[{"date_published":"2025-12-01T00:00:00Z","title":"Causes and consequences of sex-chromosome turnovers in Diptera","status":"public","year":"2025","abstract":[{"lang":"eng","text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes."}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","doi":"10.15479/AT-ISTA-20780","department":[{"_id":"BeVi"}],"article_processing_charge":"No","month":"12","date_created":"2025-12-10T23:40:14Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"20780","oa":1,"file_date_updated":"2025-12-11T11:00:53Z","author":[{"full_name":"Layana Franco, Lorena Alexandra","first_name":"Lorena Alexandra","orcid":"0000-0002-1253-6297","last_name":"Layana Franco","id":"02814589-eb8f-11eb-b029-a70074f3f18f"},{"full_name":"Toups, Melissa A","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"date_updated":"2025-12-15T11:13:32Z","oa_version":"None","has_accepted_license":"1","keyword":["Schizophora","sex chromosomes","sex-chromosome turnover","Diptera","genomic features","out-of-X movement."],"citation":{"ama":"Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>","ista":"Layana Franco LA, Toups MA, Vicoso B. 2025. Causes and consequences of sex-chromosome turnovers in Diptera, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>.","ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria, 2025.","mla":"Layana Franco, Lorena Alexandra, et al. <i>Causes and Consequences of Sex-Chromosome Turnovers in Diptera</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>.","chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">https://doi.org/10.15479/AT-ISTA-20780</a>.","apa":"Layana Franco, L. A., Toups, M. A., &#38; Vicoso, B. (2025). Causes and consequences of sex-chromosome turnovers in Diptera. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">https://doi.org/10.15479/AT-ISTA-20780</a>","short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, (2025)."},"corr_author":"1","license":"https://creativecommons.org/licenses/by/4.0/","type":"research_data","file":[{"checksum":"251e7aab01917c2ad2fbccf465492ea1","date_created":"2025-12-11T10:47:15Z","file_id":"20799","success":1,"file_name":"Perl_scripts.zip","file_size":4575,"creator":"llayanaf","access_level":"open_access","date_updated":"2025-12-11T10:47:15Z","content_type":"application/zip","relation":"main_file"},{"success":1,"file_size":19052849,"file_name":"Supplementary_Datasets.zip","date_created":"2025-12-11T10:52:17Z","file_id":"20800","checksum":"daf1c03149dd170b14e5c8e109ee3c77","content_type":"application/zip","relation":"main_file","date_updated":"2025-12-11T10:52:17Z","creator":"llayanaf","access_level":"open_access"},{"relation":"main_file","content_type":"application/zip","date_updated":"2025-12-11T10:52:11Z","access_level":"open_access","creator":"llayanaf","file_name":"Supplementary_Tables.zip","file_size":566476,"success":1,"file_id":"20801","date_created":"2025-12-11T10:52:11Z","checksum":"658d6e95a361b0a3db058b7b4e1733d4"},{"file_id":"20802","date_created":"2025-12-11T11:00:53Z","checksum":"2a2b92eb9fade0015719190596a8c5b7","file_name":"README.txt","file_size":1204,"success":1,"date_updated":"2025-12-11T11:00:53Z","access_level":"open_access","creator":"llayanaf","relation":"main_file","content_type":"text/plain"}],"publisher":"Institute of Science and Technology Austria"},{"doi":"10.1038/s41467-025-65420-9","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"11","OA_type":"gold","status":"public","date_published":"2025-11-25T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"Rapid prophase chromosome movements ensure faithful alignment of the parental homologous chromosomes and successful synapsis formation during meiosis. These movements are driven by cytoplasmic forces transmitted to the nuclear periphery, where chromosome ends are attached through transmembrane proteins. During many developmental stages a specific genome architecture with chromatin nuclear periphery contacts mediates specific gene expression. Whether chromatin is removed from the nuclear periphery as a consequence of chromosome motions or by a specific mechanism is not fully understood. Here, we identify a mechanism to remove chromatin from the nuclear periphery through vaccinia related kinase (VRK-1)–dependent phosphorylation of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early prophase of meiosis. Interfering with chromatin removal delays chromosome pairing, impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis. Long read sequencing reveals deletions and duplications in offspring lacking VRK-1 underscoring the importance of the BAF-1–VRK-1 module in preserving genome stability in gametes during rapid chromosome movements."}],"ddc":["570"],"file":[{"checksum":"a952f7ea050242b79008540de49a0e61","file_id":"20823","date_created":"2025-12-15T09:25:51Z","file_name":"2025_NatureComm_Paouneskou.pdf","file_size":8096309,"success":1,"access_level":"open_access","creator":"dernst","date_updated":"2025-12-15T09:25:51Z","relation":"main_file","content_type":"application/pdf"}],"day":"25","oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-12-15T09:28:37Z","oa_version":"Published Version","department":[{"_id":"BeVi"}],"publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"We are grateful to Monique Zetka, Nicola Silva, and Yumi Kim, Needhi Bhalla, George Krohne and Rueyling Lin for providing reagents; Scott Kennedy for sharing the multiplexed FISH library; and members of the Max Perutz Labs’ BioOptics facility (Irmgard Fischer, Josef Gotzmann, Thomas Peterbauer, Clara Bodner, and Nick Wedige) for training and support in image acquisition. We also thank the members of the NGS facility at the Vienna Biocenter. This work was funded by the Austrian Science Fund (FWF) SFB projects F 8805-B (VJ), https://doi.org/10.55776/F88, F 8809-B (ITB), and F8810-B (BV). We are also grateful to members of the V. Jantsch laboratory for helpful discussions. Some strains were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health Office of Research Infrastructure Programs (P40OD010440).","date_created":"2025-12-11T10:45:06Z","article_processing_charge":"Yes","year":"2025","publication":"Nature Communications","project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"article_type":"original","external_id":{"pmid":["41290579"]},"title":"BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity","volume":16,"OA_place":"publisher","DOAJ_listed":"1","type":"journal_article","publisher":"Springer Nature","PlanS_conform":"1","intvolume":"        16","author":[{"full_name":"Paouneskou, Dimitra","last_name":"Paouneskou","first_name":"Dimitra"},{"first_name":"Antoine","last_name":"Baudrimont","full_name":"Baudrimont, Antoine"},{"first_name":"Réka K","last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K"},{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N"},{"full_name":"Graf, Angela","last_name":"Graf","first_name":"Angela"},{"last_name":"Moukbel Ali Aldawla","first_name":"Shehab","full_name":"Moukbel Ali Aldawla, Shehab"},{"full_name":"Kölbl, Claudia","first_name":"Claudia","last_name":"Kölbl"},{"first_name":"Irene","last_name":"Tiemann-Boege","full_name":"Tiemann-Boege, Irene"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Verena","last_name":"Jantsch","full_name":"Jantsch, Verena"}],"file_date_updated":"2025-12-15T09:25:51Z","_id":"20796","citation":{"chicago":"Paouneskou, Dimitra, Antoine Baudrimont, Réka K Kelemen, Marwan N Elkrewi, Angela Graf, Shehab Moukbel Ali Aldawla, Claudia Kölbl, Irene Tiemann-Boege, Beatriz Vicoso, and Verena Jantsch. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-65420-9\">https://doi.org/10.1038/s41467-025-65420-9</a>.","apa":"Paouneskou, D., Baudrimont, A., Kelemen, R. K., Elkrewi, M. N., Graf, A., Moukbel Ali Aldawla, S., … Jantsch, V. (2025). BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-65420-9\">https://doi.org/10.1038/s41467-025-65420-9</a>","short":"D. Paouneskou, A. Baudrimont, R.K. Kelemen, M.N. Elkrewi, A. Graf, S. Moukbel Ali Aldawla, C. Kölbl, I. Tiemann-Boege, B. Vicoso, V. Jantsch, Nature Communications 16 (2025).","ama":"Paouneskou D, Baudrimont A, Kelemen RK, et al. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-65420-9\">10.1038/s41467-025-65420-9</a>","ieee":"D. Paouneskou <i>et al.</i>, “BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","ista":"Paouneskou D, Baudrimont A, Kelemen RK, Elkrewi MN, Graf A, Moukbel Ali Aldawla S, Kölbl C, Tiemann-Boege I, Vicoso B, Jantsch V. 2025. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. Nature Communications. 16, 10446.","mla":"Paouneskou, Dimitra, et al. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” <i>Nature Communications</i>, vol. 16, 10446, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-65420-9\">10.1038/s41467-025-65420-9</a>."},"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","article_number":"10446"},{"citation":{"mla":"Seabrook, Hannah, et al. “Surpassing the Loss-Noise Robustness Trade-off in Quantum Key Distribution.” <i>Physical Review Applied</i>, vol. 24, no. 2, 024072, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/xq2l-r4r7\">10.1103/xq2l-r4r7</a>.","ieee":"H. Seabrook, E. Lavie, K. T. Strömberg, M. P. Stafford, and G. Rubino, “Surpassing the loss-noise robustness trade-off in quantum key distribution,” <i>Physical Review Applied</i>, vol. 24, no. 2. American Physical Society, 2025.","ista":"Seabrook H, Lavie E, Strömberg KT, Stafford MP, Rubino G. 2025. Surpassing the loss-noise robustness trade-off in quantum key distribution. Physical Review Applied. 24(2), 024072.","ama":"Seabrook H, Lavie E, Strömberg KT, Stafford MP, Rubino G. Surpassing the loss-noise robustness trade-off in quantum key distribution. <i>Physical Review Applied</i>. 2025;24(2). doi:<a href=\"https://doi.org/10.1103/xq2l-r4r7\">10.1103/xq2l-r4r7</a>","short":"H. Seabrook, E. Lavie, K.T. Strömberg, M.P. Stafford, G. Rubino, Physical Review Applied 24 (2025).","apa":"Seabrook, H., Lavie, E., Strömberg, K. T., Stafford, M. P., &#38; Rubino, G. (2025). Surpassing the loss-noise robustness trade-off in quantum key distribution. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/xq2l-r4r7\">https://doi.org/10.1103/xq2l-r4r7</a>","chicago":"Seabrook, Hannah, Emilien Lavie, Karl T Strömberg, Matthew P. Stafford, and Giulia Rubino. “Surpassing the Loss-Noise Robustness Trade-off in Quantum Key Distribution.” <i>Physical Review Applied</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/xq2l-r4r7\">https://doi.org/10.1103/xq2l-r4r7</a>."},"quality_controlled":"1","article_number":"024072","scopus_import":"1","has_accepted_license":"1","_id":"20797","file_date_updated":"2025-12-15T09:39:12Z","author":[{"full_name":"Seabrook, Hannah","first_name":"Hannah","last_name":"Seabrook"},{"last_name":"Lavie","first_name":"Emilien","full_name":"Lavie, Emilien"},{"full_name":"Strömberg, Karl T","last_name":"Strömberg","id":"68011cd2-da32-11ee-a930-b2774c7aba5f","first_name":"Karl T"},{"first_name":"Matthew P.","last_name":"Stafford","full_name":"Stafford, Matthew P."},{"first_name":"Giulia","last_name":"Rubino","full_name":"Rubino, Giulia"}],"PlanS_conform":"1","publisher":"American Physical Society","intvolume":"        24","type":"journal_article","OA_place":"publisher","publication":"Physical Review Applied","year":"2025","volume":24,"external_id":{"arxiv":["2412.08694"]},"article_type":"original","title":"Surpassing the loss-noise robustness trade-off in quantum key distribution","publication_identifier":{"eissn":["2331-7019"]},"article_processing_charge":"Yes (in subscription journal)","date_created":"2025-12-11T10:46:28Z","acknowledgement":"We thank B. Baragiola, A. Boubriak, M. Clark, M. Jones, and P. Skrzypczyk for useful discussions. H.S. acknowledges financial support from EPSRC Quantum Engineering Centre for Doctoral Training Grant No. EP/SO23607/1. E.L. acknowledges support from the Engineering and Physical Sciences Research Council (EPSRC) Hub in Quantum Computing and Simulation (EP/T001062/1). T.S. acknowledges that they received no funding in support of this research. M.P.S. acknowledges support from the EPSRC Quantum Engineering Centre for Doctoral Training EP/SO23607/1 and the European Commission through Starting Grant No. ERC-2018-STG803665 (PEQEM). G.R. acknowledges support from the Royal Commission for the Exhibition of 1851 through a Research Fellowship, from the European Commission through Starting Grant No. ERC-2018-STG803665 (PEQEM) and Advanced Grant No. ERC-2020-ADG101021085 (FLQuant), and from EPSRC through Standard Proposal Grant No. EP/X016218/1 (Mono-Squeeze).","department":[{"_id":"OnHo"}],"arxiv":1,"oa_version":"Published Version","date_updated":"2025-12-15T09:40:58Z","issue":"2","language":[{"iso":"eng"}],"oa":1,"day":"29","file":[{"content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2025-12-15T09:39:12Z","success":1,"file_size":3028735,"file_name":"2025_PhysReviewApplied_Seabrook.pdf","checksum":"12ddb0414780f65b8e690fe0e6cfb95e","date_created":"2025-12-15T09:39:12Z","file_id":"20824"}],"ddc":["530"],"abstract":[{"lang":"eng","text":"Quantum key distribution (QKD) offers a theoretically secure method to share secret keys, yet practical implementations face challenges due to noise and loss over long-distance channels. Traditional QKD protocols require extensive noise compensation, hindering their industrial scalability and lowering the achievable key rates. Alternative protocols encode logical qubits in noise-resilient states but at the cost of using many physical qubits, increasing susceptibility to loss and limiting transmission distance. In this work, we introduce a logical-qubit encoding that uses antisymmetric Bell states in the continuous photonic degrees of freedom, frequency and time. By leveraging the continuous space, we overcome this noise-loss robustness trade-off by minimizing the number of photons per logical qubit while optimizing the encoding resilience over noise fluctuations. We analyze the security of our encoding and demonstrate its robustness compared to existing state-of-the-art protocols. This approach provides a path toward scalable, efficient QKD implementations under realistic noise conditions."}],"publication_status":"published","status":"public","date_published":"2025-08-29T00:00:00Z","OA_type":"hybrid","month":"08","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/xq2l-r4r7"},{"publisher":"bioRxiv","day":"10","type":"preprint","corr_author":"1","citation":{"ama":"Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. Structure of cytoplasmic RNA polymerase II. 2025. doi:<a href=\"https://doi.org/10.64898/2025.12.10.692585\">10.64898/2025.12.10.692585</a>","ieee":"A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, and C. Bernecky, “Structure of cytoplasmic RNA polymerase II.” bioRxiv, 2025.","mla":"Hlavata, Annamaria, et al. <i>Structure of Cytoplasmic RNA Polymerase II</i>. bioRxiv, 2025, doi:<a href=\"https://doi.org/10.64898/2025.12.10.692585\">10.64898/2025.12.10.692585</a>.","ista":"Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. 2025. Structure of cytoplasmic RNA polymerase II. <a href=\"https://doi.org/10.64898/2025.12.10.692585\">10.64898/2025.12.10.692585</a>.","chicago":"Hlavata, Annamaria, Benjamin Neuditschko, Ulla Schellhaas, Clemens Plaschka, Franz Herzog, and Carrie Bernecky. “Structure of Cytoplasmic RNA Polymerase II.” bioRxiv, 2025. <a href=\"https://doi.org/10.64898/2025.12.10.692585\">https://doi.org/10.64898/2025.12.10.692585</a>.","apa":"Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., &#38; Bernecky, C. (2025). Structure of cytoplasmic RNA polymerase II. bioRxiv. <a href=\"https://doi.org/10.64898/2025.12.10.692585\">https://doi.org/10.64898/2025.12.10.692585</a>","short":"A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, C. Bernecky, (2025)."},"date_updated":"2025-12-15T09:48:22Z","oa_version":"None","language":[{"iso":"eng"}],"_id":"20804","oa":1,"author":[{"full_name":"Hlavata, Annamaria","first_name":"Annamaria","last_name":"Hlavata","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Neuditschko","first_name":"Benjamin","full_name":"Neuditschko, Benjamin"},{"full_name":"Schellhaas, Ulla","last_name":"Schellhaas","first_name":"Ulla"},{"full_name":"Plaschka, Clemens","first_name":"Clemens","last_name":"Plaschka"},{"full_name":"Herzog, Franz","first_name":"Franz","last_name":"Herzog"},{"full_name":"Bernecky, Carrie A","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","orcid":"0000-0003-0893-7036"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}],"main_file_link":[{"url":"https://doi.org/10.64898/2025.12.10.692585","open_access":"1"}],"month":"12","article_processing_charge":"No","date_created":"2025-12-11T13:33:27Z","acknowledgement":"We thank A. Salmazo for assistance with Pol II purification. We thank staff at the VBCF Proteomics facility for immunoprecipitation-mass spectrometry analysis, and J.A. Stopp for assistance with IP-MS data visualization. This research was further supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaBe"}],"doi":"10.64898/2025.12.10.692585","abstract":[{"text":"RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters the nucleus, where it transcribes protein-coding genes. Although transcription by Pol II is intensively studied, how this central multi-subunit enzyme is made and the role of dedicated factors remains unclear. Here, we report the integrative structural analysis of a native human Pol II from the cytoplasm captured near the end of biogenesis. The complex contained Gdown1 and three biogenesis factors – RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the complex revealed how Gdown1 and RPAP2 associate with Pol II and prevent the premature association of transcription factors. Further biochemical and cryo-EM analysis revealed how RPAP2 recruits GPN1–GPN3 to the complex, and how the assembly of the RPAP2–GPN1–GPN3 complex is controlled by GTP hydrolysis. The combined results uncover a network of interactions that chaperone cytoplasmic Pol II to prevent aberrant interactions, reveal a GTP-controlled switch during the final stages of Pol II biogenesis, and suggest a general mechanism for the action of GPN-loop GTPase family of enzymes.","lang":"eng"}],"publication_status":"published","year":"2025","status":"public","date_published":"2025-12-10T00:00:00Z","title":"Structure of cytoplasmic RNA polymerase II"},{"type":"journal_article","intvolume":"        64","PlanS_conform":"1","publisher":"Springer Nature","_id":"20814","author":[{"first_name":"Matthias","last_name":"Keller","full_name":"Keller, Matthias"},{"full_name":"Lenz, Daniel","last_name":"Lenz","first_name":"Daniel"},{"first_name":"Marcel","last_name":"Schmidt","full_name":"Schmidt, Marcel"},{"full_name":"Schwarz, Michael","last_name":"Schwarz","first_name":"Michael"},{"orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","last_name":"Wirth","first_name":"Melchior","full_name":"Wirth, Melchior"}],"article_number":"6","scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","citation":{"chicago":"Keller, Matthias, Daniel Lenz, Marcel Schmidt, Michael Schwarz, and Melchior Wirth. “Boundary Representations of Intermediate Forms between a Regular Dirichlet Form and Its Active Main Part.” <i>Potential Analysis</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s11118-025-10251-y\">https://doi.org/10.1007/s11118-025-10251-y</a>.","short":"M. Keller, D. Lenz, M. Schmidt, M. Schwarz, M. Wirth, Potential Analysis 64 (2025).","apa":"Keller, M., Lenz, D., Schmidt, M., Schwarz, M., &#38; Wirth, M. (2025). Boundary representations of intermediate forms between a regular Dirichlet form and its active main part. <i>Potential Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11118-025-10251-y\">https://doi.org/10.1007/s11118-025-10251-y</a>","ama":"Keller M, Lenz D, Schmidt M, Schwarz M, Wirth M. Boundary representations of intermediate forms between a regular Dirichlet form and its active main part. <i>Potential Analysis</i>. 2025;64. doi:<a href=\"https://doi.org/10.1007/s11118-025-10251-y\">10.1007/s11118-025-10251-y</a>","ieee":"M. Keller, D. Lenz, M. Schmidt, M. Schwarz, and M. Wirth, “Boundary representations of intermediate forms between a regular Dirichlet form and its active main part,” <i>Potential Analysis</i>, vol. 64. Springer Nature, 2025.","mla":"Keller, Matthias, et al. “Boundary Representations of Intermediate Forms between a Regular Dirichlet Form and Its Active Main Part.” <i>Potential Analysis</i>, vol. 64, 6, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s11118-025-10251-y\">10.1007/s11118-025-10251-y</a>.","ista":"Keller M, Lenz D, Schmidt M, Schwarz M, Wirth M. 2025. Boundary representations of intermediate forms between a regular Dirichlet form and its active main part. Potential Analysis. 64, 6."},"department":[{"_id":"JaMa"}],"article_processing_charge":"Yes (via OA deal)","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL. The first three authors acknowledge financial support of the DFG within the priority programme Geometry at Infinity.\r\nM.W. acknowledges financial support by the German Academic Scholarship Foundation, by the Austrian Science Fund (FWF) through grant number F65 and the Esprit Programme [ESP 156], and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117).","date_created":"2025-12-14T23:02:03Z","publication_identifier":{"issn":["0926-2601"],"eissn":["1572-929X"]},"volume":64,"title":"Boundary representations of intermediate forms between a regular Dirichlet form and its active main part","article_type":"original","external_id":{"arxiv":["2301.01035"]},"publication":"Potential Analysis","project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"ESP156_N","name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"year":"2025","OA_place":"publisher","day":"03","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"date_updated":"2025-12-15T13:11:24Z","oa_version":"Published Version","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s11118-025-10251-y","OA_type":"hybrid","month":"12","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s11118-025-10251-y"}],"date_published":"2025-12-03T00:00:00Z","status":"public","ddc":["510"],"abstract":[{"text":"We characterize all semigroups sandwiched between the semigroup of a Dirichlet form and the semigroup of its active main part. In case the Dirichlet form is regular, we give a more explicit description of the quadratic forms of the sandwiched semigroups in terms of pairs consisting of an open set and a measure on an abstract boundary.","lang":"eng"}],"publication_status":"epub_ahead"},{"volume":26,"external_id":{"pmid":["41361833"]},"title":"Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants","article_type":"original","publication":"Genome Biology","year":"2025","OA_place":"publisher","department":[{"_id":"MaRo"}],"article_processing_charge":"Yes","date_created":"2025-12-14T23:02:04Z","acknowledgement":"Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006] and is currently supported by the Wellcome Trust [216767/Z/19/Z]. Genotyping of the Generation Scotland samples was carried out by the Genetics Core Laboratory at the Edinburgh Clinical Research Facility, University of Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” (STRADL) Reference 104036/Z/14/Z). The DNA methylation profiling and analysis was supported by Wellcome Investigator Award 220857/Z/20/Z and Grant 104036/Z/14/Z (PI: Prof AM McIntosh) and through funding from NARSAD (Ref: 27404; awardee: Dr DM Howard) and the Royal College of Physicians of Edinburgh (Sim Fellowship; Awardee: Prof HC Whalley).\r\nJAR is a University of Edinburgh Clinical Academic Track PhD student, supported by the Wellcome Trust (319878/Z/24/Z). ADC was supported by a Medical Research Council PhD Studentship in Precision Medicine with funding from the Medical Research Council Doctoral Training Program and the University of Edinburgh College of Medicine and Veterinary Medicine. HMS is a student on the University of Edinburgh Translational Neuroscience PhD programme funded by the Wellcome Trust (218493/Z/19/Z). CH was funded by MRC Human Genetics Unit program (QTL in Health and Disease) (grant U.MC_UU_00007/10). S.R.C. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (221890/Z/20/Z). JM and REM were supported by Alzheimer’s Society project grant AS-PG-19b-010.","publication_identifier":{"issn":["1474-7596"],"eissn":["1474-760X"]},"file_date_updated":"2025-12-15T13:18:07Z","_id":"20816","author":[{"first_name":"Josephine A.","last_name":"Robertson","full_name":"Robertson, Josephine A."},{"full_name":"Bajzik, Jakub","first_name":"Jakub","last_name":"Bajzik","id":"b995e25b-8c4b-11ed-a6d8-f71b7bcd6122"},{"first_name":"Spyros","last_name":"Vernardis","full_name":"Vernardis, Spyros"},{"full_name":"Chybowska, Aleksandra D.","first_name":"Aleksandra D.","last_name":"Chybowska"},{"full_name":"Mccartney, Daniel L.","first_name":"Daniel L.","last_name":"Mccartney"},{"full_name":"Grauslys, Arturas","first_name":"Arturas","last_name":"Grauslys"},{"full_name":"Mur, Jure","last_name":"Mur","first_name":"Jure"},{"first_name":"Hannah M.","last_name":"Smith","full_name":"Smith, Hannah M."},{"last_name":"Campbell","first_name":"Archie","full_name":"Campbell, Archie"},{"first_name":"Camilla","last_name":"Drake","full_name":"Drake, Camilla"},{"full_name":"Grant, Hannah","first_name":"Hannah","last_name":"Grant"},{"first_name":"Jamie","last_name":"Pearce","full_name":"Pearce, Jamie"},{"full_name":"Russ, Tom C.","first_name":"Tom C.","last_name":"Russ"},{"last_name":"Adkin","first_name":"Poppy","full_name":"Adkin, Poppy"},{"last_name":"White","first_name":"Matthew","full_name":"White, Matthew"},{"first_name":"Charles","last_name":"Brigden","full_name":"Brigden, Charles"},{"full_name":"Messner, Christoph B.","last_name":"Messner","first_name":"Christoph B."},{"last_name":"Porteous","first_name":"David J.","full_name":"Porteous, David J."},{"first_name":"Caroline","last_name":"Hayward","full_name":"Hayward, Caroline"},{"last_name":"Cox","first_name":"Simon R.","full_name":"Cox, Simon R."},{"last_name":"Zelezniak","first_name":"Aleksej","full_name":"Zelezniak, Aleksej"},{"last_name":"Ralser","first_name":"Markus","full_name":"Ralser, Markus"},{"last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"first_name":"Riccardo E.","last_name":"Marioni","full_name":"Marioni, Riccardo E."}],"quality_controlled":"1","scopus_import":"1","article_number":"417","has_accepted_license":"1","citation":{"chicago":"Robertson, Josephine A., Jakub Bajzik, Spyros Vernardis, Aleksandra D. Chybowska, Daniel L. Mccartney, Arturas Grauslys, Jure Mur, et al. “Methylome-Wide Association Studies and Epigenetic Biomarker Development for 133 Mass Spectrometry-Assessed Circulating Proteins in 14,671 Generation Scotland Participants.” <i>Genome Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1186/s13059-025-03892-0\">https://doi.org/10.1186/s13059-025-03892-0</a>.","short":"J.A. Robertson, J. Bajzik, S. Vernardis, A.D. Chybowska, D.L. Mccartney, A. Grauslys, J. Mur, H.M. Smith, A. Campbell, C. Drake, H. Grant, J. Pearce, T.C. Russ, P. Adkin, M. White, C. Brigden, C.B. Messner, D.J. Porteous, C. Hayward, S.R. Cox, A. Zelezniak, M. Ralser, M.R. Robinson, R.E. Marioni, Genome Biology 26 (2025).","apa":"Robertson, J. A., Bajzik, J., Vernardis, S., Chybowska, A. D., Mccartney, D. L., Grauslys, A., … Marioni, R. E. (2025). Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-025-03892-0\">https://doi.org/10.1186/s13059-025-03892-0</a>","ama":"Robertson JA, Bajzik J, Vernardis S, et al. Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants. <i>Genome Biology</i>. 2025;26. doi:<a href=\"https://doi.org/10.1186/s13059-025-03892-0\">10.1186/s13059-025-03892-0</a>","mla":"Robertson, Josephine A., et al. “Methylome-Wide Association Studies and Epigenetic Biomarker Development for 133 Mass Spectrometry-Assessed Circulating Proteins in 14,671 Generation Scotland Participants.” <i>Genome Biology</i>, vol. 26, 417, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1186/s13059-025-03892-0\">10.1186/s13059-025-03892-0</a>.","ieee":"J. A. Robertson <i>et al.</i>, “Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants,” <i>Genome Biology</i>, vol. 26. Springer Nature, 2025.","ista":"Robertson JA, Bajzik J, Vernardis S, Chybowska AD, Mccartney DL, Grauslys A, Mur J, Smith HM, Campbell A, Drake C, Grant H, Pearce J, Russ TC, Adkin P, White M, Brigden C, Messner CB, Porteous DJ, Hayward C, Cox SR, Zelezniak A, Ralser M, Robinson MR, Marioni RE. 2025. Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants. Genome Biology. 26, 417."},"DOAJ_listed":"1","type":"journal_article","intvolume":"        26","publisher":"Springer Nature","date_published":"2025-12-08T00:00:00Z","status":"public","ddc":["570"],"publication_status":"published","abstract":[{"text":"Background: DNA methylation (DNAm) can regulate gene expression, and its genome-wide patterns (epigenetic scores or EpiScores) can act as biomarkers for complex traits. The relative stability of methylation profiles may enable better assessment of chronic exposures compared to single time-point protein measures. We present the first large-scale epigenetic study of the highly-abundant serum proteome measured via ultra-high throughput mass spectrometry in 14,671 samples from the Generation Scotland cohort. We further demonstrate the first large-scale comparison of protein EpiScores and their respective proteins as predictors of incident cardiovascular disease.\r\n\r\nResults: Marginal epigenome-wide association models, adjusting for age, sex, measurement batch, estimated white cell proportions, BMI, smoking and methylation principal components, reveal 15,855 significant CpG – protein associations across 125 of 133 proteins PBonferroni < 2.71 × 10-10. Bayesian epigenome-wide association studies of the same 133 proteins reveal 697 CpG-Protein associations (posterior inclusion probability > 0.95). 112 protein EpiScores correlate significantly with their respective protein in a holdout test-set. Of these, sixteen associate significantly with incident all-cause cardiovascular disease (Nevents=191) compared to one measured protein.\r\n\r\nConclusions: We highlight a complex interplay between the blood-based methylome and proteome. Importantly, we show that protein EpiScores correlate with measured proteins and demonstrate that the, as-yet understudied, high-abundance proteome may yield clinically relevant biomarkers. The protein EpiScores demonstrate more significant associations with cardiovascular disease than directly measured proteins, suggesting their potential as clinical biomarkers for monitoring or predicting disease risk. We suggest that biomarker development could be enhanced by the consideration of protein EpiScores alongside measured proteins.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1186/s13059-025-03892-0","OA_type":"gold","month":"12","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"date_updated":"2025-12-15T13:19:41Z","oa_version":"Published Version","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2025-12-15T13:18:07Z","creator":"dernst","access_level":"open_access","success":1,"file_size":2206991,"file_name":"2025_GenomeBiology_Robertson.pdf","date_created":"2025-12-15T13:18:07Z","file_id":"20825","checksum":"7c92919af1b5820d01e91e08906a411f"}],"day":"08"},{"arxiv":1,"alternative_title":["PMLR"],"oa_version":"Published Version","date_updated":"2025-12-16T12:24:55Z","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"day":"01","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2025-12-16T12:21:49Z","file_name":"2025_ICML_Pervez.pdf","file_size":993381,"success":1,"checksum":"933cb673fb41416f537278fb990df6c3","file_id":"20827","date_created":"2025-12-16T12:21:49Z"}],"corr_author":"1","ddc":["000"],"publication_status":"published","abstract":[{"lang":"eng","text":"We present Mechanistic PDE Networks -- a model for discovery of governing partial differential equations from data. Mechanistic PDE Networks represent spatiotemporal data as space-time dependent linear partial differential equations in neural network hidden representations. The represented PDEs are then solved and decoded for specific tasks. The learned PDE representations naturally express the spatiotemporal dynamics in data in neural network hidden space, enabling increased modeling power. Solving the PDE representations in a compute and memory-efficient way, however, is a significant challenge. We develop a native, GPU-capable, parallel, sparse and differentiable multigrid solver specialized for linear partial differential equations that acts as a module in Mechanistic PDE Networks. Leveraging the PDE solver we propose a discovery architecture that can discovers nonlinear PDEs in complex settings, while being robust to noise. We validate PDE discovery on a number of PDEs including reaction-diffusion and Navier-Stokes equations."}],"status":"public","date_published":"2025-05-01T00:00:00Z","month":"05","OA_type":"gold","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Pervez, Adeel A, Efstratios Gavves, and Francesco Locatello. “Mechanistic PDE Networks for Discovery of Governing Equations.” In <i>42nd International Conference on Machine Learning</i>, 267:48962–73. ML Research Press, 2025.","short":"A.A. Pervez, E. Gavves, F. Locatello, in:, 42nd International Conference on Machine Learning, ML Research Press, 2025, pp. 48962–48973.","apa":"Pervez, A. A., Gavves, E., &#38; Locatello, F. (2025). Mechanistic PDE networks for discovery of governing equations. In <i>42nd International Conference on Machine Learning</i> (Vol. 267, pp. 48962–48973). Vancouver, Canada: ML Research Press.","ama":"Pervez AA, Gavves E, Locatello F. Mechanistic PDE networks for discovery of governing equations. In: <i>42nd International Conference on Machine Learning</i>. Vol 267. ML Research Press; 2025:48962-48973.","ieee":"A. A. Pervez, E. Gavves, and F. Locatello, “Mechanistic PDE networks for discovery of governing equations,” in <i>42nd International Conference on Machine Learning</i>, Vancouver, Canada, 2025, vol. 267, pp. 48962–48973.","ista":"Pervez AA, Gavves E, Locatello F. 2025. Mechanistic PDE networks for discovery of governing equations. 42nd International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 267, 48962–48973.","mla":"Pervez, Adeel A., et al. “Mechanistic PDE Networks for Discovery of Governing Equations.” <i>42nd International Conference on Machine Learning</i>, vol. 267, ML Research Press, 2025, pp. 48962–73."},"quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","_id":"20817","file_date_updated":"2025-12-16T12:21:49Z","author":[{"full_name":"Pervez, Adeel A","id":"fca6d90c-d47f-11ee-bc87-93ff51604981","last_name":"Pervez","first_name":"Adeel A"},{"full_name":"Gavves, Efstratios","last_name":"Gavves","first_name":"Efstratios"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"}],"publisher":"ML Research Press","intvolume":"       267","type":"conference","related_material":{"link":[{"relation":"software","url":"https://github.com/ alpz/mech-nn-discovery-pde"}]},"page":"48962-48973","OA_place":"publisher","publication":"42nd International Conference on Machine Learning","project":[{"call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"year":"2025","volume":267,"external_id":{"arxiv":["2502.18377"]},"title":"Mechanistic PDE networks for discovery of governing equations","publication_identifier":{"eissn":["2640-3498"]},"article_processing_charge":"No","date_created":"2025-12-14T23:02:04Z","acknowledgement":"AP. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.\r\nFL. This research was funded in whole or in part by the Austrian Science Fund (FWF) 10.55776/COE12. For open access purposes, the author has applied a CC BY public\r\ncopyright license to any author accepted manuscript version arising from this submission.","department":[{"_id":"FrLo"}],"conference":{"name":"ICML: International Conference on Machine Learning","location":"Vancouver, Canada","start_date":"2025-07-13","end_date":"2025-07-19"}},{"publication":"Plant Cell and Environment","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"}],"year":"2025","external_id":{"pmid":["41340422"]},"title":"The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha","article_type":"comment","department":[{"_id":"JiFr"}],"publication_identifier":{"eissn":["1365-3040"],"issn":["0140-7791"]},"article_processing_charge":"No","acknowledgement":"The authors sincerely thank Dr. Shutang Tan for experimental support and Dr. Barbara Kloeckener Gruissem for critical reading and constructive advice on the manuscript. This study was supported by the European Research Council Advanced Grant (ETAP-742985 to H.T. and J.F.), by the Ministry of Science and Technology (grant 112-2636-B-005-001- to K.-J.L.), and by the Ministry of Education (grant MOE-109-YSFAG-0006-001-P1 to K.-J.L.).","date_created":"2025-12-14T23:02:05Z","_id":"20818","author":[{"id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E","last_name":"Tang","orcid":"0000-0001-6152-6637","first_name":"Han","full_name":"Tang, Han"},{"full_name":"Smoljan, Adrijana","last_name":"Smoljan","id":"cced8a85-223e-11ed-af04-b0596c55053b","first_name":"Adrijana"},{"full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou","first_name":"Minxia"},{"last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","full_name":"Zhang, Yuzhou"},{"first_name":"Kuan Ju","last_name":"Lu","full_name":"Lu, Kuan Ju"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"citation":{"ieee":"H. Tang, A. Smoljan, M. Zou, Y. Zhang, K. J. Lu, and J. Friml, “The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha,” <i>Plant Cell and Environment</i>. Wiley, 2025.","mla":"Tang, Han, et al. “The MiniW Domain Directs Polarized Membrane Localization of Non-Canonical PINs in Marchantia Polymorpha.” <i>Plant Cell and Environment</i>, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/pce.70295\">10.1111/pce.70295</a>.","ista":"Tang H, Smoljan A, Zou M, Zhang Y, Lu KJ, Friml J. 2025. The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha. Plant Cell and Environment.","ama":"Tang H, Smoljan A, Zou M, Zhang Y, Lu KJ, Friml J. The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha. <i>Plant Cell and Environment</i>. 2025. doi:<a href=\"https://doi.org/10.1111/pce.70295\">10.1111/pce.70295</a>","apa":"Tang, H., Smoljan, A., Zou, M., Zhang, Y., Lu, K. J., &#38; Friml, J. (2025). The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha. <i>Plant Cell and Environment</i>. Wiley. <a href=\"https://doi.org/10.1111/pce.70295\">https://doi.org/10.1111/pce.70295</a>","short":"H. Tang, A. Smoljan, M. Zou, Y. Zhang, K.J. Lu, J. Friml, Plant Cell and Environment (2025).","chicago":"Tang, Han, Adrijana Smoljan, Minxia Zou, Yuzhou Zhang, Kuan Ju Lu, and Jiří Friml. “The MiniW Domain Directs Polarized Membrane Localization of Non-Canonical PINs in Marchantia Polymorpha.” <i>Plant Cell and Environment</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/pce.70295\">https://doi.org/10.1111/pce.70295</a>."},"quality_controlled":"1","scopus_import":"1","type":"journal_article","publisher":"Wiley","status":"public","date_published":"2025-12-03T00:00:00Z","abstract":[{"lang":"eng","text":"This study demonstrates that Marchantia non-canonical PINs are predominantly localized to the plasma membrane, with MpPINX and MpPINW exhibiting asymmetric distribution.\r\nA newly identified miniW domain within the MpPINW hydrophilic loop governs subcellular trafficking and asymmetric PM localization of non-canonical PINs in Marchantia."}],"publication_status":"epub_ahead","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1111/pce.70295","month":"12","OA_type":"closed access","language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"None","date_updated":"2025-12-15T13:56:26Z","day":"03"},{"month":"03","OA_type":"hybrid","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.ejc.2024.104104","ddc":["510"],"publication_status":"published","abstract":[{"text":"We continue a line of research which studies which hereditary families of digraphs have bounded dichromatic number. For a class of digraphs  C, a hero in  C  is any digraph  H\r\n  such that  H -free digraphs in  C  have bounded dichromatic number. We show that if  F\r\n  is an oriented star of degree at least five, the only heroes for the class of  F -free digraphs are transitive tournaments. For oriented stars  F  of degree exactly four, we show the only heroes in  F -free digraphs are transitive tournaments, or possibly special joins of transitive tournaments. Aboulker et al. characterized the set of heroes of  {H,K1+P2→} -free digraphs almost completely, and we show the same characterization for the class of  {H,rK1+P3→} -free digraphs. Lastly, we show that if we forbid two \"valid\" orientations of brooms, then every transitive tournament is a hero for this class of digraphs.","lang":"eng"}],"date_published":"2025-03-01T00:00:00Z","status":"public","day":"01","corr_author":"1","file":[{"access_level":"open_access","creator":"dernst","date_updated":"2025-04-16T09:16:25Z","relation":"main_file","content_type":"application/pdf","checksum":"2c75f78f40ebb93d16fe3765bda2905a","file_id":"19577","date_created":"2025-04-16T09:16:25Z","file_name":"2025_EuropJournCombinatorics_Carbonero.pdf","file_size":1110657,"success":1}],"oa_version":"Published Version","date_updated":"2025-05-19T14:06:00Z","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2025-01-05T23:01:55Z","acknowledgement":"We thank the anonymous referees for their careful proofreading which helped improve the presentation of this paper. We also thank one of the anonymous referees for pointing out our construction implies Theorem 1.7!\r\nBenjamin Moore finished this project while a postdoctoral researcher at Charles University, and was supported by project 22-17398S (Flows and cycles in graphs on surfaces) of the Czech Science Foundation. Benjamin Moore is currently funded by RANDSTRUCT No. 101076777, and appreciates the gracious support. We acknowledge the support of the Natural Sciences and Engineering Research Council of Canada (NSERC), [funding reference number RGPIN-2020-03912]. Cette recherche a été financée par le Conseil de recherches en sciences naturelles et en génie du Canada (CRSNG), [numéro de référence RGPIN-2020-03912]. This project was funded in part by the Government of Ontario .","publication_identifier":{"issn":["0195-6698"]},"department":[{"_id":"MaKw"}],"OA_place":"publisher","volume":125,"external_id":{"arxiv":["2306.04710"],"isi":["001400113700001"]},"title":"On heroes in digraphs with forbidden induced forests","article_type":"original","publication":"European Journal of Combinatorics","project":[{"grant_number":"101076777","name":"Randomness and structure in combinatorics","_id":"bd95085b-d553-11ed-ba76-e55d3349be45"}],"year":"2025","intvolume":"       125","publisher":"Elsevier","isi":1,"type":"journal_article","scopus_import":"1","article_number":"104104","quality_controlled":"1","has_accepted_license":"1","citation":{"ama":"Carbonero A, Koerts H, Moore B, Spirkl S. On heroes in digraphs with forbidden induced forests. <i>European Journal of Combinatorics</i>. 2025;125. doi:<a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">10.1016/j.ejc.2024.104104</a>","ieee":"A. Carbonero, H. Koerts, B. Moore, and S. Spirkl, “On heroes in digraphs with forbidden induced forests,” <i>European Journal of Combinatorics</i>, vol. 125. Elsevier, 2025.","mla":"Carbonero, Alvaro, et al. “On Heroes in Digraphs with Forbidden Induced Forests.” <i>European Journal of Combinatorics</i>, vol. 125, 104104, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">10.1016/j.ejc.2024.104104</a>.","ista":"Carbonero A, Koerts H, Moore B, Spirkl S. 2025. On heroes in digraphs with forbidden induced forests. European Journal of Combinatorics. 125, 104104.","chicago":"Carbonero, Alvaro, Hidde Koerts, Benjamin Moore, and Sophie Spirkl. “On Heroes in Digraphs with Forbidden Induced Forests.” <i>European Journal of Combinatorics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">https://doi.org/10.1016/j.ejc.2024.104104</a>.","short":"A. Carbonero, H. Koerts, B. Moore, S. Spirkl, European Journal of Combinatorics 125 (2025).","apa":"Carbonero, A., Koerts, H., Moore, B., &#38; Spirkl, S. (2025). On heroes in digraphs with forbidden induced forests. <i>European Journal of Combinatorics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">https://doi.org/10.1016/j.ejc.2024.104104</a>"},"file_date_updated":"2025-04-16T09:16:25Z","_id":"18753","author":[{"full_name":"Carbonero, Alvaro","last_name":"Carbonero","first_name":"Alvaro"},{"first_name":"Hidde","last_name":"Koerts","full_name":"Koerts, Hidde"},{"full_name":"Moore, Benjamin","id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","last_name":"Moore","first_name":"Benjamin"},{"last_name":"Spirkl","first_name":"Sophie","full_name":"Spirkl, Sophie"}]},{"publication_status":"published","abstract":[{"lang":"eng","text":"Exploring the molecular correlates of metabolic health measures may identify their shared and unique biological processes and pathways. Molecular proxies of these traits may also provide a more objective approach to their measurement. Here, DNA methylation (DNAm) data were used in epigenome-wide association studies (EWASs) and for training epigenetic scores (EpiScores) of six metabolic traits: body mass index (BMI), body fat percentage, waist-hip ratio, and blood-based measures of glucose, high-density lipoprotein cholesterol, and total cholesterol in >17,000 volunteers from the Generation Scotland (GS) cohort. We observed a maximum of 12,033 significant findings (p < 3.6 × 10−8) for BMI in a marginal linear regression EWAS. By contrast, a joint and conditional Bayesian penalized regression approach yielded 27 high-confidence associations with BMI. EpiScores trained in GS performed well in both Scottish and Singaporean test cohorts (Lothian Birth Cohort 1936 [LBC1936] and Health for Life in Singapore [HELIOS]). The EpiScores for BMI and total cholesterol performed best in HELIOS, explaining 20.8% and 7.1% of the variance in the measured traits, respectively. The corresponding results in LBC1936 were 14.4% and 3.2%, respectively. Differences were observed in HELIOS for body fat, where the EpiScore explained ∼9% of the variance in Chinese and Malay -subgroups but ∼3% in the Indian subgroup. The EpiScores also correlated with cognitive function in LBC1936 (standardized βrange: 0.08–0.12, false discovery rate p [pFDR] < 0.05). Accounting for the correlation structure across the methylome can vastly affect the number of lead findings in EWASs. The EpiScores of metabolic traits are broadly applicable across populations and can reflect differences in cognition."}],"ddc":["570"],"date_published":"2025-01-02T00:00:00Z","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"01","OA_type":"hybrid","doi":"10.1016/j.ajhg.2024.11.012","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","oa_version":"Published Version","date_updated":"2025-02-27T12:38:23Z","oa":1,"language":[{"iso":"eng"}],"day":"02","file":[{"file_size":2266488,"file_name":"2025_AJHG_Smith.pdf","success":1,"checksum":"891d120554f07da2c35d38388c29a690","file_id":"18776","date_created":"2025-01-08T09:26:42Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2025-01-08T09:26:42Z"}],"page":"106-115","OA_place":"publisher","related_material":{"link":[{"relation":"software","url":"https://github.com/marioni-group/Metabolic_trait"}]},"title":"DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts","article_type":"original","external_id":{"pmid":["39706196"],"isi":["001412498600001"]},"volume":112,"year":"2025","publication":"American Journal of Human Genetics","date_created":"2025-01-05T23:01:56Z","article_processing_charge":"No","publication_identifier":{"eissn":["1537-6605"],"issn":["0002-9297"]},"department":[{"_id":"MaRo"}],"has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","citation":{"ista":"Smith HM, Ng HK, Moodie JE, Gadd DA, Mccartney DL, Bernabeu E, Campbell A, Redmond P, Taylor A, Page D, Corley J, Harris SE, Tay D, Deary IJ, Evans KL, Robinson MR, Chambers JC, Loh M, Cox SR, Marioni RE, Hillary RF. 2025. DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. American Journal of Human Genetics. 112(1), 106–115.","ieee":"H. M. Smith <i>et al.</i>, “DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts,” <i>American Journal of Human Genetics</i>, vol. 112, no. 1. Elsevier, pp. 106–115, 2025.","mla":"Smith, Hannah M., et al. “DNA Methylation-Based Predictors of Metabolic Traits in Scottish and Singaporean Cohorts.” <i>American Journal of Human Genetics</i>, vol. 112, no. 1, Elsevier, 2025, pp. 106–15, doi:<a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">10.1016/j.ajhg.2024.11.012</a>.","ama":"Smith HM, Ng HK, Moodie JE, et al. DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. <i>American Journal of Human Genetics</i>. 2025;112(1):106-115. doi:<a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">10.1016/j.ajhg.2024.11.012</a>","apa":"Smith, H. M., Ng, H. K., Moodie, J. E., Gadd, D. A., Mccartney, D. L., Bernabeu, E., … Hillary, R. F. (2025). DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. <i>American Journal of Human Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">https://doi.org/10.1016/j.ajhg.2024.11.012</a>","short":"H.M. Smith, H.K. Ng, J.E. Moodie, D.A. Gadd, D.L. Mccartney, E. Bernabeu, A. Campbell, P. Redmond, A. Taylor, D. Page, J. Corley, S.E. Harris, D. Tay, I.J. Deary, K.L. Evans, M.R. Robinson, J.C. Chambers, M. Loh, S.R. Cox, R.E. Marioni, R.F. Hillary, American Journal of Human Genetics 112 (2025) 106–115.","chicago":"Smith, Hannah M., Hong Kiat Ng, Joanna E. Moodie, Danni A. Gadd, Daniel L. Mccartney, Elena Bernabeu, Archie Campbell, et al. “DNA Methylation-Based Predictors of Metabolic Traits in Scottish and Singaporean Cohorts.” <i>American Journal of Human Genetics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">https://doi.org/10.1016/j.ajhg.2024.11.012</a>."},"author":[{"first_name":"Hannah M.","last_name":"Smith","full_name":"Smith, Hannah M."},{"full_name":"Ng, Hong Kiat","last_name":"Ng","first_name":"Hong Kiat"},{"first_name":"Joanna E.","last_name":"Moodie","full_name":"Moodie, Joanna E."},{"first_name":"Danni A.","last_name":"Gadd","full_name":"Gadd, Danni A."},{"first_name":"Daniel L.","last_name":"Mccartney","full_name":"Mccartney, Daniel L."},{"full_name":"Bernabeu, Elena","first_name":"Elena","last_name":"Bernabeu"},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"first_name":"Paul","last_name":"Redmond","full_name":"Redmond, Paul"},{"full_name":"Taylor, Adele","first_name":"Adele","last_name":"Taylor"},{"last_name":"Page","first_name":"Danielle","full_name":"Page, Danielle"},{"last_name":"Corley","first_name":"Janie","full_name":"Corley, Janie"},{"last_name":"Harris","first_name":"Sarah E.","full_name":"Harris, Sarah E."},{"last_name":"Tay","first_name":"Darwin","full_name":"Tay, Darwin"},{"first_name":"Ian J.","last_name":"Deary","full_name":"Deary, Ian J."},{"full_name":"Evans, Kathryn L.","last_name":"Evans","first_name":"Kathryn L."},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"first_name":"John C.","last_name":"Chambers","full_name":"Chambers, John C."},{"first_name":"Marie","last_name":"Loh","full_name":"Loh, Marie"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"first_name":"Riccardo E.","last_name":"Marioni","full_name":"Marioni, Riccardo E."},{"full_name":"Hillary, Robert F.","last_name":"Hillary","first_name":"Robert F."}],"_id":"18754","file_date_updated":"2025-01-08T09:26:42Z","intvolume":"       112","publisher":"Elsevier","type":"journal_article","isi":1},{"author":[{"first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"full_name":"Pauler, Florian","first_name":"Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"_id":"18765","citation":{"ama":"Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Garcia-Marques J, Lee T, eds. <i>Lineage Tracing</i>. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>","ieee":"G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM),” in <i>Lineage Tracing</i>, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.","ista":"Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.","mla":"Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>.","chicago":"Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” In <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>.","short":"G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.), Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151.","apa":"Cheung, G. T., Pauler, F., &#38; Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques &#38; T. Lee (Eds.), <i>Lineage Tracing</i> (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>"},"scopus_import":"1","quality_controlled":"1","type":"book_chapter","publisher":"Springer Nature","intvolume":"      2886","editor":[{"full_name":"Garcia-Marques, Jorge","first_name":"Jorge","last_name":"Garcia-Marques"},{"last_name":"Lee","first_name":"Tzumin","full_name":"Lee, Tzumin"}],"place":"New York, NY","year":"2025","publication":"Lineage Tracing","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"title":"Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)","external_id":{"pmid":["39745639"]},"volume":2886,"page":"139-151","department":[{"_id":"SiHi"}],"publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"eisbn":["9781071643105"],"isbn":["9781071643099"]},"acknowledged_ssus":[{"_id":"Bio"}],"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. Experimental steps described were optimized with support provided by the Imaging & Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine (CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional funds: The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","date_created":"2025-01-07T08:36:47Z","article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"series_title":"MIMB","alternative_title":["Methods in Molecular Biology"],"oa_version":"None","date_updated":"2025-04-14T07:43:46Z","corr_author":"1","day":"03","status":"public","date_published":"2025-01-03T00:00:00Z","abstract":[{"lang":"eng","text":"Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution."}],"publication_status":"published","pmid":1,"doi":"10.1007/978-1-0716-4310-5_7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"closed access","month":"01"},{"oa":1,"language":[{"iso":"eng"}],"APC_amount":"12348 EUR","oa_version":"Published Version","date_updated":"2025-11-20T10:28:36Z","corr_author":"1","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2025-04-16T08:17:27Z","content_type":"application/pdf","relation":"main_file","checksum":"2919b30b271f395888e880076a680d73","date_created":"2025-04-16T08:17:27Z","file_id":"19573","success":1,"file_name":"2025_NatureStrucMolBiol_Tluckova.pdf","file_size":9306639}],"day":"01","date_published":"2025-04-01T00:00:00Z","status":"public","ddc":["570"],"abstract":[{"lang":"eng","text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41594-024-01448-7","pmid":1,"month":"04","OA_type":"hybrid","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2025-04-16T08:17:27Z","_id":"18778","author":[{"full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","last_name":"Tluckova","first_name":"Katarina"},{"full_name":"Kaczmarek, Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarek","first_name":"Beata M"},{"full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo","first_name":"Anita P"},{"first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A"}],"quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","citation":{"chicago":"Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41594-024-01448-7\">https://doi.org/10.1038/s41594-024-01448-7</a>.","short":"K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural &#38; Molecular Biology 32 (2025) 607–612.","apa":"Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., &#38; Bernecky, C. (2025). Mechanism of mammalian transcriptional repression by noncoding RNA. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01448-7\">https://doi.org/10.1038/s41594-024-01448-7</a>","ama":"Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. <i>Nature Structural &#38; Molecular Biology</i>. 2025;32:607-612. doi:<a href=\"https://doi.org/10.1038/s41594-024-01448-7\">10.1038/s41594-024-01448-7</a>","ista":"Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural &#38; Molecular Biology. 32, 607–612.","mla":"Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32, Springer Nature, 2025, pp. 607–12, doi:<a href=\"https://doi.org/10.1038/s41594-024-01448-7\">10.1038/s41594-024-01448-7</a>.","ieee":"K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32. Springer Nature, pp. 607–612, 2025."},"isi":1,"type":"journal_article","intvolume":"        32","publisher":"Springer Nature","volume":32,"title":"Mechanism of mammalian transcriptional repression by noncoding RNA","external_id":{"isi":["001390268000001"],"pmid":["39762629"]},"article_type":"original","publication":"Nature Structural & Molecular Biology","project":[{"_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30","name":"Regulation of mammalian transcription by noncoding RNA","grant_number":"P34185"}],"year":"2025","OA_place":"publisher","page":"607-612","related_material":{"record":[{"status":"public","id":"14644","relation":"earlier_version"}]},"department":[{"_id":"CaBe"}],"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We thank the members of the Bernecky laboratory for helpful discussions and A. Hlavata for providing Pol II for use in the fluorescence anisotropy binding assay. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade (Max Perutz Laboratories and Medical University of Vienna, Vienna, Austria) for the wild-type TFIIF expression plasmid. We thank N. Thompson and R. Burgess (McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA) for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant no. P34185 (DOI 10.55776/P34185) (C.B.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. This research was further supported by the Scientific Service Units of ISTA through resources provided by the Laboratory Support Facility, Electron Microscopy Facility, Scientific Computing and the Preclinical Facility.","date_created":"2025-01-08T11:20:20Z","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}]},{"abstract":[{"lang":"eng","text":"Feature selection is essential in the analysis of molecular systems and many other fields, but several uncertainties remain: What is the optimal number of features for a simplified, interpretable model that retains essential information? How should features with different units be aligned, and how should their relative importance be weighted? Here, we introduce the Differentiable Information Imbalance (DII), an automated method to rank information content between sets of features. Using distances in a ground truth feature space, DII identifies a low-dimensional subset of features that best preserves these relationships. Each feature is scaled by a weight, which is optimized by minimizing the DII through gradient descent. This allows simultaneously performing unit alignment and relative importance scaling, while preserving interpretability. DII can also produce sparse solutions and determine the optimal size of the reduced feature space. We demonstrate the usefulness of this approach on two benchmark molecular problems: (1) identifying collective variables that describe conformations of a biomolecule, and (2) selecting features for training a machine-learning force field. These results show the potential of DII in addressing feature selection challenges and optimizing dimensionality in various applications. The method is available in the Python library DADApy."}],"publication_status":"published","ddc":["570"],"status":"public","date_published":"2025-01-02T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"month":"01","OA_type":"gold","doi":"10.1038/s41467-024-55449-7","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_updated":"2025-02-27T12:41:25Z","oa":1,"language":[{"iso":"eng"}],"day":"02","file":[{"success":1,"file_name":"2025_NatureComm_Wild.pdf","file_size":1216738,"checksum":"b3d0f3568d9a87c494cf231a5324029a","date_created":"2025-01-14T06:59:25Z","file_id":"18846","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2025-01-14T06:59:25Z"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","OA_place":"publisher","year":"2025","publication":"Nature Communications","article_type":"original","external_id":{"isi":["001389959100009"],"pmid":["39747013"]},"title":"Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance","volume":16,"publication_identifier":{"eissn":["2041-1723"]},"date_created":"2025-01-12T23:04:00Z","acknowledgement":"The authors thank Dr. Matteo Carli for providing the CLN025 replica exchange MD trajectory and Matteo Allione for the fruitful discussions connected with the idea of the linear scaling estimator. This work was partially funded by NextGenerationEU through the Italian National Centre for HPC, Big Data, and Quantum Computing (Grant No. CN00000013 received by A.L.). A.L. also acknowledges financial support by the region Friuli Venezia Giulia (project F53C22001770002 received by A.L.).","article_processing_charge":"Yes","department":[{"_id":"AnSa"},{"_id":"BiCh"}],"citation":{"chicago":"Wild, Romina, Felix Wodaczek, Vittorio Del Tatto, Bingqing Cheng, and Alessandro Laio. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-024-55449-7\">https://doi.org/10.1038/s41467-024-55449-7</a>.","short":"R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, A. Laio, Nature Communications 16 (2025).","apa":"Wild, R., Wodaczek, F., Del Tatto, V., Cheng, B., &#38; Laio, A. (2025). Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-55449-7\">https://doi.org/10.1038/s41467-024-55449-7</a>","ama":"Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-024-55449-7\">10.1038/s41467-024-55449-7</a>","ieee":"R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, and A. Laio, “Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","ista":"Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. 2025. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. 16, 270.","mla":"Wild, Romina, et al. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” <i>Nature Communications</i>, vol. 16, 270, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-024-55449-7\">10.1038/s41467-024-55449-7</a>."},"has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","article_number":"270","author":[{"full_name":"Wild, Romina","first_name":"Romina","last_name":"Wild"},{"id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","last_name":"Wodaczek","orcid":"0009-0000-1457-795X","first_name":"Felix","full_name":"Wodaczek, Felix"},{"full_name":"Del Tatto, Vittorio","last_name":"Del Tatto","first_name":"Vittorio"},{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"last_name":"Laio","first_name":"Alessandro","full_name":"Laio, Alessandro"}],"file_date_updated":"2025-01-14T06:59:25Z","_id":"18820","publisher":"Springer Nature","intvolume":"        16","type":"journal_article","DOAJ_listed":"1","isi":1},{"day":"03","issue":"1","date_updated":"2025-02-27T12:41:58Z","oa_version":"Preprint","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"month":"01","OA_type":"green","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2408.10052","open_access":"1"}],"doi":"10.1103/PhysRevA.111.013303","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"Even though the one-dimensional contact interaction requires no regularization, renormalization methods have been shown to improve the convergence of numerical calculations considerably. In this work, we compare and contrast these methods: “the running coupling constant” where the two-body ground-state energy is used as a renormalization condition, and two effective interaction approaches that include information about the ground as well as excited states. In particular, we calculate the energies and densities of few-fermion systems in a harmonic oscillator with the configuration-interaction method and compare the results based upon renormalized and bare interactions. We find that the use of the running coupling constant instead of the bare interaction improves convergence significantly. A comparison with an effective interaction, which is designed to reproduce the relative part of the energy spectrum of two particles, showed a similar improvement. The effective interaction provides an additional improvement if the center-of-mass excitations are included in the construction. Finally, we discuss the transformation of observables alongside the renormalization of the potential, and demonstrate that this might be an essential ingredient for accurate numerical calculations.","lang":"eng"}],"date_published":"2025-01-03T00:00:00Z","status":"public","intvolume":"       111","publisher":"American Physical Society","type":"journal_article","isi":1,"scopus_import":"1","article_number":"013303","quality_controlled":"1","citation":{"chicago":"Brauneis, Fabian, Hans Werner Hammer, Stephanie M. Reimann, and Artem Volosniev. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” <i>Physical Review A</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">https://doi.org/10.1103/PhysRevA.111.013303</a>.","short":"F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111 (2025).","apa":"Brauneis, F., Hammer, H. W., Reimann, S. M., &#38; Volosniev, A. (2025). Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">https://doi.org/10.1103/PhysRevA.111.013303</a>","ama":"Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. <i>Physical Review A</i>. 2025;111(1). doi:<a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">10.1103/PhysRevA.111.013303</a>","ista":"Brauneis F, Hammer HW, Reimann SM, Volosniev A. 2025. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. 111(1), 013303.","mla":"Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” <i>Physical Review A</i>, vol. 111, no. 1, 013303, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">10.1103/PhysRevA.111.013303</a>.","ieee":"F. Brauneis, H. W. Hammer, S. M. Reimann, and A. Volosniev, “Comparison of renormalized interactions using one-dimensional few-body systems as a testbed,” <i>Physical Review A</i>, vol. 111, no. 1. American Physical Society, 2025."},"author":[{"first_name":"Fabian","last_name":"Brauneis","full_name":"Brauneis, Fabian"},{"full_name":"Hammer, Hans Werner","first_name":"Hans Werner","last_name":"Hammer"},{"full_name":"Reimann, Stephanie M.","first_name":"Stephanie M.","last_name":"Reimann"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"_id":"18821","date_created":"2025-01-12T23:04:00Z","acknowledgement":"We thank J. Cremon and J. Bjerlin for earlier contributions to the configuration-interaction calculations used in this work (see Refs. [49,50]). F.B. and S.M.R. acknowledge helpful discussions with Carl Heintze, Sandra Brandstetter, and Lila Chergui. We further want to thank Lila Chergui for helpful comments on the paper. This research was financially supported by the Knut and Alice Wallenberg Foundation (Grant No. KAW 2018.0217) and the Swedish Research Council (Grant No. 2022-03654 VR).","article_processing_charge":"No","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"department":[{"_id":"MiLe"}],"OA_place":"repository","title":"Comparison of renormalized interactions using one-dimensional few-body systems as a testbed","external_id":{"arxiv":["2408.10052"],"isi":["001398791400004"]},"article_type":"original","volume":111,"year":"2025","publication":"Physical Review A"},{"isi":1,"type":"journal_article","intvolume":"        71","publisher":"London Mathematical Society","file_date_updated":"2025-01-14T06:52:09Z","_id":"18822","author":[{"first_name":"Victor","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","last_name":"Wang","orcid":"0000-0002-0704-7026","full_name":"Wang, Victor"}],"scopus_import":"1","article_number":"e70008","quality_controlled":"1","has_accepted_license":"1","citation":{"chicago":"Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” <i>Mathematika</i>. London Mathematical Society, 2025. <a href=\"https://doi.org/10.1112/mtk.70008\">https://doi.org/10.1112/mtk.70008</a>.","short":"V. Wang, Mathematika 71 (2025).","apa":"Wang, V. (2025). Diagonal cubic forms and the large sieve. <i>Mathematika</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/mtk.70008\">https://doi.org/10.1112/mtk.70008</a>","ama":"Wang V. Diagonal cubic forms and the large sieve. <i>Mathematika</i>. 2025;71(1). doi:<a href=\"https://doi.org/10.1112/mtk.70008\">10.1112/mtk.70008</a>","ieee":"V. Wang, “Diagonal cubic forms and the large sieve,” <i>Mathematika</i>, vol. 71, no. 1. London Mathematical Society, 2025.","mla":"Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” <i>Mathematika</i>, vol. 71, no. 1, e70008, London Mathematical Society, 2025, doi:<a href=\"https://doi.org/10.1112/mtk.70008\">10.1112/mtk.70008</a>.","ista":"Wang V. 2025. Diagonal cubic forms and the large sieve. Mathematika. 71(1), e70008."},"department":[{"_id":"TiBr"}],"article_processing_charge":"Yes (via OA deal)","date_created":"2025-01-12T23:04:01Z","acknowledgement":"I thank Peter Sarnak for suggesting projects that ultimately led to the present paper. I also thank him for many encouraging discussions, helpful comments, and references. Thanks also to Tim Browning, Trevor Wooley, and Nina Zubrilina for helpful comments, and to Levent Alpöge and Will Sawin for some interesting old discussions. I thank Yang Liu, Evan O'Dorney, Ashwin Sah, and Mark Sellke for conversations illuminating the combinatorics of an older, counting version of the present Lemma 4.9. Finally, special thanks are due to the editors and referees for their patience and help with the exposition. This work was partially supported by NSF Grant DMS-1802211, and the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","publication_identifier":{"eissn":["2041-7942"],"issn":["0025-5793"]},"volume":71,"title":"Diagonal cubic forms and the large sieve","external_id":{"isi":["001388255500001"]},"article_type":"original","project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"publication":"Mathematika","year":"2025","OA_place":"publisher","corr_author":"1","file":[{"date_created":"2025-01-14T06:52:09Z","file_id":"18845","checksum":"700a8596b4bffce2320d074120962c22","success":1,"file_name":"2025_Mathematika_Wang.pdf","file_size":309893,"date_updated":"2025-01-14T06:52:09Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"day":"02","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"date_updated":"2025-04-14T07:54:56Z","oa_version":"Published Version","issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1112/mtk.70008","OA_type":"hybrid","month":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2025-01-02T00:00:00Z","status":"public","ddc":["510"],"publication_status":"published","abstract":[{"text":"Let N(X) be the number of integral zeros (mathematical equation). Works of Hooley and Heath-Brown imply (mathematical equation), if one assumes automorphy and grand Riemann hypothesis for certain Hasse–Weil L-functions. Assuming instead a natural large sieve inequality, we recover the same bound on N(X). This is part of a more general statement, for diagonal cubic forms in (mathematical equation) variables, where we allow approximations to Hasse–Weil L-functions.","lang":"eng"}]},{"day":"01","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2025-07-15T08:17:25Z","creator":"dernst","access_level":"open_access","success":1,"file_size":1214018,"file_name":"2025_PlantPhysiology_Cao.pdf","date_created":"2025-07-15T08:17:25Z","file_id":"20023","checksum":"a9b2a12d7bc6174f27e28413e9c77a9c"}],"corr_author":"1","date_updated":"2025-07-15T08:18:19Z","oa_version":"Published Version","issue":"1","oa":1,"language":[{"iso":"eng"}],"month":"01","OA_type":"hybrid","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1093/plphys/kiae651","ddc":["580"],"publication_status":"published","status":"public","date_published":"2025-01-01T00:00:00Z","publisher":"Oxford University Press","intvolume":"       197","isi":1,"type":"journal_article","citation":{"chicago":"Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” <i>Plant Physiology</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/plphys/kiae651\">https://doi.org/10.1093/plphys/kiae651</a>.","short":"D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025).","apa":"Cao, D., &#38; De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures: DNA methylation alterations across generations. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiae651\">https://doi.org/10.1093/plphys/kiae651</a>","ama":"Cao D, De Jaeger-Braet JG. Memory of maternal temperatures: DNA methylation alterations across generations. <i>Plant Physiology</i>. 2025;197(1). doi:<a href=\"https://doi.org/10.1093/plphys/kiae651\">10.1093/plphys/kiae651</a>","ista":"Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. 197(1), kiae651.","ieee":"D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation alterations across generations,” <i>Plant Physiology</i>, vol. 197, no. 1. Oxford University Press, 2025.","mla":"Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” <i>Plant Physiology</i>, vol. 197, no. 1, kiae651, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/plphys/kiae651\">10.1093/plphys/kiae651</a>."},"scopus_import":"1","quality_controlled":"1","article_number":"kiae651","has_accepted_license":"1","_id":"18823","file_date_updated":"2025-07-15T08:17:25Z","author":[{"first_name":"Dechang","last_name":"Cao","full_name":"Cao, Dechang"},{"full_name":"De Jaeger-Braet, Joke G","last_name":"De Jaeger-Braet","id":"26bd38d3-c59a-11ee-a1af-d7a988cafcc5","first_name":"Joke G"}],"publication_identifier":{"eissn":["1532-2548"]},"article_processing_charge":"Yes (in subscription journal)","date_created":"2025-01-12T23:04:02Z","department":[{"_id":"XiFe"}],"OA_place":"publisher","publication":"Plant Physiology","year":"2025","volume":197,"article_type":"original","external_id":{"isi":["001382979900001"],"pmid":["39691053"]},"title":"Memory of maternal temperatures: DNA methylation alterations across generations"},{"department":[{"_id":"JoDa"}],"doi":"10.15479/AT:ISTA:18837","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","orcid":"0000-0003-1286-7368","contributor_type":"researcher"},{"contributor_type":"researcher","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","last_name":"Truckenbrodt","first_name":"Sven M"},{"first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"last_name":"Inumella","id":"F8660870-D756-11E9-98C5-34DFE5697425","first_name":"Syamala","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Vistunou","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","first_name":"Vitali"},{"orcid":"0000-0003-1216-9105","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","contributor_type":"researcher"},{"contributor_type":"researcher","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli","first_name":"Mojtaba"},{"first_name":"Nathalie","last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"first_name":"Jakob","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","first_name":"Marek","contributor_type":"researcher"},{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"contributor_type":"researcher","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"contributor_type":"researcher","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973"}],"date_created":"2025-01-13T09:51:29Z","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","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"month":"04","article_processing_charge":"No","year":"2025","status":"public","title":"Research Data for the publication \"Super-resolution expansion microscopy in plant roots\"","date_published":"2025-04-01T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"19003"}]},"abstract":[{"lang":"eng","text":"Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. 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Research Data for the publication ‘Super-resolution expansion microscopy in plant roots’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18837\">10.15479/AT:ISTA:18837</a>.","ieee":"J. G. Danzl and C. Kreuzinger, “Research Data for the publication ‘Super-resolution expansion microscopy in plant roots.’” Institute of Science and Technology Austria, 2025.","mla":"Danzl, Johann G., and Caroline Kreuzinger. <i>Research Data for the Publication “Super-Resolution Expansion Microscopy in Plant Roots.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18837\">10.15479/AT:ISTA:18837</a>.","ama":"Danzl JG, Kreuzinger C. Research Data for the publication “Super-resolution expansion microscopy in plant roots.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18837\">10.15479/AT:ISTA:18837</a>","short":"J.G. Danzl, C. Kreuzinger, (2025).","apa":"Danzl, J. G., &#38; Kreuzinger, C. (2025). Research Data for the publication “Super-resolution expansion microscopy in plant roots.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18837\">https://doi.org/10.15479/AT:ISTA:18837</a>","chicago":"Danzl, Johann G, and Caroline Kreuzinger. “Research Data for the Publication ‘Super-Resolution Expansion Microscopy in Plant Roots.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:18837\">https://doi.org/10.15479/AT:ISTA:18837</a>."},"has_accepted_license":"1","oa_version":"None","date_updated":"2025-10-08T08:43:55Z"},{"day":"07","file":[{"date_created":"2025-01-22T14:35:22Z","file_id":"18869","checksum":"885e96690620790d5c9f188a1587b4cd","success":1,"file_name":"2025_NatureComm_Ocampo.pdf","file_size":5450660,"date_updated":"2025-01-22T14:35:22Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2025-07-03T11:58:22Z","language":[{"iso":"eng"}],"oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_type":"gold","month":"01","pmid":1,"doi":"10.1038/s41467-024-55573-4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains for DNA recognition. The sgRNA can be truncated by up to ~25% yet still retain activity in vivo. Using ancestral sequence reconstruction, we generated compact nucleases capable of efficient genome editing in mammalian cells. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for future re-engineering of minimal RNA-guided DNA endonucleases."}],"ddc":["570"],"date_published":"2025-01-07T00:00:00Z","status":"public","intvolume":"        16","publisher":"Springer Nature","type":"journal_article","DOAJ_listed":"1","has_accepted_license":"1","scopus_import":"1","article_number":"457","quality_controlled":"1","citation":{"chicago":"Ocampo, Rodrigo Fregoso, Jack Peter Kelly Bravo, Tyler L. Dangerfield, Isabel Nocedal, Samatar A. Jirde, Lisa M. Alexander, Nicole C. Thomas, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-024-55573-4\">https://doi.org/10.1038/s41467-024-55573-4</a>.","apa":"Ocampo, R. F., Bravo, J. P. K., Dangerfield, T. L., Nocedal, I., Jirde, S. A., Alexander, L. M., … Taylor, D. W. (2025). DNA targeting by compact Cas9d and its resurrected ancestor. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-55573-4\">https://doi.org/10.1038/s41467-024-55573-4</a>","short":"R.F. Ocampo, J.P.K. Bravo, T.L. Dangerfield, I. Nocedal, S.A. Jirde, L.M. Alexander, N.C. Thomas, A. Das, S. Nielson, K.A. Johnson, C.T. Brown, C.N. Butterfield, D.S.A. Goltsman, D.W. Taylor, Nature Communications 16 (2025).","ama":"Ocampo RF, Bravo JPK, Dangerfield TL, et al. DNA targeting by compact Cas9d and its resurrected ancestor. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-024-55573-4\">10.1038/s41467-024-55573-4</a>","mla":"Ocampo, Rodrigo Fregoso, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” <i>Nature Communications</i>, vol. 16, 457, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-024-55573-4\">10.1038/s41467-024-55573-4</a>.","ieee":"R. F. Ocampo <i>et al.</i>, “DNA targeting by compact Cas9d and its resurrected ancestor,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","ista":"Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor DW. 2025. DNA targeting by compact Cas9d and its resurrected ancestor. Nature Communications. 16, 457."},"author":[{"full_name":"Ocampo, Rodrigo Fregoso","last_name":"Ocampo","first_name":"Rodrigo Fregoso"},{"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":"Dangerfield, Tyler L.","last_name":"Dangerfield","first_name":"Tyler L."},{"full_name":"Nocedal, Isabel","first_name":"Isabel","last_name":"Nocedal"},{"full_name":"Jirde, Samatar A.","last_name":"Jirde","first_name":"Samatar A."},{"first_name":"Lisa M.","last_name":"Alexander","full_name":"Alexander, Lisa M."},{"last_name":"Thomas","first_name":"Nicole C.","full_name":"Thomas, Nicole C."},{"last_name":"Das","first_name":"Anjali","full_name":"Das, Anjali"},{"first_name":"Sarah","last_name":"Nielson","full_name":"Nielson, Sarah"},{"full_name":"Johnson, Kenneth A.","last_name":"Johnson","first_name":"Kenneth A."},{"full_name":"Brown, Christopher T.","last_name":"Brown","first_name":"Christopher T."},{"full_name":"Butterfield, Cristina N.","last_name":"Butterfield","first_name":"Cristina N."},{"last_name":"Goltsman","first_name":"Daniela S.A.","full_name":"Goltsman, Daniela S.A."},{"last_name":"Taylor","first_name":"David W.","full_name":"Taylor, David W."}],"file_date_updated":"2025-01-22T14:35:22Z","_id":"18848","date_created":"2025-01-19T23:01:50Z","acknowledgement":"We would like to thank M. Ocampo Camacho and M.F. Canedo Ocampo for assistance with the figures. We thank M. Hooper for assistance developing the GFP assay and operating the CE machine for in vitro cleavage analysis. We thank E. Schwartz and A. Brilot for expert cryo-EM support in the Sauer Structural Biology Laboratory at UT Austin. This work was funded, in part, by a sponsored research agreement with Metagenomi, Inc. (to D.W.T), a Welch Foundation Research Grant F-1938 (to D.W.T), and the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation Medical Research Grant (to D.W.T), and a grant from the National Institute of Allergy and Infectious Diseases (NIAID 1R01AI110577 to K.A.J.).","article_processing_charge":"Yes","publication_identifier":{"eissn":["2041-1723"]},"department":[{"_id":"JaBr"}],"OA_place":"publisher","article_type":"original","title":"DNA targeting by compact Cas9d and its resurrected ancestor","external_id":{"pmid":["39774105"]},"volume":16,"year":"2025","publication":"Nature Communications"},{"date_published":"2025-01-07T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks."}],"ddc":["570"],"pmid":1,"doi":"10.1073/pnas.2402925121","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"month":"01","OA_type":"hybrid","language":[{"iso":"eng"}],"oa":1,"issue":"1","date_updated":"2026-02-16T12:26:51Z","oa_version":"Published Version","corr_author":"1","file":[{"success":1,"file_name":"2025_PNAS_Sokolowski.pdf","file_size":19073585,"checksum":"8dbfc7d495413340225ebfae69b0cf9a","date_created":"2025-01-20T10:10:04Z","file_id":"18862","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2025-01-20T10:10:04Z"}],"day":"07","title":"Deriving a genetic regulatory network from an optimization principle","article_type":"original","external_id":{"pmid":["39752518"],"isi":["001392772400001"]},"volume":122,"year":"2025","publication":"Proceedings of the National Academy of Sciences","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF"},{"_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"}],"OA_place":"publisher","department":[{"_id":"GaTk"}],"date_created":"2025-01-19T23:01:50Z","acknowledgement":"We thank Nicholas H. Barton for his comments on the manuscript, Benjamin Zoller for helpful discussions, and Aleksandra Walczak and Curtis Callan for early collaborations that shaped this work. Special thanks to Eric F. Wieschaus for many persistently inspiring conversations. This work was supported in part by the Human Frontiers Science Program; the Austrian Science Fund (FWF P28844); by the European Research Council grant DynaTrans (101118866); by U.S. NSF, through the Center for the Physics of Biological Function (PHY–1734030); by NIH Grants R01GM097275, U01DA047730, and U01DK127429; by the John Simon Guggenheim Memorial Foundation; and by the LOEWE priority program “Center for Multiscale Modeling in Life Sciences” (CMMS), sponsored by the Hessian Ministry for Science and Research, Arts and Culture (HMWK).","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"author":[{"first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"_id":"18849","file_date_updated":"2025-01-20T10:10:04Z","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","article_number":"e2402925121","citation":{"ieee":"T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic regulatory network from an optimization principle,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1. National Academy of Sciences, 2025.","ista":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. 2025. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. 122(1), e2402925121.","mla":"Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>.","ama":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory network from an optimization principle. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(1). doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>","short":"T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025).","apa":"Sokolowski, T. R., Gregor, T., Bialek, W., &#38; Tkačik, G. (2025). Deriving a genetic regulatory network from an optimization principle. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2402925121\">https://doi.org/10.1073/pnas.2402925121</a>","chicago":"Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2402925121\">https://doi.org/10.1073/pnas.2402925121</a>."},"type":"journal_article","isi":1,"intvolume":"       122","publisher":"National Academy of Sciences"},{"file_date_updated":"2025-01-20T09:38:32Z","_id":"18850","author":[{"full_name":"Perkins, Mindy Liu","first_name":"Mindy Liu","last_name":"Perkins"},{"full_name":"Crocker, Justin","first_name":"Justin","last_name":"Crocker"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"citation":{"apa":"Perkins, M. L., Crocker, J., &#38; Tkačik, G. (2025). Chromatin enables precise and scalable gene regulation with factors of limited specificity. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2411887121\">https://doi.org/10.1073/pnas.2411887121</a>","short":"M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025).","chicago":"Perkins, Mindy Liu, Justin Crocker, and Gašper Tkačik. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2411887121\">https://doi.org/10.1073/pnas.2411887121</a>.","ista":"Perkins ML, Crocker J, Tkačik G. 2025. Chromatin enables precise and scalable gene regulation with factors of limited specificity. Proceedings of the National Academy of Sciences. 122(1), e2411887121.","ieee":"M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable gene regulation with factors of limited specificity,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1. National Academy of Sciences, 2025.","mla":"Perkins, Mindy Liu, et al. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1, e2411887121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2411887121\">10.1073/pnas.2411887121</a>.","ama":"Perkins ML, Crocker J, Tkačik G. Chromatin enables precise and scalable gene regulation with factors of limited specificity. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(1). doi:<a href=\"https://doi.org/10.1073/pnas.2411887121\">10.1073/pnas.2411887121</a>"},"scopus_import":"1","article_number":"e2411887121","quality_controlled":"1","has_accepted_license":"1","isi":1,"type":"journal_article","publisher":"National Academy of Sciences","intvolume":"       122","project":[{"grant_number":"101118866","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"}],"publication":"Proceedings of the National Academy of Sciences","year":"2025","volume":122,"external_id":{"pmid":["39793086"],"isi":["001392765300001"]},"title":"Chromatin enables precise and scalable gene regulation with factors of limited specificity","article_type":"original","related_material":{"link":[{"url":"https://github.com/officerredshirt/network_crosstalk","relation":"software"}]},"OA_place":"publisher","department":[{"_id":"GaTk"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_processing_charge":"No","acknowledgement":"M.L.P. was supported by the European Molecular Biology Laboratory (EMBL) Interdisciplinary Postdoc Programme (EIPOD4 fellowships), cofunded by Marie SkÅ‚odowska-Curie Actions (Grant Agreement No. 847543). J.C. and M.L.P. were supported by EMBL Core Funding and Theory@EMBL. This work is supported by European Research Council Grant DynaTrans (101118866) to G.T. We would like to thank the members of the J.C. and G.T. groups, especially Natalia Misunou, Michal Hledík, and Réka Borbély, for helpful feedback and discussion. We also thank EMBL IT Services for the use of high performance computing resources.","date_created":"2025-01-19T23:01:51Z","APC_amount":"2750 USD","oa":1,"language":[{"iso":"eng"}],"date_updated":"2026-02-16T12:27:25Z","oa_version":"Published Version","issue":"1","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2025-01-20T09:38:32Z","file_name":"2025_PNAS_Perkins.pdf","file_size":30943709,"success":1,"checksum":"86a8d25a6e282aeb4128f1d0b86ff911","file_id":"18859","date_created":"2025-01-20T09:38:32Z"}],"corr_author":"1","day":"07","status":"public","date_published":"2025-01-07T00:00:00Z","ddc":["570"],"abstract":[{"lang":"eng","text":"Biophysical constraints limit the specificity with which transcription factors (TFs) can target regulatory DNA. While individual nontarget binding events may be low affinity, the sheer number of such interactions could present a challenge for gene regulation by degrading its precision or possibly leading to an erroneous induction state. Chromatin can prevent nontarget binding by rendering DNA physically inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by pioneer factors (PFs). Under what conditions and by how much can chromatin reduce regulatory errors on a global scale? We use a theoretical approach to compare two scenarios for gene regulation: one that relies on TF binding to free DNA alone and one that uses a combination of TFs and chromatin-regulating PFs to achieve desired gene expression patterns. We find, first, that chromatin effectively silences groups of genes that should be simultaneously OFF, thereby allowing more accurate graded control of expression for the remaining ON genes. Second, chromatin buffers the deleterious consequences of nontarget binding as the number of OFF genes grows, permitting a substantial expansion in regulatory complexity. Third, chromatin-based regulation productively co-opts nontarget TF binding for ON genes in order to establish a “leaky” baseline expression level, which targeted activator or repressor binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin simultaneously alleviates pressure for high specificity of regulatory interactions and enables an increase in genome size with minimal impact on global expression error."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1073/pnas.2411887121","pmid":1,"OA_type":"hybrid","month":"01","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"}}]