[{"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"acknowledgement":"We thank Rotem Sorek (Weizmann Institute of Science) for the Lambda Gam mutant and Ian Molineux (University of Texas) for T4Δgp2. We thank You Yu (Zhejiang University-University of Edinburgh Institute) and J. De La Cruz (MSK) for assistance with cryo-EM data collection and Lyuqin Zheng (MSK) for discussions on structural analysis. We thank the Imaging and Microscopy Centre (IMC) at the University of Southampton. This work was supported by Royal Society grant RGS\\R2\\222312 to F.L.N.; Welch Foundation grant F-1938 and National Institutes of Health R35GM138348 to D.W.T.; Wessex Medical Research Innovation grant AE06 to T.A.; and NIH grant GM145888 and Maloris Foundation and Memorial Sloan-Kettering Core grant (P30-CA008748) to D.J.P. In addition to MSKCC cryo-EM resources, some of this work was performed at the National Center for CryoEM Access and Training (NCCAT) and the Simons Electron Microscopy Center located at the New York Structural Biology Center, supported by the NIH Common Fund Transformative High Resolution Cryo-Electron Microscopy program (U24 GM129539) and Simons Foundation (SF349247) and NY State Assembly grants. This research used NSLS-II MX X-ray User Resources (FMX) of the National Synchrotron Light Source II, operated for the DOE Office of Science by Brookhaven National Laboratory under contract no. DE-SC0012704. The Center for BioMolecular Structure (CBMS) is primarily supported by the NIH, the National Institute of General Medical Sciences (NIGMS) through a Center Core P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental Research (KP1605010). R.K. and E.V.K. are supported by the Intramural Research Program of the NIH (National Library of Medicine).","abstract":[{"lang":"eng","text":"Bacteria and archaea deploy diverse antiviral defense systems, many of which remain mechanistically uncharacterized. Here, we characterize Kiwa, a widespread two-component system composed of the transmembrane sensor KwaA and the DNA-binding effector KwaB. Cryogenic electron microscopy (cryo-EM) analysis reveals that KwaA and KwaB assemble into a large, membrane-associated supercomplex. Upon phage binding, KwaA senses infection at the membrane, leading to KwaB binding of ejected phage DNA and inhibition of replication and late transcription, without inducing host cell death. Although KwaB can bind DNA independently, its antiviral activity requires association with KwaA, suggesting spatial or conformational regulation. We show that the phage-encoded DNA-mimic protein Gam directly binds and inhibits KwaB but that co-expression with the Gam-targeted RecBCD system restores protection by Kiwa. Our findings support a model in which Kiwa coordinates membrane-associated detection of phage infection with downstream DNA binding by its effector, forming a spatially coordinated antiviral mechanism."}],"type":"journal_article","file_date_updated":"2025-12-29T14:15:25Z","month":"10","external_id":{"isi":["001603560700005"],"pmid":["40730155"]},"title":"Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","doi":"10.1016/j.cell.2025.07.002","date_created":"2025-08-07T05:00:04Z","department":[{"_id":"JaBr"}],"publication_status":"published","intvolume":"       188","pmid":1,"language":[{"iso":"eng"}],"date_published":"2025-10-16T00:00:00Z","isi":1,"_id":"20143","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","article_type":"original","oa":1,"volume":188,"PlanS_conform":"1","issue":"21","day":"16","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Cell","status":"public","page":"5862-5877.e23","OA_type":"hybrid","citation":{"short":"Z. Zhang, T.C. Todeschini, Y. Wu, R. Kogay, A. Naji, J. Cardenas Rodriguez, R. Mondi, D. Kaganovich, D.W. Taylor, J.P.K. Bravo, M. Teplova, T. Amen, E. Koonin, D.J. Patel, F.L. Nobrega, Cell 188 (2025) 5862–5877.e23.","ista":"Zhang Z, Todeschini TC, Wu Y, Kogay R, Naji A, Cardenas Rodriguez J, Mondi R, Kaganovich D, Taylor DW, Bravo JPK, Teplova M, Amen T, Koonin E, Patel DJ, Nobrega FL. 2025. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. Cell. 188(21), 5862–5877.e23.","chicago":"Zhang, Zhiying, Thomas C. Todeschini, Yi Wu, Roman Kogay, Ameena Naji, Joaquin Cardenas Rodriguez, Rupavidhya Mondi, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” <i>Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">https://doi.org/10.1016/j.cell.2025.07.002</a>.","apa":"Zhang, Z., Todeschini, T. C., Wu, Y., Kogay, R., Naji, A., Cardenas Rodriguez, J., … Nobrega, F. L. (2025). Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">https://doi.org/10.1016/j.cell.2025.07.002</a>","mla":"Zhang, Zhiying, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” <i>Cell</i>, vol. 188, no. 21, Elsevier, 2025, p. 5862–5877.e23, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">10.1016/j.cell.2025.07.002</a>.","ieee":"Z. Zhang <i>et al.</i>, “Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites,” <i>Cell</i>, vol. 188, no. 21. Elsevier, p. 5862–5877.e23, 2025.","ama":"Zhang Z, Todeschini TC, Wu Y, et al. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. <i>Cell</i>. 2025;188(21):5862-5877.e23. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.07.002\">10.1016/j.cell.2025.07.002</a>"},"ddc":["570"],"scopus_import":"1","has_accepted_license":"1","publisher":"Elsevier","file":[{"content_type":"application/pdf","file_size":32104588,"checksum":"b944de5fbd7455f58e1ff338ad352239","success":1,"date_created":"2025-12-29T14:15:25Z","access_level":"open_access","date_updated":"2025-12-29T14:15:25Z","file_id":"20875","relation":"main_file","file_name":"2025_Cell_Zhang.pdf","creator":"dernst"}],"date_updated":"2025-12-29T14:15:58Z","year":"2025","author":[{"full_name":"Zhang, Zhiying","first_name":"Zhiying","last_name":"Zhang"},{"full_name":"Todeschini, Thomas C.","last_name":"Todeschini","first_name":"Thomas C."},{"full_name":"Wu, Yi","last_name":"Wu","first_name":"Yi"},{"full_name":"Kogay, Roman","first_name":"Roman","last_name":"Kogay"},{"first_name":"Ameena","last_name":"Naji","full_name":"Naji, Ameena"},{"last_name":"Cardenas Rodriguez","first_name":"Joaquin","full_name":"Cardenas Rodriguez, Joaquin"},{"full_name":"Mondi, Rupavidhya","last_name":"Mondi","first_name":"Rupavidhya"},{"full_name":"Kaganovich, Daniel","first_name":"Daniel","last_name":"Kaganovich"},{"first_name":"David W.","last_name":"Taylor","full_name":"Taylor, David W."},{"orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly"},{"full_name":"Teplova, Marianna","first_name":"Marianna","last_name":"Teplova"},{"full_name":"Amen, Triana","last_name":"Amen","first_name":"Triana"},{"first_name":"Eugene","last_name":"Koonin","full_name":"Koonin, Eugene"},{"full_name":"Patel, Dinshaw J.","last_name":"Patel","first_name":"Dinshaw J."},{"first_name":"Franklin L.","last_name":"Nobrega","full_name":"Nobrega, Franklin L."}]},{"scopus_import":"1","has_accepted_license":"1","ec_funded":1,"file":[{"access_level":"open_access","date_updated":"2025-01-27T08:46:33Z","success":1,"date_created":"2025-01-27T08:46:33Z","checksum":"d5a818edc32d249cdf75e1bb5b70a4b7","file_size":14082343,"content_type":"application/pdf","creator":"dernst","file_name":"2025_Cell_Watson.pdf","relation":"main_file","file_id":"18884"}],"publisher":"Elsevier","publication":"Cell","status":"public","ddc":["570"],"OA_type":"hybrid","citation":{"ista":"Watson J, Vargas Barroso VM, Morse R, Navas Olivé AC, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. 2025. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell. 188(2), 501–514.e18.","chicago":"Watson, Jake, Victor M Vargas Barroso, Rebecca Morse, Andrea C Navas Olivé, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">https://doi.org/10.1016/j.cell.2024.11.022</a>.","short":"J. Watson, V.M. Vargas Barroso, R. Morse, A.C. Navas Olivé, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, Cell 188 (2025) 501–514.e18.","apa":"Watson, J., Vargas Barroso, V. M., Morse, R., Navas Olivé, A. C., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (2025). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">https://doi.org/10.1016/j.cell.2024.11.022</a>","ama":"Watson J, Vargas Barroso VM, Morse R, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>Cell</i>. 2025;188(2):501-514.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">10.1016/j.cell.2024.11.022</a>","mla":"Watson, Jake, et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>Cell</i>, vol. 188, no. 2, Elsevier, 2025, p. 501–514.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">10.1016/j.cell.2024.11.022</a>.","ieee":"J. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>Cell</i>, vol. 188, no. 2. Elsevier, p. 501–514.e18, 2025."},"page":"501-514.e18","year":"2025","author":[{"orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake","full_name":"Watson, Jake"},{"id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","first_name":"Victor M","last_name":"Vargas Barroso","full_name":"Vargas Barroso, Victor M"},{"id":"ceb89ae7-dc8d-11ea-abe3-da3301d0eab4","last_name":"Morse","first_name":"Rebecca","full_name":"Morse, Rebecca"},{"last_name":"Navas Olivé","first_name":"Andrea C","full_name":"Navas Olivé, Andrea C","orcid":"0000-0002-9280-8597","id":"739d26c9-52e8-11ee-8d72-f14d3893b4ce"},{"orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli","first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba"},{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"full_name":"Tomschik, Matthias","first_name":"Matthias","last_name":"Tomschik"},{"full_name":"Rössler, Karl","last_name":"Rössler","first_name":"Karl"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"date_updated":"2026-04-14T08:34:32Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"quality_controlled":"1","article_type":"original","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","volume":188,"issue":"2","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"       188","pmid":1,"_id":"18879","isi":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"18688"}]},"date_published":"2025-01-23T00:00:00Z","abstract":[{"text":"Our brain has remarkable computational power, generating sophisticated behaviors, storing memories over an individual’s lifetime, and producing higher cognitive functions. However, little of our neuroscience knowledge covers the human brain. Is this organ truly unique, or is it a scaled version of the extensively studied rodent brain? Combining multicellular patch-clamp recording with expansion-based superresolution microscopy and full-scale modeling, we determined the cellular and microcircuit properties of the human hippocampal CA3 region, a fundamental circuit for memory storage. In contrast to neocortical networks, human hippocampal CA3 displayed sparse connectivity, providing a circuit architecture that maximizes associational power. Human synapses showed unique reliability, high precision, and long integration times, exhibiting both species- and circuit-specific properties. Together with expanded neuronal numbers, these circuit characteristics greatly enhanced the memory storage capacity of CA3. Our results reveal distinct microcircuit properties of the human hippocampus and begin to unravel the inner workings of our most complex organ. ","lang":"eng"}],"month":"01","file_date_updated":"2025-01-27T08:46:33Z","type":"journal_article","project":[{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"grant_number":"W1232","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"PAT 4178023","name":"Synaptic networks of human brain","_id":"8d9195e9-16d5-11f0-9cad-d075be887a1e"},{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"external_id":{"pmid":["39667938"],"isi":["001408395600001"]},"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"corr_author":"1","acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, Walter Kaufmann for assistance with handling frozen tissue, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, Miba Machine Shop, and Scientific Computing. We are particularly grateful to the patient donors for their support of this project and also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff; Romana Hoeftberger and the Division of Neuropathology and Neurochemistry; Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology; and Christoph Baumgartner, Martha Feucht, and Ekaterina Pataraia for their clinical care of the patients included in this study. We thank Laura Jonkman, the NABCA biobank, and postmortem brain sample donors for their support of this research. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (advanced grant no. 692692 to P.J. and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J. and grant DK W1232 to M.R.T. and J.G.D.), the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.), and a NOMIS-ISTA fellowship (to A.N.-O.).","department":[{"_id":"JoDa"},{"_id":"PeJo"},{"_id":"GradSch"}],"title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","article_processing_charge":"Yes (via OA deal)","date_created":"2025-01-26T23:01:49Z","doi":"10.1016/j.cell.2024.11.022","oa_version":"Published Version"},{"pmid":1,"publication_status":"published","intvolume":"       188","language":[{"iso":"eng"}],"date_published":"2025-05-29T00:00:00Z","_id":"19602","isi":1,"related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/from-bacterial-immunity-to-plant-sex/","relation":"press_release"}]},"corr_author":"1","acknowledgement":"We thank Sir Richard Roberts (NEB) for the kind gift of anti-4mC antibodies. We are also grateful to the JIC Small Molecule Mass Spectrometry (Lionel Hill) and Chemistry (Martin Rejzek) platforms as well as the High Resolution Metabolomics Laboratory (Manfred Beckmann, Aberystwyth University) for their assistance with LC-MS. Additionally, we acknowledge the assistance of the JIC Bioimaging Facility and ISTA Imaging and Optics Facility for microscopy. Finally, we appreciate the High Performance Computing resources provided by the ISTA Scientific Computing Facility and Norwich BioScience Institute Partnership Computing Infrastructure. This work was funded by a Sainsbury Charitable Foundation studentship (J.W.), a UKRI-BBSRC Doctoral Training Partnerships studentship (BBT0087171 to J.T.), a European Research Council Starting Grant (“SexMeth” 804981 to J.W., S.X., and X.F.), two Biotechnology and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111 to J.Z., M.V., and X.F.), an EMBO Long Term Fellowship (Y.L.), an ISTA Bridge Fellowship (S.X.), and ISTA core funding (Y.Y. and X.F.).","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"project":[{"_id":"bdb51a6e-d553-11ed-ba76-c2025f3d5725","grant_number":"804981","name":"Establishment, modulation and inheritance of sexual lineage specific DNA methylation in plants","call_identifier":"H2020"}],"external_id":{"isi":["001504744800006"],"pmid":["40209706"]},"abstract":[{"lang":"eng","text":"N4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but its relevance and even its presence in eukaryotes have been mysterious. Here we show that spermatogenesis in the liverwort Marchantia polymorpha involves two waves of extensive DNA methylation reprogramming. First, 5-methylcytosine (5mC) expands from transposons to the entire genome. Notably, the second wave installs 4mC throughout genic regions, covering over 50% of CG sites in sperm. 4mC requires a methyltransferase (MpDN4MT1a) that is specifically expressed during late spermiogenesis. Deletion of MpDN4MT1a alters the sperm transcriptome, causes sperm swimming and fertility defects, and impairs post-fertilization development. Our results reveal extensive 4mC in a eukaryote, identify a family of eukaryotic methyltransferases, and elucidate the biological functions of 4mC in reproductive development, thereby expanding the repertoire of functional eukaryotic DNA modifications."}],"type":"journal_article","file_date_updated":"2025-12-29T13:40:32Z","month":"05","article_processing_charge":"Yes (via OA deal)","date_created":"2025-04-20T22:01:28Z","doi":"10.1016/j.cell.2025.03.014","oa_version":"Published Version","title":"Extensive N4 cytosine methylation is essential for Marchantia sperm function","department":[{"_id":"XiFe"}],"page":"2890-2906.e14","ddc":["570"],"citation":{"ista":"Walker J, Zhang J, Liu Y, Xu S, Yu Y, Vickers M, Ouyang W, Tálas J, Dolan L, Nakajima K, Feng X. 2025. Extensive N4 cytosine methylation is essential for Marchantia sperm function. Cell. 188(11), 2890–2906.e14.","short":"J. Walker, J. Zhang, Y. Liu, S. Xu, Y. Yu, M. Vickers, W. Ouyang, J. Tálas, L. Dolan, K. Nakajima, X. Feng, Cell 188 (2025) 2890–2906.e14.","chicago":"Walker, James, Jingyi Zhang, Yalin Liu, Shujuan Xu, Yiming Yu, Martin Vickers, Weizhi Ouyang, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia Sperm Function.” <i>Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">https://doi.org/10.1016/j.cell.2025.03.014</a>.","ieee":"J. Walker <i>et al.</i>, “Extensive N4 cytosine methylation is essential for Marchantia sperm function,” <i>Cell</i>, vol. 188, no. 11. Elsevier, p. 2890–2906.e14, 2025.","apa":"Walker, J., Zhang, J., Liu, Y., Xu, S., Yu, Y., Vickers, M., … Feng, X. (2025). Extensive N4 cytosine methylation is essential for Marchantia sperm function. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">https://doi.org/10.1016/j.cell.2025.03.014</a>","mla":"Walker, James, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia Sperm Function.” <i>Cell</i>, vol. 188, no. 11, Elsevier, 2025, p. 2890–2906.e14, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">10.1016/j.cell.2025.03.014</a>.","ama":"Walker J, Zhang J, Liu Y, et al. Extensive N4 cytosine methylation is essential for Marchantia sperm function. <i>Cell</i>. 2025;188(11):2890-2906.e14. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">10.1016/j.cell.2025.03.014</a>"},"OA_type":"hybrid","status":"public","publication":"Cell","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","publisher":"Elsevier","file":[{"date_updated":"2025-12-29T13:40:32Z","access_level":"open_access","date_created":"2025-12-29T13:40:32Z","success":1,"checksum":"0dcc2feb368dfe7c4890093366b2dacb","file_size":11622960,"content_type":"application/pdf","creator":"dernst","file_name":"2025_Cell_Walker.pdf","relation":"main_file","file_id":"20871"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"date_updated":"2026-04-28T13:36:51Z","year":"2025","author":[{"last_name":"Walker","first_name":"James","full_name":"Walker, James"},{"first_name":"Jingyi","last_name":"Zhang","full_name":"Zhang, Jingyi"},{"first_name":"Yalin","last_name":"Liu","full_name":"Liu, Yalin"},{"full_name":"Xu, Shujuan","last_name":"Xu","first_name":"Shujuan","id":"9724dd9d-f591-11ee-bd51-e97ed0652286"},{"full_name":"Yu, Yiming","first_name":"Yiming","last_name":"Yu","orcid":"0000-0002-9919-7282","id":"318e643b-8b61-11ed-b69e-aafa103ec8dd"},{"full_name":"Vickers, Martin","last_name":"Vickers","first_name":"Martin"},{"full_name":"Ouyang, Weizhi","first_name":"Weizhi","last_name":"Ouyang","id":"fec73395-8b60-11ed-b69e-927fda99c743"},{"full_name":"Tálas, Judit","first_name":"Judit","last_name":"Tálas"},{"last_name":"Dolan","first_name":"Liam","full_name":"Dolan, Liam"},{"full_name":"Nakajima, Keiji","last_name":"Nakajima","first_name":"Keiji"},{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"quality_controlled":"1","article_type":"original","issue":"11","volume":188,"PlanS_conform":"1","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"29"},{"author":[{"full_name":"Kuhn, Andre","last_name":"Kuhn","first_name":"Andre"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"last_name":"Mutte","first_name":"Sumanth","full_name":"Mutte, Sumanth"},{"last_name":"Dubey","first_name":"Shiv Mani","full_name":"Dubey, Shiv Mani"},{"first_name":"Vanessa Polet","last_name":"Carrillo Carrasco","full_name":"Carrillo Carrasco, Vanessa Polet"},{"full_name":"Boeren, Sjef","last_name":"Boeren","first_name":"Sjef"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer","full_name":"Monzer, Aline"},{"full_name":"Koehorst, Jasper","first_name":"Jasper","last_name":"Koehorst"},{"full_name":"Kohchi, Takayuki","last_name":"Kohchi","first_name":"Takayuki"},{"full_name":"Nishihama, Ryuichi","last_name":"Nishihama","first_name":"Ryuichi"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","first_name":"Matyas","last_name":"Fendrych"},{"last_name":"Sprakel","first_name":"Joris","full_name":"Sprakel, Joris"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"}],"year":"2024","date_updated":"2026-04-07T11:48:32Z","publisher":"Elsevier","file":[{"file_id":"14874","relation":"main_file","file_name":"2024_Cell_Kuhn.pdf","creator":"dernst","success":1,"date_created":"2024-01-22T13:41:41Z","date_updated":"2024-01-22T13:41:41Z","access_level":"open_access","file_size":13194060,"checksum":"06fd236a9ee0b46ccb05f44695bfc34b","content_type":"application/pdf"}],"has_accepted_license":"1","scopus_import":"1","ec_funded":1,"citation":{"ista":"Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17.","short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17.","chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>.","mla":"Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>.","ieee":"A. Kuhn <i>et al.</i>, “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” <i>Cell</i>, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024.","ama":"Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. 2024;187(1):130-148.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>"},"page":"130-148.e17","ddc":["580"],"status":"public","publication":"Cell","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"04","issue":"1","volume":187,"oa":1,"article_type":"original","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"keyword":["General Biochemistry","Genetics and Molecular Biology"],"related_material":{"record":[{"id":"19395","relation":"dissertation_contains","status":"public"}]},"_id":"14826","isi":1,"date_published":"2024-01-04T00:00:00Z","language":[{"iso":"eng"}],"pmid":1,"intvolume":"       187","publication_status":"published","department":[{"_id":"JiFr"}],"date_created":"2024-01-17T12:45:40Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","oa_version":"Published Version","doi":"10.1016/j.cell.2023.11.021","article_processing_charge":"Yes (in subscription journal)","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","external_id":{"isi":["001152705700001"],"pmid":["38128538"]},"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF"}],"file_date_updated":"2024-01-22T13:41:41Z","month":"01","type":"journal_article","abstract":[{"lang":"eng","text":"The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage."}],"acknowledgement":"We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]}},{"date_published":"2022-02-22T00:00:00Z","_id":"10825","isi":1,"pmid":1,"intvolume":"       185","publication_status":"published","language":[{"iso":"eng"}],"date_created":"2022-03-06T23:01:52Z","oa_version":"Published Version","doi":"10.1016/j.cell.2022.01.022","article_processing_charge":"No","title":"Cell surface fluctuations regulate early embryonic lineage sorting","department":[{"_id":"EdHa"}],"acknowledgement":"We are grateful to H. Niwa for Dox regulatable PB vector; G. Charras for EzrinT567D cDNA; K. Jones for tdTomato ESCs, R26-Confetti ESCs, and laboratory assistance; M. Kinoshita for pPB-CAG-H2B-BFP plasmid; P. Humphreys and D. Clements for imaging support; G. Chu, P. Attlesey, and staff for animal husbandry; S. Pallett for laboratory assistance; C. Mulas for critical feedback on the project; T. Boroviak for single-cell RNA-seq; the EMBL Genomics Core Facility for sequencing; and M. Merkel for developing and sharing the original version of the 3D Voronoi code. This work was financially supported by BBSRC ( BB/Moo4023/1 and BB/T007044/1 to K.J.C. and J.N., Alert16 grant BB/R000042 to E.K.P.), Leverhulme Trust ( RPG-2014-080 to K.J.C. and J.N.), European Research Council ( 772798 -CellFateTech to K.J.C., 311637 -MorphoCorDiv and 820188 -NanoMechShape to E.K.P., Starting Grant 851288 to E.H., and 772426 -MeChemGui to K.F.), the Isaac Newton Trust (to E.K.P.), Medical Research Council UK (MRC program award MC_UU_00012/5 to E.K.P.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 641639 ( ITN Biopol , H.D.B. and E.K.P.), the Alexander von Humboldt Foundation (Alexander von Humboldt Professorship to K.F.), EMBO ALTF 522-2021 (to P.S.), Centre for Trophoblast Research (Next Generation fellowship to S.A.), and JSPS Overseas Research Fellowships (to A.Y.). The Wellcome-MRC Cambridge Stem Cell Institute receives core funding from Wellcome Trust ( 203151/Z/16/Z ) and MRC ( MC_PC_17230 ). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"external_id":{"pmid":["35196500"],"isi":["000796293700007"]},"project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"type":"journal_article","month":"02","file_date_updated":"2022-03-07T07:55:23Z","abstract":[{"text":"In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages.","lang":"eng"}],"date_updated":"2025-07-10T11:50:00Z","author":[{"last_name":"Yanagida","first_name":"Ayaka","full_name":"Yanagida, Ayaka"},{"first_name":"Elena","last_name":"Corujo-Simon","full_name":"Corujo-Simon, Elena"},{"first_name":"Christopher K.","last_name":"Revell","full_name":"Revell, Christopher K."},{"id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","first_name":"Preeti","last_name":"Sahu","full_name":"Sahu, Preeti"},{"full_name":"Stirparo, Giuliano G.","last_name":"Stirparo","first_name":"Giuliano G."},{"full_name":"Aspalter, Irene M.","first_name":"Irene M.","last_name":"Aspalter"},{"full_name":"Winkel, Alex K.","last_name":"Winkel","first_name":"Alex K."},{"first_name":"Ruby","last_name":"Peters","full_name":"Peters, Ruby"},{"full_name":"De Belly, Henry","last_name":"De Belly","first_name":"Henry"},{"last_name":"Cassani","first_name":"Davide A.D.","full_name":"Cassani, Davide A.D."},{"last_name":"Achouri","first_name":"Sarra","full_name":"Achouri, Sarra"},{"full_name":"Blumenfeld, Raphael","first_name":"Raphael","last_name":"Blumenfeld"},{"full_name":"Franze, Kristian","last_name":"Franze","first_name":"Kristian"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paluch","first_name":"Ewa K.","full_name":"Paluch, Ewa K."},{"first_name":"Jennifer","last_name":"Nichols","full_name":"Nichols, Jennifer"},{"first_name":"Kevin J.","last_name":"Chalut","full_name":"Chalut, Kevin J."}],"year":"2022","page":"777-793.e20","citation":{"ama":"Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. 2022;185(5):777-793.e20. doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>","ieee":"A. Yanagida <i>et al.</i>, “Cell surface fluctuations regulate early embryonic lineage sorting,” <i>Cell</i>, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022.","apa":"Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter, I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>","mla":"Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20, doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>.","ista":"Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 185(5), 777–793.e20.","chicago":"Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>.","short":"A. Yanagida, E. Corujo-Simon, C.K. Revell, P. Sahu, G.G. Stirparo, I.M. Aspalter, A.K. Winkel, R. Peters, H. De Belly, D.A.D. Cassani, S. Achouri, R. Blumenfeld, K. Franze, E.B. Hannezo, E.K. Paluch, J. Nichols, K.J. Chalut, Cell 185 (2022) 777–793.e20."},"ddc":["570"],"publication":"Cell","status":"public","publisher":"Cell Press","file":[{"date_created":"2022-03-07T07:55:23Z","success":1,"date_updated":"2022-03-07T07:55:23Z","access_level":"open_access","file_size":8478995,"content_type":"application/pdf","checksum":"ae305060e8031297771b89dae9e36a29","relation":"main_file","file_id":"10831","creator":"dernst","file_name":"2022_Cell_Yanagida.pdf"}],"has_accepted_license":"1","scopus_import":"1","ec_funded":1,"issue":"5","volume":185,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"article_type":"original","quality_controlled":"1"},{"language":[{"iso":"eng"}],"publication_status":"published","intvolume":"       184","_id":"10573","isi":1,"date_published":"2021-12-22T00:00:00Z","abstract":[{"lang":"eng","text":"How tissues acquire complex shapes is a fundamental question in biology and regenerative medicine. Zebrafish semicircular canals form from invaginations in the otic epithelium (buds) that extend and fuse to form the hubs of each canal. We find that conventional actomyosin-driven behaviors are not required. Instead, local secretion of hyaluronan, made by the enzymes uridine 5′-diphosphate dehydrogenase (ugdh) and hyaluronan synthase 3 (has3), drives canal morphogenesis. Charged hyaluronate polymers osmotically swell with water and generate isotropic extracellular pressure to deform the overlying epithelium into buds. The mechanical anisotropy needed to shape buds into tubes is conferred by a polarized distribution of actomyosin and E-cadherin-rich membrane tethers, which we term cytocinches. Most work on tissue morphogenesis ascribes actomyosin contractility as the driving force, while the extracellular matrix shapes tissues through differential stiffness. Our work inverts this expectation. Hyaluronate pressure shaped by anisotropic tissue stiffness may be a widespread mechanism for powering morphological change in organogenesis and tissue engineering."}],"month":"12","type":"journal_article","external_id":{"isi":["000735387500002"]},"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"acknowledgement":"We thank Ian Swinburne, Sandy Nandagopal, and Toru Kawanishi for support, discussions, and reagents. We thank Vanessa Barone, Joseph Nasser, and members of the Megason lab for useful comments on the manuscript and general feedback. We are grateful to the Heisenberg and Knaut labs for transgenic fish. Diagrams on the right in the graphical abstract were created using BioRender. This work was supported by NIH R01DC015478 and NIH R01GM107733 to S.G.M. A.M. was supported by Human Frontiers Science Program LTF and NIH K99HD098918.","department":[{"_id":"EdHa"}],"title":"Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis","article_processing_charge":"No","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.09.28.316042","open_access":"1"}],"doi":"10.1016/j.cell.2021.11.025","oa_version":"Preprint","date_created":"2021-12-26T23:01:26Z","scopus_import":"1","publisher":"Elsevier","publication":"Cell","status":"public","page":"6313-6325.e18","citation":{"mla":"Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” <i>Cell</i>, vol. 184, no. 26, Elsevier, 2021, p. 6313–6325.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">10.1016/j.cell.2021.11.025</a>.","ieee":"A. Munjal, E. B. Hannezo, T. Y. C. Tsai, T. J. Mitchison, and S. G. Megason, “Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis,” <i>Cell</i>, vol. 184, no. 26. Elsevier, p. 6313–6325.e18, 2021.","ama":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. <i>Cell</i>. 2021;184(26):6313-6325.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">10.1016/j.cell.2021.11.025</a>","apa":"Munjal, A., Hannezo, E. B., Tsai, T. Y. C., Mitchison, T. J., &#38; Megason, S. G. (2021). Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">https://doi.org/10.1016/j.cell.2021.11.025</a>","short":"A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 6313–6325.e18.","chicago":"Munjal, Akankshi, Edouard B Hannezo, Tony Y.C. Tsai, Timothy J. Mitchison, and Sean G. Megason. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” <i>Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">https://doi.org/10.1016/j.cell.2021.11.025</a>.","ista":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. 2021. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 184(26), 6313–6325.e18."},"year":"2021","author":[{"first_name":"Akankshi","last_name":"Munjal","full_name":"Munjal, Akankshi"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"Tsai, Tony Y.C.","first_name":"Tony Y.C.","last_name":"Tsai"},{"last_name":"Mitchison","first_name":"Timothy J.","full_name":"Mitchison, Timothy J."},{"last_name":"Megason","first_name":"Sean G.","full_name":"Megason, Sean G."}],"date_updated":"2025-05-14T11:26:20Z","quality_controlled":"1","article_type":"original","oa":1,"day":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":184,"issue":"26"},{"date_published":"2021-04-01T00:00:00Z","_id":"9316","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/embryonic-tissue-undergoes-phase-transition/"}]},"isi":1,"intvolume":"       184","publication_status":"published","pmid":1,"language":[{"iso":"eng"}],"title":"Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions","oa_version":"Published Version","doi":"10.1016/j.cell.2021.02.017","date_created":"2021-04-11T22:01:14Z","article_processing_charge":"No","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"acknowledgement":"We thank Carl Goodrich and the members of the Heisenberg and Hannezo groups, in particular Reka Korei, for help, technical advice, and discussions; and the Bioimaging and zebrafish facilities of the IST Austria for continuous support. This work was supported by the Elise Richter Program of Austrian Science Fund (FWF) to N.I.P. ( V 736-B26 ) and the European Union (European Research Council Advanced Grant 742573 to C.-P.H. and European Research Council Starting Grant 851288 to E.H.).","corr_author":"1","month":"04","file_date_updated":"2021-06-08T10:04:10Z","type":"journal_article","abstract":[{"lang":"eng","text":"Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin to phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context."}],"external_id":{"isi":["000636734000022"],"pmid":["33730596"]},"project":[{"call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"_id":"2693FD8C-B435-11E9-9278-68D0E5697425","grant_number":"V00736","name":"Tissue material properties in embryonic development","call_identifier":"FWF"}],"date_updated":"2025-07-10T12:01:42Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"author":[{"orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","full_name":"Petridou, Nicoletta","first_name":"Nicoletta","last_name":"Petridou"},{"first_name":"Bernat","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"year":"2021","publication":"Cell","status":"public","ddc":["570"],"citation":{"apa":"Petridou, N., Corominas-Murtra, B., Heisenberg, C.-P. J., &#38; Hannezo, E. B. (2021). Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">https://doi.org/10.1016/j.cell.2021.02.017</a>","mla":"Petridou, Nicoletta, et al. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” <i>Cell</i>, vol. 184, no. 7, Elsevier, 2021, p. 1914–1928.e19, doi:<a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">10.1016/j.cell.2021.02.017</a>.","ieee":"N. Petridou, B. Corominas-Murtra, C.-P. J. Heisenberg, and E. B. Hannezo, “Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions,” <i>Cell</i>, vol. 184, no. 7. Elsevier, p. 1914–1928.e19, 2021.","ama":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. <i>Cell</i>. 2021;184(7):1914-1928.e19. doi:<a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">10.1016/j.cell.2021.02.017</a>","ista":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. 2021. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 184(7), 1914–1928.e19.","short":"N. Petridou, B. Corominas-Murtra, C.-P.J. Heisenberg, E.B. Hannezo, Cell 184 (2021) 1914–1928.e19.","chicago":"Petridou, Nicoletta, Bernat Corominas-Murtra, Carl-Philipp J Heisenberg, and Edouard B Hannezo. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” <i>Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cell.2021.02.017\">https://doi.org/10.1016/j.cell.2021.02.017</a>."},"page":"1914-1928.e19","publisher":"Elsevier","file":[{"content_type":"application/pdf","checksum":"1e5295fbd9c2a459173ec45a0e8a7c2e","file_size":11405875,"date_created":"2021-06-08T10:04:10Z","success":1,"access_level":"open_access","date_updated":"2021-06-08T10:04:10Z","file_id":"9534","relation":"main_file","file_name":"2021_Cell_Petridou.pdf","creator":"cziletti"}],"has_accepted_license":"1","ec_funded":1,"scopus_import":"1","volume":184,"issue":"7","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","quality_controlled":"1","oa":1},{"year":"2020","author":[{"full_name":"Dekoninck, Sophie","last_name":"Dekoninck","first_name":"Sophie"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"full_name":"Sifrim, Alejandro","last_name":"Sifrim","first_name":"Alejandro"},{"full_name":"Miroshnikova, Yekaterina A.","first_name":"Yekaterina A.","last_name":"Miroshnikova"},{"first_name":"Mariaceleste","last_name":"Aragona","full_name":"Aragona, Mariaceleste"},{"full_name":"Malfait, Milan","last_name":"Malfait","first_name":"Milan"},{"last_name":"Gargouri","first_name":"Souhir","full_name":"Gargouri, Souhir"},{"full_name":"De Neunheuser, Charlotte","first_name":"Charlotte","last_name":"De Neunheuser"},{"full_name":"Dubois, Christine","last_name":"Dubois","first_name":"Christine"},{"full_name":"Voet, Thierry","last_name":"Voet","first_name":"Thierry"},{"full_name":"Wickström, Sara A.","first_name":"Sara A.","last_name":"Wickström"},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"},{"first_name":"Cédric","last_name":"Blanpain","full_name":"Blanpain, Cédric"}],"date_updated":"2025-07-10T11:54:47Z","scopus_import":"1","has_accepted_license":"1","publisher":"Elsevier","file":[{"content_type":"application/pdf","file_size":17992888,"checksum":"e2114902f4e9d75a752e9efb5ae06011","date_created":"2020-05-04T10:20:55Z","access_level":"open_access","date_updated":"2020-07-14T12:48:03Z","relation":"main_file","file_id":"7795","creator":"dernst","file_name":"2020_Cell_Dekoninck.pdf"}],"page":"604-620.e22","citation":{"ista":"Dekoninck S, Hannezo EB, Sifrim A, Miroshnikova YA, Aragona M, Malfait M, Gargouri S, De Neunheuser C, Dubois C, Voet T, Wickström SA, Simons BD, Blanpain C. 2020. Defining the design principles of skin epidermis postnatal growth. Cell. 181(3), 604–620.e22.","chicago":"Dekoninck, Sophie, Edouard B Hannezo, Alejandro Sifrim, Yekaterina A. Miroshnikova, Mariaceleste Aragona, Milan Malfait, Souhir Gargouri, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” <i>Cell</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.cell.2020.03.015\">https://doi.org/10.1016/j.cell.2020.03.015</a>.","short":"S. Dekoninck, E.B. Hannezo, A. Sifrim, Y.A. Miroshnikova, M. Aragona, M. Malfait, S. Gargouri, C. De Neunheuser, C. Dubois, T. Voet, S.A. Wickström, B.D. Simons, C. Blanpain, Cell 181 (2020) 604–620.e22.","ieee":"S. Dekoninck <i>et al.</i>, “Defining the design principles of skin epidermis postnatal growth,” <i>Cell</i>, vol. 181, no. 3. Elsevier, p. 604–620.e22, 2020.","mla":"Dekoninck, Sophie, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” <i>Cell</i>, vol. 181, no. 3, Elsevier, 2020, p. 604–620.e22, doi:<a href=\"https://doi.org/10.1016/j.cell.2020.03.015\">10.1016/j.cell.2020.03.015</a>.","ama":"Dekoninck S, Hannezo EB, Sifrim A, et al. Defining the design principles of skin epidermis postnatal growth. <i>Cell</i>. 2020;181(3):604-620.e22. doi:<a href=\"https://doi.org/10.1016/j.cell.2020.03.015\">10.1016/j.cell.2020.03.015</a>","apa":"Dekoninck, S., Hannezo, E. B., Sifrim, A., Miroshnikova, Y. A., Aragona, M., Malfait, M., … Blanpain, C. (2020). Defining the design principles of skin epidermis postnatal growth. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2020.03.015\">https://doi.org/10.1016/j.cell.2020.03.015</a>"},"ddc":["570"],"status":"public","publication":"Cell","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","issue":"3","volume":181,"oa":1,"quality_controlled":"1","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"_id":"7789","isi":1,"date_published":"2020-04-30T00:00:00Z","language":[{"iso":"eng"}],"pmid":1,"publication_status":"published","intvolume":"       181","department":[{"_id":"EdHa"}],"article_processing_charge":"No","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2020-05-03T22:00:48Z","doi":"10.1016/j.cell.2020.03.015","title":"Defining the design principles of skin epidermis postnatal growth","external_id":{"isi":["000530708400016"],"pmid":["32259486"]},"abstract":[{"lang":"eng","text":"During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, andin vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues."}],"type":"journal_article","file_date_updated":"2020-07-14T12:48:03Z","month":"04","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]}},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_updated":"2026-04-29T22:30:09Z","year":"2019","author":[{"full_name":"Shamipour, Shayan","last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland","first_name":"Roland","last_name":"Kardos"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","last_name":"Xue","full_name":"Xue, Shi-lei"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"page":"1463-1479.e18","citation":{"chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>.","ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” <i>Cell</i>, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. 2019;177(6):1463-1479.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>."},"status":"public","publication":"Cell","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","publisher":"Elsevier","file":[{"file_name":"2019_Cell_Shamipour_accepted.pdf","creator":"dernst","file_id":"8686","relation":"main_file","checksum":"aea43726d80e35ce3885073a5f05c3e3","file_size":3356292,"content_type":"application/pdf","date_updated":"2020-10-21T07:22:34Z","access_level":"open_access","success":1,"date_created":"2020-10-21T07:22:34Z"}],"issue":"6","volume":177,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","oa":1,"quality_controlled":"1","article_type":"original","date_published":"2019-05-30T00:00:00Z","_id":"6508","isi":1,"related_material":{"record":[{"status":"public","id":"8350","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/","relation":"press_release"}]},"pmid":1,"publication_status":"published","intvolume":"       177","language":[{"iso":"eng"}],"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.04.030","open_access":"1"}],"doi":"10.1016/j.cell.2019.04.030","oa_version":"Published Version","date_created":"2019-06-02T21:59:12Z","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["31080065"],"isi":["000469415100013"]},"abstract":[{"text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.","lang":"eng"}],"file_date_updated":"2020-10-21T07:22:34Z","type":"journal_article","month":"05"},{"department":[{"_id":"CaHe"},{"_id":"BjHo"}],"doi":"10.1016/j.cell.2019.10.006","oa_version":"Submitted Version","date_created":"2019-11-12T12:51:06Z","article_processing_charge":"No","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","external_id":{"isi":["000493898000012"],"pmid":["31675500"]},"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020"}],"month":"10","type":"journal_article","file_date_updated":"2020-10-21T07:09:45Z","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"isi":1,"_id":"7001","related_material":{"link":[{"description":"News auf IST Website","url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","relation":"press_release"}],"record":[{"status":"public","id":"7186","relation":"dissertation_contains"},{"id":"8350","relation":"dissertation_contains","status":"public"}]},"date_published":"2019-10-31T00:00:00Z","language":[{"iso":"eng"}],"pmid":1,"intvolume":"       179","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"31","issue":"4","volume":179,"oa":1,"article_type":"original","quality_controlled":"1","author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226","last_name":"Schwayer","first_name":"Cornelia","full_name":"Schwayer, Cornelia"},{"last_name":"Shamipour","first_name":"Shayan","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","first_name":"Kornelija"},{"orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","first_name":"Alexandra","last_name":"Schauer"},{"last_name":"Balda","first_name":"M","full_name":"Balda, M"},{"last_name":"Tada","first_name":"M","full_name":"Tada, M"},{"first_name":"K","last_name":"Matter","full_name":"Matter, K"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"year":"2019","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"date_updated":"2026-04-29T22:30:09Z","file":[{"file_size":8805878,"content_type":"application/pdf","checksum":"33dac4bb77ee630e2666e936b4d57980","access_level":"open_access","date_updated":"2020-10-21T07:09:45Z","success":1,"date_created":"2020-10-21T07:09:45Z","creator":"dernst","file_name":"2019_Cell_Schwayer_accepted.pdf","relation":"main_file","file_id":"8684"}],"publisher":"Cell Press","scopus_import":"1","has_accepted_license":"1","ec_funded":1,"citation":{"ieee":"C. Schwayer <i>et al.</i>, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” <i>Cell</i>, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>.","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. 2019;179(4):937-952.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18."},"page":"937-952.e18","ddc":["570"],"publication":"Cell","status":"public"},{"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"type":"journal_article","month":"09","external_id":{"pmid":["31539498"],"isi":["000486618500011"]},"title":"The neural crest pitches in to remove apoptotic debris","article_processing_charge":"No","date_created":"2019-09-15T22:00:46Z","oa_version":"None","doi":"10.1016/j.cell.2019.08.047","department":[{"_id":"MiSi"}],"publication_status":"published","intvolume":"       179","pmid":1,"language":[{"iso":"eng"}],"date_published":"2019-09-19T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","id":"6891","status":"public"}]},"_id":"6877","isi":1,"quality_controlled":"1","article_type":"original","volume":179,"issue":"1","day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Cell","status":"public","citation":{"apa":"Kopf, A., &#38; Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">https://doi.org/10.1016/j.cell.2019.08.047</a>","mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” <i>Cell</i>, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">10.1016/j.cell.2019.08.047</a>.","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” <i>Cell</i>, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. <i>Cell</i>. 2019;179(1):51-53. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">10.1016/j.cell.2019.08.047</a>","ista":"Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53.","chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">https://doi.org/10.1016/j.cell.2019.08.047</a>.","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53."},"page":"51-53","scopus_import":"1","publisher":"Elsevier","date_updated":"2026-04-29T22:30:36Z","year":"2019","author":[{"orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja","last_name":"Kopf","first_name":"Aglaja"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}]},{"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","article_processing_charge":"No","date_created":"2019-04-28T21:59:14Z","doi":"10.1016/j.cell.2019.04.015","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing."}],"month":"05","type":"journal_article","file_date_updated":"2020-07-14T12:47:28Z","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"external_id":{"isi":["000466843000015"],"pmid":["31051107"]},"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"corr_author":"1","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/"}],"record":[{"status":"public","id":"9992","relation":"dissertation_contains"}]},"_id":"6351","isi":1,"date_published":"2019-05-02T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"       177","pmid":1,"day":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":177,"issue":"4","quality_controlled":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2019","author":[{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavá","first_name":"Petra","full_name":"Marhavá, Petra"},{"orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer"},{"first_name":"Saiko","last_name":"Yoshida","full_name":"Yoshida, Saiko","orcid":"0000-0001-6111-9353","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marhavy","first_name":"Peter","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-29T22:30:38Z","acknowledged_ssus":[{"_id":"Bio"}],"has_accepted_license":"1","scopus_import":"1","ec_funded":1,"file":[{"file_id":"6411","relation":"main_file","file_name":"2019_Cell_Marhava.pdf","creator":"dernst","content_type":"application/pdf","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","file_size":10272032,"date_created":"2019-05-13T06:12:45Z","date_updated":"2020-07-14T12:47:28Z","access_level":"open_access"}],"publisher":"Elsevier","publication":"Cell","status":"public","citation":{"chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>.","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13.","short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., &#38; Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>","mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>.","ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” <i>Cell</i>, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.","ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. 2019;177(4):957-969.e13. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>"},"ddc":["570"],"page":"957-969.e13"},{"page":"1286-1297","citation":{"chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014."},"publication":"Cell","status":"public","publisher":"Elsevier","scopus_import":"1","extern":"1","date_updated":"2021-12-14T08:22:36Z","author":[{"last_name":"Huff","first_name":"Jason T.","full_name":"Huff, Jason T."},{"last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"year":"2014","oa":1,"article_type":"original","quality_controlled":"1","issue":"6","volume":156,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"13","pmid":1,"intvolume":"       156","publication_status":"published","language":[{"iso":"eng"}],"date_published":"2014-03-13T00:00:00Z","_id":"9458","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"external_id":{"pmid":["24630728"]},"month":"03","type":"journal_article","abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"oa_version":"Published Version","date_created":"2021-06-04T12:00:16Z","doi":"10.1016/j.cell.2014.01.029","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2014.01.029"}],"article_processing_charge":"No","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","department":[{"_id":"DaZi"}]},{"author":[{"full_name":"Zemach, Assaf","first_name":"Assaf","last_name":"Zemach"},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr","first_name":"Devin"},{"first_name":"Leor","last_name":"Eshed-Williams","full_name":"Eshed-Williams, Leor"},{"full_name":"Thao, Ka","first_name":"Ka","last_name":"Thao"},{"full_name":"Harmer, Stacey L.","last_name":"Harmer","first_name":"Stacey L."},{"first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"year":"2013","date_updated":"2021-12-14T08:25:35Z","extern":"1","publisher":"Elsevier","scopus_import":"1","status":"public","publication":"Cell","citation":{"mla":"Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>.","ieee":"A. Zemach <i>et al.</i>, “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” <i>Cell</i>, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.","ama":"Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. 2013;153(1):193-205. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>","apa":"Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>","short":"A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.","ista":"Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205.","chicago":"Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>."},"page":"193-205","day":"28","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":153,"issue":"1","article_type":"original","quality_controlled":"1","oa":1,"_id":"9459","date_published":"2013-03-28T00:00:00Z","language":[{"iso":"eng"}],"intvolume":"       153","publication_status":"published","pmid":1,"department":[{"_id":"DaZi"}],"title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","doi":"10.1016/j.cell.2013.02.033","oa_version":"Published Version","date_created":"2021-06-04T12:23:28Z","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.02.033"}],"month":"03","type":"journal_article","abstract":[{"text":"Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway.","lang":"eng"}],"external_id":{"pmid":["23540698"]},"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]}}]