"publisher":"Elsevier","status":"public","_id":"12190","oa_version":"None"},{"extern":"1","article_number":"42530","type":"journal_article","doi":"10.7554/elife.42530","oa":1,"title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","publication_identifier":{"issn":["2050-084X"]},"author":[{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"first_name":"Martin","full_name":"Vickers, Martin","last_name":"Vickers"},{"first_name":"Jingyi","last_name":"Zhang","full_name":"Zhang, Jingyi"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"}],"publication":"eLife","scopus_import":"1","quality_controlled":"1","article_processing_charge":"No","date_created":"2023-01-16T09:17:21Z","month":"05","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"XiFe"}],"volume":8,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"article_type":"original","fulldoi":"https://doi.org/10.7554/elife.42530","date_published":"2019-05-28T00:00:00Z","has_accepted_license":"1","ddc":["580"],"abstract":[{"text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.","lang":"eng"}],"file_date_updated":"2023-02-07T09:42:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-01-14T14:31:41Z","intvolume":"         8","file":[{"file_size":2493837,"date_created":"2023-02-07T09:42:46Z","file_name":"2019_elife_He.pdf","success":1,"file_id":"12525","creator":"alisjak","content_type":"application/pdf","date_updated":"2023-02-07T09:42:46Z","checksum":"ea6b89c20d59e5eb3646916fe5d568ad","access_level":"open_access","relation":"main_file"}],"external_id":{"unknown":["31135340"]},"publisher":"eLife Sciences Publications","acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","year":"2019","citation":{"ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.42530\">10.7554/elife.42530</a>","ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","apa":"He, S., Vickers, M., Zhang, J., &#38; Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.42530\">https://doi.org/10.7554/elife.42530</a>","ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.42530\">https://doi.org/10.7554/elife.42530</a>.","mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” <i>ELife</i>, vol. 8, 42530, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.42530\">10.7554/elife.42530</a>.","short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019)."},"day":"28","oa_version":"Published Version","_id":"12192","status":"public"}]