--- OA_place: publisher OA_type: hybrid _id: '22956' abstract: - lang: eng text: Tissue regeneration requires de novo patterning, which has been proposed to be facilitated by cellular heterogeneity. Yet how such heterogeneities are integrated with the mechanochemical state of the tissue and stabilized at the chromatin level into stable, spatially organized fates remains poorly understood. Using in vivo mouse intestinal regeneration models and organoids, we identify a critical density regime that produces a permissive window for heterogeneity in the mechanosensor Yes-associated protein 1 (YAP1). We show that YAP1 heterogeneity is coupled to lineage-biased chromatin accessibility and is decoded through FOXA1, which integrates the permissive chromatin state to Delta-Notch supracellular feedback and lineage commitment. This circuit generates fate bistability and preserves a memory of transient YAP1 activity, thereby maintaining spatial patterning as tissues return to homeostasis after injury. Together, our findings establish a multiscale framework in which tissue-scale mechanics tune single-cell competence and, through FOXA1-mediated bistability, convert transient heterogeneity into stable and self-organized tissue architecture. acknowledgement: We thank the Liberali group, M. Verbeek, and C. Soneson for fruitful discussions; E. Tagliavini for IT support; J. Lüthi for Fractal support; H. Köhler for FACS sorting; T.O. Buchholz for help on cell segmentation; B. Treutlein and A. Xavier da Silveira dos Santos for help with library preparation of single-cell ATAC-seq; M. Garioni for help with mouse salivary organoids; M. Kahnwald for help with human intestinal organoids; M. Lütolf, M. Nikolaev, and O. Mitrofanova for providing material and initial training for microwell experiments; J. Tchorz and V. Orsini for intestinal tissue sections of the YAP1 activator experiment in homeostasis; R. Kageyama for DLL1-Venus-T2A-mCherry mice; J.-F. Spetz for technical assistance; C. Lambert and N. Accart for help with sample preparation; Claudia Flandoli for graphic design of schemes; and Zuzana Nascakova for the graphical abstract. We thank the Foundation Hubrecht Organoid Technology (now Foundation Hubrecht Organoid Biobank, https://www.hubrechtorganoidbiobank.org/) for the duodenal organoid line used in this study (HUB-04-A2-001). We thank C.P. Heisenberg, M. Lütolf, C. Tsiairis, J. Zaugg, G. D’Angelo, L. Giorgetti, S. Arber, and the Liberali group for reading the manuscript. C.S. was supported by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 660-2020) and the Human Frontier Science Program (HFSP) LT000746/2021-L. D.B.B. was supported by the NOMIS Foundation as a NOMIS fellow, an EMBO Postdoctoral Fellowship (ALTF 343-2022), and the Austrian Academy of Sciences through an APART-MINT Fellowship. B.S. was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust (FC001159). This work received funding from ERC to E.H. (grant number 851288) and to P.L. (grant number 758617) and from SNSF (310030_208162 and SNSF ERC TMCG-3_223263). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Cornelia full_name: Schwayer, Cornelia id: 3436488C-F248-11E8-B48F-1D18A9856A87 last_name: Schwayer orcid: 0000-0001-5130-2226 - first_name: Silvia full_name: Barbiero, Silvia last_name: Barbiero - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Koen C. full_name: Oost, Koen C. last_name: Oost - first_name: Clara full_name: Baader, Clara last_name: Baader - first_name: Nicole A. full_name: Repina, Nicole A. last_name: Repina - first_name: Jinse full_name: Kim, Jinse last_name: Kim - first_name: Oscar E. full_name: Diaz, Oscar E. last_name: Diaz - first_name: Isa full_name: Uccelli, Isa last_name: Uccelli - first_name: Laura full_name: Capolupo, Laura last_name: Capolupo - first_name: Ludivine Challet full_name: Meylan, Ludivine Challet last_name: Meylan - first_name: Veronique full_name: Kalck, Veronique last_name: Kalck - first_name: Franziska full_name: Moos, Franziska last_name: Moos - first_name: Simon full_name: Suppinger, Simon last_name: Suppinger - first_name: Qiutan full_name: Yang, Qiutan last_name: Yang - first_name: Jakob full_name: Schnabl, Jakob last_name: Schnabl - first_name: Umut full_name: Kilik, Umut last_name: Kilik - first_name: Matthieu full_name: Bourdon, Matthieu last_name: Bourdon - first_name: J. Gray full_name: Camp, J. Gray last_name: Camp - first_name: Brigitta full_name: Stockinger, Brigitta last_name: Stockinger - first_name: Alessandra full_name: Ferrari, Alessandra last_name: Ferrari - first_name: Marc full_name: Bühler, Marc last_name: Bühler - first_name: Michael B. full_name: Stadler, Michael B. last_name: Stadler - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Prisca full_name: Liberali, Prisca last_name: Liberali citation: ama: Schwayer C, Barbiero S, Brückner D, et al. Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. Cell. 2026;189(17):5266-5282.e17. doi:10.1016/j.cell.2026.06.009 apa: Schwayer, C., Barbiero, S., Brückner, D., Oost, K. C., Baader, C., Repina, N. A., … Liberali, P. (2026). Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. Cell. Cell Press. https://doi.org/10.1016/j.cell.2026.06.009 chicago: Schwayer, Cornelia, Silvia Barbiero, David Brückner, Koen C. Oost, Clara Baader, Nicole A. Repina, Jinse Kim, et al. “Multiscale Integration of Tissue and Chromatin Context Converts Cell Heterogeneity into Stable Intestinal Patterning.” Cell. Cell Press, 2026. https://doi.org/10.1016/j.cell.2026.06.009. ieee: C. Schwayer et al., “Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning,” Cell, vol. 189, no. 17. Cell Press, p. 5266–5282.e17, 2026. ista: Schwayer C, Barbiero S, Brückner D, Oost KC, Baader C, Repina NA, Kim J, Diaz OE, Uccelli I, Capolupo L, Meylan LC, Kalck V, Moos F, Suppinger S, Yang Q, Schnabl J, Kilik U, Bourdon M, Camp JG, Stockinger B, Ferrari A, Bühler M, Stadler MB, Hannezo EB, Liberali P. 2026. Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. Cell. 189(17), 5266–5282.e17. mla: Schwayer, Cornelia, et al. “Multiscale Integration of Tissue and Chromatin Context Converts Cell Heterogeneity into Stable Intestinal Patterning.” Cell, vol. 189, no. 17, Cell Press, 2026, p. 5266–5282.e17, doi:10.1016/j.cell.2026.06.009. short: C. Schwayer, S. Barbiero, D. Brückner, K.C. Oost, C. Baader, N.A. Repina, J. Kim, O.E. Diaz, I. Uccelli, L. Capolupo, L.C. Meylan, V. Kalck, F. Moos, S. Suppinger, Q. Yang, J. Schnabl, U. Kilik, M. Bourdon, J.G. Camp, B. Stockinger, A. Ferrari, M. Bühler, M.B. Stadler, E.B. Hannezo, P. Liberali, Cell 189 (2026) 5266–5282.e17. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: "All sequencing data have been deposited at the Gene Expression Omnibus (GEO) under accession number GEO: GSE283662.\r\nAnalysis of imaging and sequencing data was developed in the Liberali lab and is available at https://github.com/LiberaliLab/symmetry-breaking-2026. Detailed information on the packages used is provided in the STAR Methods section.\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request." date_created: 2026-09-17T11:06:12Z date_published: 2026-08-20T00:00:00Z date_updated: 2026-10-01T08:42:00Z day: '20' ddc: - '570' doi: 10.1016/j.cell.2026.06.009 ec_funded: 1 external_id: pmid: - '42379166' file: - access_level: open_access checksum: 3ff0f4f8be0e79940ba11b18af318ae3 content_type: application/pdf creator: dernst date_created: 2026-10-01T08:34:11Z date_updated: 2026-10-01T08:34:11Z file_id: '23014' file_name: 2026_Cell_Schwayer.pdf file_size: 15536364 relation: main_file success: 1 file_date_updated: 2026-10-01T08:34:11Z fulldoi: https://doi.org/10.1016/j.cell.2026.06.009 has_accepted_license: '1' intvolume: ' 189' issue: '17' keyword: - tissue patterning - heterogeneity - mechanics - intestinal regeneration - epigenetic competence - multiscale integration - modeling - organoids - image-based phenotyping - Yap1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 5266-5282.e17 pmid: 1 project: - _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b grant_number: ALTF 343-2022 name: A mechano-chemical theory for stem cell fate decisions in organoid development - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 189 year: '2026' ... --- OA_type: closed access _id: '22144' abstract: - lang: eng text: Most cells polarize and migrate in response to electrical fields. In this issue of Cell, Belliveau et al. identify TMEM154/Galvanin, a receptor that serves as a cellular antenna to sense electrical gradients and guide migration toward the cathode. article_processing_charge: No article_type: comment author: - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Riedl M, Sixt MK. A new sense for electrical fields. Cell. 2026;189(13):3845-3846. doi:10.1016/j.cell.2026.05.038 apa: Riedl, M., & Sixt, M. K. (2026). A new sense for electrical fields. Cell. Cell Press. https://doi.org/10.1016/j.cell.2026.05.038 chicago: Riedl, Michael, and Michael K Sixt. “A New Sense for Electrical Fields.” Cell. Cell Press, 2026. https://doi.org/10.1016/j.cell.2026.05.038. ieee: M. Riedl and M. K. Sixt, “A new sense for electrical fields,” Cell, vol. 189, no. 13. Cell Press, pp. 3845–3846, 2026. ista: Riedl M, Sixt MK. 2026. A new sense for electrical fields. Cell. 189(13), 3845–3846. mla: Riedl, Michael, and Michael K. Sixt. “A New Sense for Electrical Fields.” Cell, vol. 189, no. 13, Cell Press, 2026, pp. 3845–46, doi:10.1016/j.cell.2026.05.038. short: M. Riedl, M.K. Sixt, Cell 189 (2026) 3845–3846. corr_author: '1' das_tickbox: '0' date_created: 2026-06-28T22:01:34Z date_published: 2026-06-25T00:00:00Z date_updated: 2026-10-20T09:00:16Z day: '25' department: - _id: MiSi doi: 10.1016/j.cell.2026.05.038 fulldoi: https://doi.org/10.1016/j.cell.2026.05.038 intvolume: ' 189' issue: '13' language: - iso: eng month: '06' oa_version: None page: 3845-3846 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: A new sense for electrical fields type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 189 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22955' abstract: - lang: eng text: The regulation of 3D cell shape is a fundamental problem of life. In multicellular tissues, cell shape emerges through the balance of forces inside and outside the cell. In epithelia, the basement membrane (BM) is the first extracellular barrier that cells sense biochemically and mechanically. Despite this, little is known about how BM mechanical properties are regulated and how they impact cell shape. Through mathematical modeling, we show that the stress relaxation time of the BM can regulate cell shape. Using molecular dynamics simulations, we show that the stress relaxation time of a collagen IV network can be inferred from the lifetime of collagen IV molecules. To measure collagen IV lifetime in vivo, we develop a fluorescent timer reporter for collagen IV and show that perlecan modifies collagen IV lifetime. This cross-disciplinary approach establishes a multiscale framework to probe matrix turnover, and its regulation and function in cell shape control. acknowledgement: "We thank all members of the Mao lab for insightful discussions throughout the project, and we thank Giulia Paci and Nargess Khalilgharibi for critical reading of the manuscript. We thank Jonathan Chubb for molecular biology guidance and WellGenetics for generating the timer protein fly lines.\r\nR.B. was funded by a UCL COMPLEX PhD studentship and a Leverhulme Trust project grant RPG-2020-068 awarded to Y.M. B.M. and A.S. were funded by the European Union Horizon 2020 research and innovation programme (ERC starting grant no. 802960). S.B. was funded by NIH R35 GM143042. G.C. was funded by EPSRC Physics of Life, grants EP/W023806 and EP/W023865. B.J.S.S. and B.M.S. are funded by the Wellcome Trust (grant no. 301803/Z/23/Z to B.M.S.). E.K.P. was funded by the Medical Research Council UK (MRC programme award MC_UU_12018/5). Y.M. was funded by MRC award MR/W027437/1, a Lister Institute Research Prize, and the EMBO Young Investigator Programme." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ricardo full_name: Barrientos, Ricardo last_name: Barrientos - first_name: Billie full_name: Meadowcroft, Billie id: a4725fd6-932b-11ed-81e2-c098c7f37ae1 last_name: Meadowcroft orcid: 0000-0003-3441-1337 - first_name: Besaiz J. full_name: Sánchez-Sánchez, Besaiz J. last_name: Sánchez-Sánchez - first_name: Brian M. full_name: Stramer, Brian M. last_name: Stramer - first_name: Ewa K. full_name: Paluch, Ewa K. last_name: Paluch - first_name: Guillaume full_name: Charras, Guillaume last_name: Charras - first_name: Shiladitya full_name: Banerjee, Shiladitya last_name: Banerjee - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Yanlan full_name: Mao, Yanlan last_name: Mao citation: ama: Barrientos R, Meadowcroft B, Sánchez-Sánchez BJ, et al. Basement membrane turnover controls cell shape. Cell. 2026;189(18):5611-5624.e4. doi:10.1016/j.cell.2026.07.010 apa: Barrientos, R., Meadowcroft, B., Sánchez-Sánchez, B. J., Stramer, B. M., Paluch, E. K., Charras, G., … Mao, Y. (2026). Basement membrane turnover controls cell shape. Cell. Cell Press. https://doi.org/10.1016/j.cell.2026.07.010 chicago: Barrientos, Ricardo, Billie Meadowcroft, Besaiz J. Sánchez-Sánchez, Brian M. Stramer, Ewa K. Paluch, Guillaume Charras, Shiladitya Banerjee, Anđela Šarić, and Yanlan Mao. “Basement Membrane Turnover Controls Cell Shape.” Cell. Cell Press, 2026. https://doi.org/10.1016/j.cell.2026.07.010. ieee: R. Barrientos et al., “Basement membrane turnover controls cell shape,” Cell, vol. 189, no. 18. Cell Press, p. 5611–5624.e4, 2026. ista: Barrientos R, Meadowcroft B, Sánchez-Sánchez BJ, Stramer BM, Paluch EK, Charras G, Banerjee S, Šarić A, Mao Y. 2026. Basement membrane turnover controls cell shape. Cell. 189(18), 5611–5624.e4. mla: Barrientos, Ricardo, et al. “Basement Membrane Turnover Controls Cell Shape.” Cell, vol. 189, no. 18, Cell Press, 2026, p. 5611–5624.e4, doi:10.1016/j.cell.2026.07.010. short: R. Barrientos, B. Meadowcroft, B.J. Sánchez-Sánchez, B.M. Stramer, E.K. Paluch, G. Charras, S. Banerjee, A. Šarić, Y. Mao, Cell 189 (2026) 5611–5624.e4. das_tickbox: '1' dataavailabilitystatement: "The fly line generated in this study is available from the lead contact without restriction.\r\nData and code availability\r\n•\r\nCollagen IV fluorescent timer image data and associated data analysis code have been deposited in the UCL Research Data Repository at https://doi.org/10.5522/04/32647191 and are publicly available as of the date of publication.\r\n•\r\nAll original code associated with the tissue mechanics model has also been deposited in the UCL Research Data Repository at https://doi.org/10.5522/04/32647191 and is publicly available as of the date of publication.\r\n•\r\nAll original code associated with the collagen IV network model has been deposited on Zenodo at https://doi.org/10.5281/zenodo.20719515 and is publicly available as of the date of publication.\r\n•\r\nAny additional information reported in this paper is available from the lead contact upon request." date_created: 2026-09-17T11:06:06Z date_published: 2026-09-03T00:00:00Z date_updated: 2026-10-20T09:04:52Z day: '03' ddc: - '570' department: - _id: AnSa doi: 10.1016/j.cell.2026.07.010 ec_funded: 1 external_id: pmid: - '42532043' file: - access_level: open_access checksum: 01e74f866223ca9ea8680b617d4aa4e3 content_type: application/pdf creator: dernst date_created: 2026-09-24T12:35:11Z date_updated: 2026-09-24T12:35:11Z file_id: '22990' file_name: 2026_Cell_Barrientos.pdf file_size: 5642382 relation: main_file success: 1 file_date_updated: 2026-09-24T12:35:11Z fulldoi: https://doi.org/10.1016/j.cell.2026.07.010 has_accepted_license: '1' intvolume: ' 189' issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 5611-5624.e4 pmid: 1 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Basement membrane turnover controls cell shape tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 189 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '18879' abstract: - lang: eng text: 'Our brain has remarkable computational power, generating sophisticated behaviors, storing memories over an individual’s lifetime, and producing higher cognitive functions. However, little of our neuroscience knowledge covers the human brain. Is this organ truly unique, or is it a scaled version of the extensively studied rodent brain? Combining multicellular patch-clamp recording with expansion-based superresolution microscopy and full-scale modeling, we determined the cellular and microcircuit properties of the human hippocampal CA3 region, a fundamental circuit for memory storage. In contrast to neocortical networks, human hippocampal CA3 displayed sparse connectivity, providing a circuit architecture that maximizes associational power. Human synapses showed unique reliability, high precision, and long integration times, exhibiting both species- and circuit-specific properties. Together with expanded neuronal numbers, these circuit characteristics greatly enhanced the memory storage capacity of CA3. Our results reveal distinct microcircuit properties of the human hippocampus and begin to unravel the inner workings of our most complex organ. ' acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: ScienComp acknowledgement: We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, Walter Kaufmann for assistance with handling frozen tissue, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, Miba Machine Shop, and Scientific Computing. We are particularly grateful to the patient donors for their support of this project and also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff; Romana Hoeftberger and the Division of Neuropathology and Neurochemistry; Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology; and Christoph Baumgartner, Martha Feucht, and Ekaterina Pataraia for their clinical care of the patients included in this study. We thank Laura Jonkman, the NABCA biobank, and postmortem brain sample donors for their support of this research. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (advanced grant no. 692692 to P.J. and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J. and grant DK W1232 to M.R.T. and J.G.D.), the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.), and a NOMIS-ISTA fellowship (to A.N.-O.). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Victor M full_name: Vargas Barroso, Victor M id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87 last_name: Vargas Barroso - first_name: Rebecca full_name: Morse, Rebecca id: ceb89ae7-dc8d-11ea-abe3-da3301d0eab4 last_name: Morse - first_name: Andrea C full_name: Navas Olivé, Andrea C id: 739d26c9-52e8-11ee-8d72-f14d3893b4ce last_name: Navas Olivé orcid: 0000-0002-9280-8597 - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Matthias full_name: Tomschik, Matthias last_name: Tomschik - first_name: Karl full_name: Rössler, Karl last_name: Rössler - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Watson J, Vargas Barroso VM, Morse R, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell. 2025;188(2):501-514.e18. doi:10.1016/j.cell.2024.11.022 apa: Watson, J., Vargas Barroso, V. M., Morse, R., Navas Olivé, A. C., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (2025). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell. Cell Press. https://doi.org/10.1016/j.cell.2024.11.022 chicago: Watson, Jake, Victor M Vargas Barroso, Rebecca Morse, Andrea C Navas Olivé, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” Cell. Cell Press, 2025. https://doi.org/10.1016/j.cell.2024.11.022. ieee: J. Watson et al., “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” Cell, vol. 188, no. 2. Cell Press, p. 501–514.e18, 2025. ista: Watson J, Vargas Barroso VM, Morse R, Navas Olivé AC, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. 2025. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell. 188(2), 501–514.e18. mla: Watson, Jake, et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” Cell, vol. 188, no. 2, Cell Press, 2025, p. 501–514.e18, doi:10.1016/j.cell.2024.11.022. short: J. Watson, V.M. Vargas Barroso, R. Morse, A.C. Navas Olivé, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, Cell 188 (2025) 501–514.e18. corr_author: '1' date_created: 2025-01-26T23:01:49Z date_published: 2025-01-23T00:00:00Z date_updated: 2026-10-20T08:20:04Z day: '23' ddc: - '570' department: - _id: JoDa - _id: PeJo - _id: GradSch doi: 10.1016/j.cell.2024.11.022 ec_funded: 1 external_id: isi: - '001408395600001' pmid: - '39667938' file: - access_level: open_access checksum: d5a818edc32d249cdf75e1bb5b70a4b7 content_type: application/pdf creator: dernst date_created: 2025-01-27T08:46:33Z date_updated: 2025-01-27T08:46:33Z file_id: '18884' file_name: 2025_Cell_Watson.pdf file_size: 14082343 relation: main_file success: 1 file_date_updated: 2025-01-27T08:46:33Z fulldoi: https://doi.org/10.1016/j.cell.2024.11.022 has_accepted_license: '1' intvolume: ' 188' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 501-514.e18 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9 call_identifier: H2020 grant_number: '101026635' name: Synaptic computations of the hippocampal CA3 circuitry - _id: 6285a163-2b32-11ec-9570-8e204ca2dba5 grant_number: '26137' name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets - _id: 8d9195e9-16d5-11f0-9cad-d075be887a1e grant_number: PAT 4178023 name: Synaptic networks of human brain - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '18688' relation: earlier_version status: public scopus_import: '1' status: public title: Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 188 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '19602' abstract: - lang: eng text: N4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but its relevance and even its presence in eukaryotes have been mysterious. Here we show that spermatogenesis in the liverwort Marchantia polymorpha involves two waves of extensive DNA methylation reprogramming. First, 5-methylcytosine (5mC) expands from transposons to the entire genome. Notably, the second wave installs 4mC throughout genic regions, covering over 50% of CG sites in sperm. 4mC requires a methyltransferase (MpDN4MT1a) that is specifically expressed during late spermiogenesis. Deletion of MpDN4MT1a alters the sperm transcriptome, causes sperm swimming and fertility defects, and impairs post-fertilization development. Our results reveal extensive 4mC in a eukaryote, identify a family of eukaryotic methyltransferases, and elucidate the biological functions of 4mC in reproductive development, thereby expanding the repertoire of functional eukaryotic DNA modifications. acknowledged_ssus: - _id: Bio - _id: ScienComp acknowledgement: We thank Sir Richard Roberts (NEB) for the kind gift of anti-4mC antibodies. We are also grateful to the JIC Small Molecule Mass Spectrometry (Lionel Hill) and Chemistry (Martin Rejzek) platforms as well as the High Resolution Metabolomics Laboratory (Manfred Beckmann, Aberystwyth University) for their assistance with LC-MS. Additionally, we acknowledge the assistance of the JIC Bioimaging Facility and ISTA Imaging and Optics Facility for microscopy. Finally, we appreciate the High Performance Computing resources provided by the ISTA Scientific Computing Facility and Norwich BioScience Institute Partnership Computing Infrastructure. This work was funded by a Sainsbury Charitable Foundation studentship (J.W.), a UKRI-BBSRC Doctoral Training Partnerships studentship (BBT0087171 to J.T.), a European Research Council Starting Grant (“SexMeth” 804981 to J.W., S.X., and X.F.), two Biotechnology and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111 to J.Z., M.V., and X.F.), an EMBO Long Term Fellowship (Y.L.), an ISTA Bridge Fellowship (S.X.), and ISTA core funding (Y.Y. and X.F.). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: James full_name: Walker, James last_name: Walker - first_name: Jingyi full_name: Zhang, Jingyi last_name: Zhang - first_name: Yalin full_name: Liu, Yalin last_name: Liu - first_name: Shujuan full_name: Xu, Shujuan id: 9724dd9d-f591-11ee-bd51-e97ed0652286 last_name: Xu - first_name: Yiming full_name: Yu, Yiming id: 318e643b-8b61-11ed-b69e-aafa103ec8dd last_name: Yu orcid: 0000-0002-9919-7282 - first_name: Martin full_name: Vickers, Martin last_name: Vickers - first_name: Weizhi full_name: Ouyang, Weizhi id: fec73395-8b60-11ed-b69e-927fda99c743 last_name: Ouyang - first_name: Judit full_name: Tálas, Judit last_name: Tálas - first_name: Liam full_name: Dolan, Liam last_name: Dolan - first_name: Keiji full_name: Nakajima, Keiji last_name: Nakajima - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 citation: ama: Walker J, Zhang J, Liu Y, et al. Extensive N4 cytosine methylation is essential for Marchantia sperm function. Cell. 2025;188(11):2890-2906.e14. doi:10.1016/j.cell.2025.03.014 apa: Walker, J., Zhang, J., Liu, Y., Xu, S., Yu, Y., Vickers, M., … Feng, X. (2025). Extensive N4 cytosine methylation is essential for Marchantia sperm function. Cell. Cell Press. https://doi.org/10.1016/j.cell.2025.03.014 chicago: Walker, James, Jingyi Zhang, Yalin Liu, Shujuan Xu, Yiming Yu, Martin Vickers, Weizhi Ouyang, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia Sperm Function.” Cell. Cell Press, 2025. https://doi.org/10.1016/j.cell.2025.03.014. ieee: J. Walker et al., “Extensive N4 cytosine methylation is essential for Marchantia sperm function,” Cell, vol. 188, no. 11. Cell Press, p. 2890–2906.e14, 2025. ista: Walker J, Zhang J, Liu Y, Xu S, Yu Y, Vickers M, Ouyang W, Tálas J, Dolan L, Nakajima K, Feng X. 2025. Extensive N4 cytosine methylation is essential for Marchantia sperm function. Cell. 188(11), 2890–2906.e14. mla: Walker, James, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia Sperm Function.” Cell, vol. 188, no. 11, Cell Press, 2025, p. 2890–2906.e14, doi:10.1016/j.cell.2025.03.014. short: J. Walker, J. Zhang, Y. Liu, S. Xu, Y. Yu, M. Vickers, W. Ouyang, J. Tálas, L. Dolan, K. Nakajima, X. Feng, Cell 188 (2025) 2890–2906.e14. corr_author: '1' date_created: 2025-04-20T22:01:28Z date_published: 2025-05-29T00:00:00Z date_updated: 2026-10-20T08:22:21Z day: '29' ddc: - '570' department: - _id: XiFe doi: 10.1016/j.cell.2025.03.014 ec_funded: 1 external_id: isi: - '001504744800006' pmid: - '40209706' file: - access_level: open_access checksum: 0dcc2feb368dfe7c4890093366b2dacb content_type: application/pdf creator: dernst date_created: 2025-12-29T13:40:32Z date_updated: 2025-12-29T13:40:32Z file_id: '20871' file_name: 2025_Cell_Walker.pdf file_size: 11622960 relation: main_file success: 1 file_date_updated: 2025-12-29T13:40:32Z fulldoi: https://doi.org/10.1016/j.cell.2025.03.014 has_accepted_license: '1' intvolume: ' 188' isi: 1 issue: '11' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 2890-2906.e14 pmid: 1 project: - _id: bdb51a6e-d553-11ed-ba76-c2025f3d5725 call_identifier: H2020 grant_number: '804981' name: Establishment, modulation and inheritance of sexual lineage specific DNA methylation in plants publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/from-bacterial-immunity-to-plant-sex/ scopus_import: '1' status: public title: Extensive N4 cytosine methylation is essential for Marchantia sperm function tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 188 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20143' abstract: - lang: eng text: Bacteria and archaea deploy diverse antiviral defense systems, many of which remain mechanistically uncharacterized. Here, we characterize Kiwa, a widespread two-component system composed of the transmembrane sensor KwaA and the DNA-binding effector KwaB. Cryogenic electron microscopy (cryo-EM) analysis reveals that KwaA and KwaB assemble into a large, membrane-associated supercomplex. Upon phage binding, KwaA senses infection at the membrane, leading to KwaB binding of ejected phage DNA and inhibition of replication and late transcription, without inducing host cell death. Although KwaB can bind DNA independently, its antiviral activity requires association with KwaA, suggesting spatial or conformational regulation. We show that the phage-encoded DNA-mimic protein Gam directly binds and inhibits KwaB but that co-expression with the Gam-targeted RecBCD system restores protection by Kiwa. Our findings support a model in which Kiwa coordinates membrane-associated detection of phage infection with downstream DNA binding by its effector, forming a spatially coordinated antiviral mechanism. acknowledgement: We thank Rotem Sorek (Weizmann Institute of Science) for the Lambda Gam mutant and Ian Molineux (University of Texas) for T4Δgp2. We thank You Yu (Zhejiang University-University of Edinburgh Institute) and J. De La Cruz (MSK) for assistance with cryo-EM data collection and Lyuqin Zheng (MSK) for discussions on structural analysis. We thank the Imaging and Microscopy Centre (IMC) at the University of Southampton. This work was supported by Royal Society grant RGS\R2\222312 to F.L.N.; Welch Foundation grant F-1938 and National Institutes of Health R35GM138348 to D.W.T.; Wessex Medical Research Innovation grant AE06 to T.A.; and NIH grant GM145888 and Maloris Foundation and Memorial Sloan-Kettering Core grant (P30-CA008748) to D.J.P. In addition to MSKCC cryo-EM resources, some of this work was performed at the National Center for CryoEM Access and Training (NCCAT) and the Simons Electron Microscopy Center located at the New York Structural Biology Center, supported by the NIH Common Fund Transformative High Resolution Cryo-Electron Microscopy program (U24 GM129539) and Simons Foundation (SF349247) and NY State Assembly grants. This research used NSLS-II MX X-ray User Resources (FMX) of the National Synchrotron Light Source II, operated for the DOE Office of Science by Brookhaven National Laboratory under contract no. DE-SC0012704. The Center for BioMolecular Structure (CBMS) is primarily supported by the NIH, the National Institute of General Medical Sciences (NIGMS) through a Center Core P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental Research (KP1605010). R.K. and E.V.K. are supported by the Intramural Research Program of the NIH (National Library of Medicine). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Zhiying full_name: Zhang, Zhiying last_name: Zhang - first_name: Thomas C. full_name: Todeschini, Thomas C. last_name: Todeschini - first_name: Yi full_name: Wu, Yi last_name: Wu - first_name: Roman full_name: Kogay, Roman last_name: Kogay - first_name: Ameena full_name: Naji, Ameena last_name: Naji - first_name: Joaquin full_name: Cardenas Rodriguez, Joaquin last_name: Cardenas Rodriguez - first_name: Rupavidhya full_name: Mondi, Rupavidhya last_name: Mondi - first_name: Daniel full_name: Kaganovich, Daniel last_name: Kaganovich - first_name: David W. full_name: Taylor, David W. last_name: Taylor - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Marianna full_name: Teplova, Marianna last_name: Teplova - first_name: Triana full_name: Amen, Triana last_name: Amen - first_name: Eugene full_name: Koonin, Eugene last_name: Koonin - first_name: Dinshaw J. full_name: Patel, Dinshaw J. last_name: Patel - first_name: Franklin L. full_name: Nobrega, Franklin L. last_name: Nobrega citation: ama: Zhang Z, Todeschini TC, Wu Y, et al. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. Cell. 2025;188(21):5862-5877.e23. doi:10.1016/j.cell.2025.07.002 apa: Zhang, Z., Todeschini, T. C., Wu, Y., Kogay, R., Naji, A., Cardenas Rodriguez, J., … Nobrega, F. L. (2025). Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. Cell. Cell Press. https://doi.org/10.1016/j.cell.2025.07.002 chicago: Zhang, Zhiying, Thomas C. Todeschini, Yi Wu, Roman Kogay, Ameena Naji, Joaquin Cardenas Rodriguez, Rupavidhya Mondi, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” Cell. Cell Press, 2025. https://doi.org/10.1016/j.cell.2025.07.002. ieee: Z. Zhang et al., “Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites,” Cell, vol. 188, no. 21. Cell Press, p. 5862–5877.e23, 2025. ista: Zhang Z, Todeschini TC, Wu Y, Kogay R, Naji A, Cardenas Rodriguez J, Mondi R, Kaganovich D, Taylor DW, Bravo JPK, Teplova M, Amen T, Koonin E, Patel DJ, Nobrega FL. 2025. Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites. Cell. 188(21), 5862–5877.e23. mla: Zhang, Zhiying, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated at Phage Attachment Sites.” Cell, vol. 188, no. 21, Cell Press, 2025, p. 5862–5877.e23, doi:10.1016/j.cell.2025.07.002. short: Z. Zhang, T.C. Todeschini, Y. Wu, R. Kogay, A. Naji, J. Cardenas Rodriguez, R. Mondi, D. Kaganovich, D.W. Taylor, J.P.K. Bravo, M. Teplova, T. Amen, E. Koonin, D.J. Patel, F.L. Nobrega, Cell 188 (2025) 5862–5877.e23. date_created: 2025-08-07T05:00:04Z date_published: 2025-10-16T00:00:00Z date_updated: 2026-10-20T08:23:33Z day: '16' ddc: - '570' department: - _id: JaBr doi: 10.1016/j.cell.2025.07.002 external_id: isi: - '001603560700005' pmid: - '40730155' file: - access_level: open_access checksum: b944de5fbd7455f58e1ff338ad352239 content_type: application/pdf creator: dernst date_created: 2025-12-29T14:15:25Z date_updated: 2025-12-29T14:15:25Z file_id: '20875' file_name: 2025_Cell_Zhang.pdf file_size: 32104588 relation: main_file success: 1 file_date_updated: 2025-12-29T14:15:25Z fulldoi: https://doi.org/10.1016/j.cell.2025.07.002 has_accepted_license: '1' intvolume: ' 188' isi: 1 issue: '21' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 5862-5877.e23 pmid: 1 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 188 year: '2025' ... --- _id: '14826' abstract: - lang: eng text: The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage. acknowledgement: 'We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Andre full_name: Kuhn, Andre last_name: Kuhn - first_name: Mark full_name: Roosjen, Mark last_name: Roosjen - first_name: Sumanth full_name: Mutte, Sumanth last_name: Mutte - first_name: Shiv Mani full_name: Dubey, Shiv Mani last_name: Dubey - first_name: Vanessa Polet full_name: Carrillo Carrasco, Vanessa Polet last_name: Carrillo Carrasco - first_name: Sjef full_name: Boeren, Sjef last_name: Boeren - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Jasper full_name: Koehorst, Jasper last_name: Koehorst - first_name: Takayuki full_name: Kohchi, Takayuki last_name: Kohchi - first_name: Ryuichi full_name: Nishihama, Ryuichi last_name: Nishihama - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Joris full_name: Sprakel, Joris last_name: Sprakel - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers citation: ama: Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 2024;187(1):130-148.e17. doi:10.1016/j.cell.2023.11.021 apa: Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.11.021 chicago: Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” Cell. Elsevier, 2024. https://doi.org/10.1016/j.cell.2023.11.021. ieee: A. Kuhn et al., “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” Cell, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024. ista: Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17. mla: Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” Cell, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:10.1016/j.cell.2023.11.021. short: A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17. das_tickbox: '1' dataavailabilitystatement: "Phosphoproteome data are available in the ProteomeXchange PRIDE database: PXD038369 and PXD038363. Transcriptome data are available in the NCBI Sequence Read Archive: PRJNA881051. Data underlying RAF-like kinase phylogeny is deposited at the iTOL: https://itol.embl.de/shared/dolfweijers. This paper analyzes existing, publicly available data phospho-proteome data. The accession number for the datasets are listed in the key resources table.\r\n\r\nCode for the AuxPhos app and for MATlab code for analysis of cytoplasmic streaming are available at Github: https://github.com/WeijersLab/AuxPhos and https://github.com/jorissprakel/RAF_track_analysis.\r\n\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead author upon request." date_created: 2024-01-17T12:45:40Z date_published: 2024-01-04T00:00:00Z date_updated: 2026-10-15T08:06:16Z day: '04' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.cell.2023.11.021 ec_funded: 1 external_id: isi: - '001152705700001' pmid: - '38128538' file: - access_level: open_access checksum: 06fd236a9ee0b46ccb05f44695bfc34b content_type: application/pdf creator: dernst date_created: 2024-01-22T13:41:41Z date_updated: 2024-01-22T13:41:41Z file_id: '14874' file_name: 2024_Cell_Kuhn.pdf file_size: 13194060 relation: main_file success: 1 file_date_updated: 2024-01-22T13:41:41Z fulldoi: https://doi.org/10.1016/j.cell.2023.11.021 has_accepted_license: '1' intvolume: ' 187' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 130-148.e17 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 262EF96E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29988 name: RNA-directed DNA methylation in plant development publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '19395' relation: dissertation_contains status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: RAF-like protein kinases mediate a deeply conserved, rapid auxin response tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 187 year: '2024' ... --- _id: '10825' abstract: - lang: eng text: In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages. acknowledgement: We are grateful to H. Niwa for Dox regulatable PB vector; G. Charras for EzrinT567D cDNA; K. Jones for tdTomato ESCs, R26-Confetti ESCs, and laboratory assistance; M. Kinoshita for pPB-CAG-H2B-BFP plasmid; P. Humphreys and D. Clements for imaging support; G. Chu, P. Attlesey, and staff for animal husbandry; S. Pallett for laboratory assistance; C. Mulas for critical feedback on the project; T. Boroviak for single-cell RNA-seq; the EMBL Genomics Core Facility for sequencing; and M. Merkel for developing and sharing the original version of the 3D Voronoi code. This work was financially supported by BBSRC ( BB/Moo4023/1 and BB/T007044/1 to K.J.C. and J.N., Alert16 grant BB/R000042 to E.K.P.), Leverhulme Trust ( RPG-2014-080 to K.J.C. and J.N.), European Research Council ( 772798 -CellFateTech to K.J.C., 311637 -MorphoCorDiv and 820188 -NanoMechShape to E.K.P., Starting Grant 851288 to E.H., and 772426 -MeChemGui to K.F.), the Isaac Newton Trust (to E.K.P.), Medical Research Council UK (MRC program award MC_UU_00012/5 to E.K.P.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 641639 ( ITN Biopol , H.D.B. and E.K.P.), the Alexander von Humboldt Foundation (Alexander von Humboldt Professorship to K.F.), EMBO ALTF 522-2021 (to P.S.), Centre for Trophoblast Research (Next Generation fellowship to S.A.), and JSPS Overseas Research Fellowships (to A.Y.). The Wellcome-MRC Cambridge Stem Cell Institute receives core funding from Wellcome Trust ( 203151/Z/16/Z ) and MRC ( MC_PC_17230 ). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. article_processing_charge: No article_type: original author: - first_name: Ayaka full_name: Yanagida, Ayaka last_name: Yanagida - first_name: Elena full_name: Corujo-Simon, Elena last_name: Corujo-Simon - first_name: Christopher K. full_name: Revell, Christopher K. last_name: Revell - first_name: Preeti full_name: Sahu, Preeti id: 55BA52EE-A185-11EA-88FD-18AD3DDC885E last_name: Sahu - first_name: Giuliano G. full_name: Stirparo, Giuliano G. last_name: Stirparo - first_name: Irene M. full_name: Aspalter, Irene M. last_name: Aspalter - first_name: Alex K. full_name: Winkel, Alex K. last_name: Winkel - first_name: Ruby full_name: Peters, Ruby last_name: Peters - first_name: Henry full_name: De Belly, Henry last_name: De Belly - first_name: Davide A.D. full_name: Cassani, Davide A.D. last_name: Cassani - first_name: Sarra full_name: Achouri, Sarra last_name: Achouri - first_name: Raphael full_name: Blumenfeld, Raphael last_name: Blumenfeld - first_name: Kristian full_name: Franze, Kristian last_name: Franze - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Ewa K. full_name: Paluch, Ewa K. last_name: Paluch - first_name: Jennifer full_name: Nichols, Jennifer last_name: Nichols - first_name: Kevin J. full_name: Chalut, Kevin J. last_name: Chalut citation: ama: Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 2022;185(5):777-793.e20. doi:10.1016/j.cell.2022.01.022 apa: Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter, I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic lineage sorting. Cell. Cell Press. https://doi.org/10.1016/j.cell.2022.01.022 chicago: Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” Cell. Cell Press, 2022. https://doi.org/10.1016/j.cell.2022.01.022. ieee: A. Yanagida et al., “Cell surface fluctuations regulate early embryonic lineage sorting,” Cell, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022. ista: Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 185(5), 777–793.e20. mla: Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” Cell, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20, doi:10.1016/j.cell.2022.01.022. short: A. Yanagida, E. Corujo-Simon, C.K. Revell, P. Sahu, G.G. Stirparo, I.M. Aspalter, A.K. Winkel, R. Peters, H. De Belly, D.A.D. Cassani, S. Achouri, R. Blumenfeld, K. Franze, E.B. Hannezo, E.K. Paluch, J. Nichols, K.J. Chalut, Cell 185 (2022) 777–793.e20. date_created: 2022-03-06T23:01:52Z date_published: 2022-02-22T00:00:00Z date_updated: 2025-07-10T11:50:00Z day: '22' ddc: - '570' department: - _id: EdHa doi: 10.1016/j.cell.2022.01.022 ec_funded: 1 external_id: isi: - '000796293700007' pmid: - '35196500' file: - access_level: open_access checksum: ae305060e8031297771b89dae9e36a29 content_type: application/pdf creator: dernst date_created: 2022-03-07T07:55:23Z date_updated: 2022-03-07T07:55:23Z file_id: '10831' file_name: 2022_Cell_Yanagida.pdf file_size: 8478995 relation: main_file success: 1 file_date_updated: 2022-03-07T07:55:23Z fulldoi: https://doi.org/10.1016/j.cell.2022.01.022 has_accepted_license: '1' intvolume: ' 185' isi: 1 issue: '5' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 777-793.e20 pmid: 1 project: - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Cell surface fluctuations regulate early embryonic lineage sorting tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 185 year: '2022' ... --- _id: '10573' abstract: - lang: eng text: How tissues acquire complex shapes is a fundamental question in biology and regenerative medicine. Zebrafish semicircular canals form from invaginations in the otic epithelium (buds) that extend and fuse to form the hubs of each canal. We find that conventional actomyosin-driven behaviors are not required. Instead, local secretion of hyaluronan, made by the enzymes uridine 5′-diphosphate dehydrogenase (ugdh) and hyaluronan synthase 3 (has3), drives canal morphogenesis. Charged hyaluronate polymers osmotically swell with water and generate isotropic extracellular pressure to deform the overlying epithelium into buds. The mechanical anisotropy needed to shape buds into tubes is conferred by a polarized distribution of actomyosin and E-cadherin-rich membrane tethers, which we term cytocinches. Most work on tissue morphogenesis ascribes actomyosin contractility as the driving force, while the extracellular matrix shapes tissues through differential stiffness. Our work inverts this expectation. Hyaluronate pressure shaped by anisotropic tissue stiffness may be a widespread mechanism for powering morphological change in organogenesis and tissue engineering. acknowledgement: We thank Ian Swinburne, Sandy Nandagopal, and Toru Kawanishi for support, discussions, and reagents. We thank Vanessa Barone, Joseph Nasser, and members of the Megason lab for useful comments on the manuscript and general feedback. We are grateful to the Heisenberg and Knaut labs for transgenic fish. Diagrams on the right in the graphical abstract were created using BioRender. This work was supported by NIH R01DC015478 and NIH R01GM107733 to S.G.M. A.M. was supported by Human Frontiers Science Program LTF and NIH K99HD098918. article_processing_charge: No article_type: original author: - first_name: Akankshi full_name: Munjal, Akankshi last_name: Munjal - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Tony Y.C. full_name: Tsai, Tony Y.C. last_name: Tsai - first_name: Timothy J. full_name: Mitchison, Timothy J. last_name: Mitchison - first_name: Sean G. full_name: Megason, Sean G. last_name: Megason citation: ama: Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 2021;184(26):6313-6325.e18. doi:10.1016/j.cell.2021.11.025 apa: Munjal, A., Hannezo, E. B., Tsai, T. Y. C., Mitchison, T. J., & Megason, S. G. (2021). Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.11.025 chicago: Munjal, Akankshi, Edouard B Hannezo, Tony Y.C. Tsai, Timothy J. Mitchison, and Sean G. Megason. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.11.025. ieee: A. Munjal, E. B. Hannezo, T. Y. C. Tsai, T. J. Mitchison, and S. G. Megason, “Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis,” Cell, vol. 184, no. 26. Elsevier, p. 6313–6325.e18, 2021. ista: Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. 2021. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 184(26), 6313–6325.e18. mla: Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” Cell, vol. 184, no. 26, Elsevier, 2021, p. 6313–6325.e18, doi:10.1016/j.cell.2021.11.025. short: A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 6313–6325.e18. date_created: 2021-12-26T23:01:26Z date_published: 2021-12-22T00:00:00Z date_updated: 2025-05-14T11:26:20Z day: '22' department: - _id: EdHa doi: 10.1016/j.cell.2021.11.025 external_id: isi: - '000735387500002' fulldoi: https://doi.org/10.1016/j.cell.2021.11.025 intvolume: ' 184' isi: 1 issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.09.28.316042 month: '12' oa: 1 oa_version: Preprint page: 6313-6325.e18 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 184 year: '2021' ... --- _id: '9316' abstract: - lang: eng text: Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin to phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context. acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: We thank Carl Goodrich and the members of the Heisenberg and Hannezo groups, in particular Reka Korei, for help, technical advice, and discussions; and the Bioimaging and zebrafish facilities of the IST Austria for continuous support. This work was supported by the Elise Richter Program of Austrian Science Fund (FWF) to N.I.P. ( V 736-B26 ) and the European Union (European Research Council Advanced Grant 742573 to C.-P.H. and European Research Council Starting Grant 851288 to E.H.). article_processing_charge: No article_type: original author: - first_name: Nicoletta full_name: Petridou, Nicoletta id: 2A003F6C-F248-11E8-B48F-1D18A9856A87 last_name: Petridou orcid: 0000-0002-8451-1195 - first_name: Bernat full_name: Corominas-Murtra, Bernat id: 43BE2298-F248-11E8-B48F-1D18A9856A87 last_name: Corominas-Murtra orcid: 0000-0001-9806-5643 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 2021;184(7):1914-1928.e19. doi:10.1016/j.cell.2021.02.017 apa: Petridou, N., Corominas-Murtra, B., Heisenberg, C.-P. J., & Hannezo, E. B. (2021). Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.02.017 chicago: Petridou, Nicoletta, Bernat Corominas-Murtra, Carl-Philipp J Heisenberg, and Edouard B Hannezo. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.02.017. ieee: N. Petridou, B. Corominas-Murtra, C.-P. J. Heisenberg, and E. B. Hannezo, “Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions,” Cell, vol. 184, no. 7. Elsevier, p. 1914–1928.e19, 2021. ista: Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. 2021. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 184(7), 1914–1928.e19. mla: Petridou, Nicoletta, et al. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” Cell, vol. 184, no. 7, Elsevier, 2021, p. 1914–1928.e19, doi:10.1016/j.cell.2021.02.017. short: N. Petridou, B. Corominas-Murtra, C.-P.J. Heisenberg, E.B. Hannezo, Cell 184 (2021) 1914–1928.e19. corr_author: '1' date_created: 2021-04-11T22:01:14Z date_published: 2021-04-01T00:00:00Z date_updated: 2025-07-10T12:01:42Z day: '01' ddc: - '570' department: - _id: CaHe - _id: EdHa doi: 10.1016/j.cell.2021.02.017 ec_funded: 1 external_id: isi: - '000636734000022' pmid: - '33730596' file: - access_level: open_access checksum: 1e5295fbd9c2a459173ec45a0e8a7c2e content_type: application/pdf creator: cziletti date_created: 2021-06-08T10:04:10Z date_updated: 2021-06-08T10:04:10Z file_id: '9534' file_name: 2021_Cell_Petridou.pdf file_size: 11405875 relation: main_file success: 1 file_date_updated: 2021-06-08T10:04:10Z fulldoi: https://doi.org/10.1016/j.cell.2021.02.017 has_accepted_license: '1' intvolume: ' 184' isi: 1 issue: '7' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1914-1928.e19 pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis - _id: 2693FD8C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: V00736 name: Tissue material properties in embryonic development publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/embryonic-tissue-undergoes-phase-transition/ scopus_import: '1' status: public title: Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 184 year: '2021' ... --- _id: '7789' abstract: - lang: eng text: During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, andin vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues. article_processing_charge: No article_type: original author: - first_name: Sophie full_name: Dekoninck, Sophie last_name: Dekoninck - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Alejandro full_name: Sifrim, Alejandro last_name: Sifrim - first_name: Yekaterina A. full_name: Miroshnikova, Yekaterina A. last_name: Miroshnikova - first_name: Mariaceleste full_name: Aragona, Mariaceleste last_name: Aragona - first_name: Milan full_name: Malfait, Milan last_name: Malfait - first_name: Souhir full_name: Gargouri, Souhir last_name: Gargouri - first_name: Charlotte full_name: De Neunheuser, Charlotte last_name: De Neunheuser - first_name: Christine full_name: Dubois, Christine last_name: Dubois - first_name: Thierry full_name: Voet, Thierry last_name: Voet - first_name: Sara A. full_name: Wickström, Sara A. last_name: Wickström - first_name: Benjamin D. full_name: Simons, Benjamin D. last_name: Simons - first_name: Cédric full_name: Blanpain, Cédric last_name: Blanpain citation: ama: Dekoninck S, Hannezo EB, Sifrim A, et al. Defining the design principles of skin epidermis postnatal growth. Cell. 2020;181(3):604-620.e22. doi:10.1016/j.cell.2020.03.015 apa: Dekoninck, S., Hannezo, E. B., Sifrim, A., Miroshnikova, Y. A., Aragona, M., Malfait, M., … Blanpain, C. (2020). Defining the design principles of skin epidermis postnatal growth. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.03.015 chicago: Dekoninck, Sophie, Edouard B Hannezo, Alejandro Sifrim, Yekaterina A. Miroshnikova, Mariaceleste Aragona, Milan Malfait, Souhir Gargouri, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell. Elsevier, 2020. https://doi.org/10.1016/j.cell.2020.03.015. ieee: S. Dekoninck et al., “Defining the design principles of skin epidermis postnatal growth,” Cell, vol. 181, no. 3. Elsevier, p. 604–620.e22, 2020. ista: Dekoninck S, Hannezo EB, Sifrim A, Miroshnikova YA, Aragona M, Malfait M, Gargouri S, De Neunheuser C, Dubois C, Voet T, Wickström SA, Simons BD, Blanpain C. 2020. Defining the design principles of skin epidermis postnatal growth. Cell. 181(3), 604–620.e22. mla: Dekoninck, Sophie, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell, vol. 181, no. 3, Elsevier, 2020, p. 604–620.e22, doi:10.1016/j.cell.2020.03.015. short: S. Dekoninck, E.B. Hannezo, A. Sifrim, Y.A. Miroshnikova, M. Aragona, M. Malfait, S. Gargouri, C. De Neunheuser, C. Dubois, T. Voet, S.A. Wickström, B.D. Simons, C. Blanpain, Cell 181 (2020) 604–620.e22. date_created: 2020-05-03T22:00:48Z date_published: 2020-04-30T00:00:00Z date_updated: 2025-07-10T11:54:47Z day: '30' ddc: - '570' department: - _id: EdHa doi: 10.1016/j.cell.2020.03.015 external_id: isi: - '000530708400016' pmid: - '32259486' file: - access_level: open_access checksum: e2114902f4e9d75a752e9efb5ae06011 content_type: application/pdf creator: dernst date_created: 2020-05-04T10:20:55Z date_updated: 2020-07-14T12:48:03Z file_id: '7795' file_name: 2020_Cell_Dekoninck.pdf file_size: 17992888 relation: main_file file_date_updated: 2020-07-14T12:48:03Z fulldoi: https://doi.org/10.1016/j.cell.2020.03.015 has_accepted_license: '1' intvolume: ' 181' isi: 1 issue: '3' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 604-620.e22 pmid: 1 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Defining the design principles of skin epidermis postnatal growth tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 181 year: '2020' ... --- _id: '6508' abstract: - lang: eng text: Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation. acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.). article_processing_charge: No article_type: original author: - first_name: Shayan full_name: Shamipour, Shayan id: 40B34FE2-F248-11E8-B48F-1D18A9856A87 last_name: Shamipour - first_name: Roland full_name: Kardos, Roland id: 4039350E-F248-11E8-B48F-1D18A9856A87 last_name: Kardos - first_name: Shi-lei full_name: Xue, Shi-lei id: 31D2C804-F248-11E8-B48F-1D18A9856A87 last_name: Xue - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 2019;177(6):1463-1479.e18. doi:10.1016/j.cell.2019.04.030 apa: Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.030 chicago: Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.030. ieee: S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” Cell, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019. ista: Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18. mla: Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:10.1016/j.cell.2019.04.030. short: S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18. date_created: 2019-06-02T21:59:12Z date_published: 2019-05-30T00:00:00Z date_updated: 2026-10-22T22:30:23Z day: '30' ddc: - '570' department: - _id: CaHe - _id: EdHa - _id: BjHo doi: 10.1016/j.cell.2019.04.030 ec_funded: 1 external_id: isi: - '000469415100013' pmid: - '31080065' file: - access_level: open_access checksum: aea43726d80e35ce3885073a5f05c3e3 content_type: application/pdf creator: dernst date_created: 2020-10-21T07:22:34Z date_updated: 2020-10-21T07:22:34Z file_id: '8686' file_name: 2019_Cell_Shamipour_accepted.pdf file_size: 3356292 relation: main_file success: 1 file_date_updated: 2020-10-21T07:22:34Z fulldoi: https://doi.org/10.1016/j.cell.2019.04.030 has_accepted_license: '1' intvolume: ' 177' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2019.04.030 month: '05' oa: 1 oa_version: Published Version page: 1463-1479.e18 pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 268294B6-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31639 name: Active mechano-chemical description of the cell cytoskeleton publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/ record: - id: '8350' relation: dissertation_contains status: public scopus_import: '1' status: public title: Bulk actin dynamics drive phase segregation in zebrafish oocytes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 177 year: '2019' ... --- _id: '7001' acknowledged_ssus: - _id: PreCl - _id: Bio article_processing_charge: No article_type: original author: - first_name: Cornelia full_name: Schwayer, Cornelia id: 3436488C-F248-11E8-B48F-1D18A9856A87 last_name: Schwayer orcid: 0000-0001-5130-2226 - first_name: Shayan full_name: Shamipour, Shayan id: 40B34FE2-F248-11E8-B48F-1D18A9856A87 last_name: Shamipour - first_name: Kornelija full_name: Pranjic-Ferscha, Kornelija id: 4362B3C2-F248-11E8-B48F-1D18A9856A87 last_name: Pranjic-Ferscha - first_name: Alexandra full_name: Schauer, Alexandra id: 30A536BA-F248-11E8-B48F-1D18A9856A87 last_name: Schauer orcid: 0000-0001-7659-9142 - first_name: M full_name: Balda, M last_name: Balda - first_name: M full_name: Tada, M last_name: Tada - first_name: K full_name: Matter, K last_name: Matter - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18. doi:10.1016/j.cell.2019.10.006 apa: Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006 chicago: Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006. ieee: C. Schwayer et al., “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019. ista: Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18. mla: Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:10.1016/j.cell.2019.10.006. short: C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18. date_created: 2019-11-12T12:51:06Z date_published: 2019-10-31T00:00:00Z date_updated: 2026-10-22T22:30:23Z day: '31' ddc: - '570' department: - _id: CaHe - _id: BjHo doi: 10.1016/j.cell.2019.10.006 ec_funded: 1 external_id: isi: - '000493898000012' pmid: - '31675500' file: - access_level: open_access checksum: 33dac4bb77ee630e2666e936b4d57980 content_type: application/pdf creator: dernst date_created: 2020-10-21T07:09:45Z date_updated: 2020-10-21T07:09:45Z file_id: '8684' file_name: 2019_Cell_Schwayer_accepted.pdf file_size: 8805878 relation: main_file success: 1 file_date_updated: 2020-10-21T07:09:45Z fulldoi: https://doi.org/10.1016/j.cell.2019.10.006 has_accepted_license: '1' intvolume: ' 179' isi: 1 issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 937-952.e18 pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News auf IST Website relation: press_release url: https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/ record: - id: '7186' relation: dissertation_contains status: public - id: '8350' relation: dissertation_contains status: public scopus_import: '1' status: public title: Mechanosensation of tight junctions depends on ZO-1 phase separation and flow type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 179 year: '2019' ... --- _id: '6877' article_processing_charge: No article_type: original author: - first_name: Aglaja full_name: Kopf, Aglaja id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87 last_name: Kopf orcid: 0000-0002-2187-6656 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell. 2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047 apa: Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047 chicago: Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047. ieee: A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019. ista: Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53. mla: Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047. short: A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53. date_created: 2019-09-15T22:00:46Z date_published: 2019-09-19T00:00:00Z date_updated: 2026-10-22T22:30:25Z day: '19' department: - _id: MiSi doi: 10.1016/j.cell.2019.08.047 external_id: isi: - '000486618500011' pmid: - '31539498' fulldoi: https://doi.org/10.1016/j.cell.2019.08.047 intvolume: ' 179' isi: 1 issue: '1' language: - iso: eng month: '09' oa_version: None page: 51-53 pmid: 1 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '6891' relation: dissertation_contains status: public scopus_import: '1' status: public title: The neural crest pitches in to remove apoptotic debris type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 179 year: '2019' ... --- _id: '6351' abstract: - lang: eng text: "A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing." acknowledged_ssus: - _id: Bio article_processing_charge: No author: - first_name: Petra full_name: Marhavá, Petra id: 44E59624-F248-11E8-B48F-1D18A9856A87 last_name: Marhavá - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Saiko full_name: Yoshida, Saiko id: 2E46069C-F248-11E8-B48F-1D18A9856A87 last_name: Yoshida orcid: 0000-0001-6111-9353 - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015 apa: Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., & Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.015 chicago: Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.015. ieee: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” Cell, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019. ista: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13. mla: Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:10.1016/j.cell.2019.04.015. short: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13. corr_author: '1' date_created: 2019-04-28T21:59:14Z date_published: 2019-05-02T00:00:00Z date_updated: 2026-10-22T22:30:27Z day: '02' ddc: - '570' department: - _id: JiFr - _id: EvBe doi: 10.1016/j.cell.2019.04.015 ec_funded: 1 external_id: isi: - '000466843000015' pmid: - '31051107' file: - access_level: open_access checksum: 4ceba04a96a74f5092ec3ce2c579a0c7 content_type: application/pdf creator: dernst date_created: 2019-05-13T06:12:45Z date_updated: 2020-07-14T12:47:28Z file_id: '6411' file_name: 2019_Cell_Marhava.pdf file_size: 10272032 relation: main_file file_date_updated: 2020-07-14T12:47:28Z fulldoi: https://doi.org/10.1016/j.cell.2019.04.015 has_accepted_license: '1' intvolume: ' 177' isi: 1 issue: '4' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 957-969.e13 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/ record: - id: '9992' relation: dissertation_contains status: public scopus_import: '1' status: public title: Re-activation of stem cell pathways for pattern restoration in plant wound healing tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 177 year: '2019' ... --- _id: '9458' abstract: - lang: eng text: Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints. article_processing_charge: No article_type: original author: - first_name: Jason T. full_name: Huff, Jason T. last_name: Huff - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029 apa: Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029 chicago: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.01.029. ieee: J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014. ista: Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297. mla: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029. short: J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297. date_created: 2021-06-04T12:00:16Z date_published: 2014-03-13T00:00:00Z date_updated: 2021-12-14T08:22:36Z day: '13' department: - _id: DaZi doi: 10.1016/j.cell.2014.01.029 extern: '1' external_id: pmid: - '24630728' fulldoi: https://doi.org/10.1016/j.cell.2014.01.029 intvolume: ' 156' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2014.01.029 month: '03' oa: 1 oa_version: Published Version page: 1286-1297 pmid: 1 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 156 year: '2014' ... --- _id: '9459' abstract: - lang: eng text: Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway. article_processing_charge: No article_type: original author: - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Ping-Hung full_name: Hsieh, Ping-Hung last_name: Hsieh - first_name: Devin full_name: Coleman-Derr, Devin last_name: Coleman-Derr - first_name: Leor full_name: Eshed-Williams, Leor last_name: Eshed-Williams - first_name: Ka full_name: Thao, Ka last_name: Thao - first_name: Stacey L. full_name: Harmer, Stacey L. last_name: Harmer - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033 apa: Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.02.033 chicago: Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033. ieee: A. Zemach et al., “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” Cell, vol. 153, no. 1. Elsevier, pp. 193–205, 2013. ista: Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205. mla: Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” Cell, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:10.1016/j.cell.2013.02.033. short: A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205. date_created: 2021-06-04T12:23:28Z date_published: 2013-03-28T00:00:00Z date_updated: 2021-12-14T08:25:35Z day: '28' department: - _id: DaZi doi: 10.1016/j.cell.2013.02.033 extern: '1' external_id: pmid: - '23540698' fulldoi: https://doi.org/10.1016/j.cell.2013.02.033 intvolume: ' 153' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2013.02.033 month: '03' oa: 1 oa_version: Published Version page: 193-205 pmid: 1 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 153 year: '2013' ... --- OA_place: publisher OA_type: free access _id: '2996' abstract: - lang: eng text: "Plants, compared to animals, exhibit an amazing adaptability and plasticity in their development. This is largely dependent on the ability of plants to form new organs, such as lateral roots, leaves, and flowers during postembryonic development. Organ primordia develop from founder cell populations into organs by coordinated cell division and differentiation. Here, we show that organ formation in Arabidopsis involves dynamic gradients of the signaling molecule auxin with maxima at the primordia tips. These gradients are mediated by cellular efflux requiring asymmetrically localized PIN proteins, which represent a functionally redundant network for auxin distribution in both aerial and underground organs. PIN1 polar localization undergoes a dynamic rearrangement, which correlates with establishment of auxin gradients and primordium development. Our results suggest that PIN-dependent, local auxin gradients represent a common module for formation of all plant organs, regardless of their mature morphology or developmental origin.\r\n" article_processing_charge: No article_type: original author: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Marta full_name: Michniewicz, Marta last_name: Michniewicz - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Thomas full_name: Teichmann, Thomas last_name: Teichmann - first_name: Daniela full_name: Seifertová, Daniela last_name: Seifertová - first_name: Gerd full_name: Jürgens, Gerd last_name: Jürgens - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Benková E, Michniewicz M, Sauer M, et al. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell. 2003;115(5):591-602. doi:10.1016/S0092-8674(03)00924-3 apa: Benková, E., Michniewicz, M., Sauer, M., Teichmann, T., Seifertová, D., Jürgens, G., & Friml, J. (2003). Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell. Cell Press. https://doi.org/10.1016/S0092-8674(03)00924-3 chicago: Benková, Eva, Marta Michniewicz, Michael Sauer, Thomas Teichmann, Daniela Seifertová, Gerd Jürgens, and Jiří Friml. “Local, Efflux-Dependent Auxin Gradients as a Common Module for Plant Organ Formation.” Cell. Cell Press, 2003. https://doi.org/10.1016/S0092-8674(03)00924-3. ieee: E. Benková et al., “Local, efflux-dependent auxin gradients as a common module for plant organ formation,” Cell, vol. 115, no. 5. Cell Press, pp. 591–602, 2003. ista: Benková E, Michniewicz M, Sauer M, Teichmann T, Seifertová D, Jürgens G, Friml J. 2003. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell. 115(5), 591–602. mla: Benková, Eva, et al. “Local, Efflux-Dependent Auxin Gradients as a Common Module for Plant Organ Formation.” Cell, vol. 115, no. 5, Cell Press, 2003, pp. 591–602, doi:10.1016/S0092-8674(03)00924-3. short: E. Benková, M. Michniewicz, M. Sauer, T. Teichmann, D. Seifertová, G. Jürgens, J. Friml, Cell 115 (2003) 591–602. date_created: 2018-12-11T12:00:46Z date_published: 2003-11-26T00:00:00Z date_updated: 2026-05-22T08:47:43Z day: '26' doi: 10.1016/S0092-8674(03)00924-3 extern: '1' external_id: pmid: - '14651850' fulldoi: https://doi.org/10.1016/S0092-8674(03)00924-3 intvolume: ' 115' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/S0092-8674(03)00924-3 month: '11' oa: 1 oa_version: Published Version page: 591 - 602 pmid: 1 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press publist_id: '3706' quality_controlled: '1' status: public title: Local, efflux-dependent auxin gradients as a common module for plant organ formation type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 115 year: '2003' ...