[{"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."}],"citation":{"mla":"Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>.","apa":"Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>","short":"A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17.","chicago":"Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">https://doi.org/10.1016/j.cell.2023.11.021</a>.","ieee":"A. Kuhn <i>et al.</i>, “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” <i>Cell</i>, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024.","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.","ama":"Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. <i>Cell</i>. 2024;187(1):130-148.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.11.021\">10.1016/j.cell.2023.11.021</a>"},"year":"2024","date_created":"2024-01-17T12:45:40Z","file":[{"creator":"dernst","file_id":"14874","content_type":"application/pdf","checksum":"06fd236a9ee0b46ccb05f44695bfc34b","file_name":"2024_Cell_Kuhn.pdf","access_level":"open_access","success":1,"date_updated":"2024-01-22T13:41:41Z","file_size":13194060,"date_created":"2024-01-22T13:41:41Z","relation":"main_file"}],"_id":"14826","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"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_type":"original","scopus_import":"1","doi":"10.1016/j.cell.2023.11.021","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","file_date_updated":"2024-01-22T13:41:41Z","publication_status":"published","title":"RAF-like protein kinases mediate a deeply conserved, rapid auxin response","intvolume":"       187","date_updated":"2024-01-22T13:43:40Z","ec_funded":1,"publication":"Cell","department":[{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"first_name":"Sumanth","last_name":"Mutte","full_name":"Mutte, Sumanth"},{"full_name":"Dubey, Shiv Mani","last_name":"Dubey","first_name":"Shiv Mani"},{"last_name":"Carrillo Carrasco","first_name":"Vanessa Polet","full_name":"Carrillo Carrasco, Vanessa Polet"},{"first_name":"Sjef","last_name":"Boeren","full_name":"Boeren, Sjef"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","first_name":"Aline"},{"last_name":"Koehorst","first_name":"Jasper","full_name":"Koehorst, Jasper"},{"first_name":"Takayuki","last_name":"Kohchi","full_name":"Kohchi, Takayuki"},{"full_name":"Nishihama, Ryuichi","last_name":"Nishihama","first_name":"Ryuichi"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Sprakel, Joris","last_name":"Sprakel","first_name":"Joris"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"}],"volume":187,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","has_accepted_license":"1","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"P29988","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development"}],"issue":"1","day":"04","page":"130-148.e17","quality_controlled":"1","keyword":["General Biochemistry","Genetics and Molecular Biology"],"ddc":["580"],"language":[{"iso":"eng"}],"status":"public","month":"01","pmid":1,"publisher":"Elsevier","type":"journal_article","date_published":"2024-01-04T00:00:00Z","external_id":{"pmid":["38128538"]}},{"status":"public","month":"12","isi":1,"language":[{"iso":"eng"}],"external_id":{"isi":["000735387500002"]},"date_published":"2021-12-22T00:00:00Z","type":"journal_article","publisher":"Elsevier ; Cell Press","issue":"26","quality_controlled":"1","day":"22","page":"6313-6325.e18","publication":"Cell","date_updated":"2023-08-17T06:28:25Z","department":[{"_id":"EdHa"}],"intvolume":"       184","oa":1,"volume":184,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Akankshi","last_name":"Munjal","full_name":"Munjal, Akankshi"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"last_name":"Tsai","first_name":"Tony Y.C.","full_name":"Tsai, Tony Y.C."},{"first_name":"Timothy J.","last_name":"Mitchison","full_name":"Mitchison, Timothy J."},{"first_name":"Sean G.","last_name":"Megason","full_name":"Megason, Sean G."}],"_id":"10573","date_created":"2021-12-26T23:01:26Z","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."}],"year":"2021","citation":{"ama":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. <i>Cell</i>. 2021;184(26):6313-6325.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">10.1016/j.cell.2021.11.025</a>","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.","ieee":"A. Munjal, E. B. Hannezo, T. Y. C. Tsai, T. J. Mitchison, and S. G. Megason, “Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis,” <i>Cell</i>, vol. 184, no. 26. Elsevier ; Cell Press, p. 6313–6325.e18, 2021.","apa":"Munjal, A., Hannezo, E. B., Tsai, T. Y. C., Mitchison, T. J., &#38; Megason, S. G. (2021). Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. <i>Cell</i>. Elsevier ; Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">https://doi.org/10.1016/j.cell.2021.11.025</a>","short":"A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 6313–6325.e18.","chicago":"Munjal, Akankshi, Edouard B Hannezo, Tony Y.C. Tsai, Timothy J. Mitchison, and Sean G. Megason. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” <i>Cell</i>. Elsevier ; Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">https://doi.org/10.1016/j.cell.2021.11.025</a>.","mla":"Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” <i>Cell</i>, vol. 184, no. 26, Elsevier ; Cell Press, 2021, p. 6313–6325.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">10.1016/j.cell.2021.11.025</a>."},"oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","title":"Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis","article_type":"original","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.","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.09.28.316042","open_access":"1"}],"doi":"10.1016/j.cell.2021.11.025","scopus_import":"1"},{"type":"journal_article","external_id":{"isi":["000493898000012"],"pmid":["31675500"]},"date_published":"2019-10-31T00:00:00Z","pmid":1,"publisher":"Cell Press","status":"public","isi":1,"month":"10","ddc":["570"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"31","page":"937-952.e18","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020"}],"has_accepted_license":"1","issue":"4","volume":179,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7186"},{"id":"8350","status":"public","relation":"dissertation_contains"}],"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/"}]},"oa":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","first_name":"Cornelia"},{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan"},{"first_name":"Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","full_name":"Pranjic-Ferscha, Kornelija"},{"last_name":"Schauer","first_name":"Alexandra","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"M","last_name":"Balda","full_name":"Balda, M"},{"last_name":"Tada","first_name":"M","full_name":"Tada, M"},{"full_name":"Matter, K","first_name":"K","last_name":"Matter"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"ec_funded":1,"date_updated":"2024-03-25T23:30:21Z","publication":"Cell","department":[{"_id":"CaHe"},{"_id":"BjHo"}],"intvolume":"       179","article_processing_charge":"No","oa_version":"Submitted Version","file_date_updated":"2020-10-21T07:09:45Z","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","publication_status":"published","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"article_type":"original","scopus_import":"1","doi":"10.1016/j.cell.2019.10.006","file":[{"file_name":"2019_Cell_Schwayer_accepted.pdf","success":1,"access_level":"open_access","date_created":"2020-10-21T07:09:45Z","file_size":8805878,"date_updated":"2020-10-21T07:09:45Z","relation":"main_file","file_id":"8684","creator":"dernst","content_type":"application/pdf","checksum":"33dac4bb77ee630e2666e936b4d57980"}],"date_created":"2019-11-12T12:51:06Z","_id":"7001","citation":{"ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. 2019;179(4):937-952.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","ieee":"C. Schwayer <i>et al.</i>, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” <i>Cell</i>, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>.","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18."},"year":"2019"},{"department":[{"_id":"MiSi"}],"publication":"Cell","date_updated":"2024-03-25T23:30:22Z","intvolume":"       179","related_material":{"record":[{"id":"6891","relation":"dissertation_contains","status":"public"}]},"volume":179,"author":[{"full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","last_name":"Kopf","first_name":"Aglaja"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6877","date_created":"2019-09-15T22:00:46Z","year":"2019","citation":{"ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. <i>Cell</i>. 2019;179(1):51-53. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">10.1016/j.cell.2019.08.047</a>","ista":"Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53.","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” <i>Cell</i>, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” <i>Cell</i>, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">10.1016/j.cell.2019.08.047</a>.","apa":"Kopf, A., &#38; Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">https://doi.org/10.1016/j.cell.2019.08.047</a>","chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">https://doi.org/10.1016/j.cell.2019.08.047</a>.","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53."},"title":"The neural crest pitches in to remove apoptotic debris","publication_status":"published","oa_version":"None","article_processing_charge":"No","doi":"10.1016/j.cell.2019.08.047","scopus_import":"1","article_type":"original","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"month":"09","isi":1,"status":"public","language":[{"iso":"eng"}],"date_published":"2019-09-19T00:00:00Z","external_id":{"isi":["000486618500011"],"pmid":["31539498"]},"type":"journal_article","publisher":"Elsevier","pmid":1,"issue":"1","quality_controlled":"1","page":"51-53","day":"19"},{"year":"2014","citation":{"ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>"},"abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"_id":"9458","date_created":"2021-06-04T12:00:16Z","doi":"10.1016/j.cell.2014.01.029","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"scopus_import":"1","article_type":"original","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","intvolume":"       156","department":[{"_id":"DaZi"}],"publication":"Cell","date_updated":"2021-12-14T08:22:36Z","author":[{"full_name":"Huff, Jason T.","first_name":"Jason T.","last_name":"Huff"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"volume":156,"issue":"6","page":"1286-1297","day":"13","quality_controlled":"1","language":[{"iso":"eng"}],"extern":"1","month":"03","status":"public","publisher":"Elsevier","pmid":1,"date_published":"2014-03-13T00:00:00Z","external_id":{"pmid":["24630728"]},"type":"journal_article"},{"oa":1,"volume":153,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"full_name":"Kim, M. Yvonne","first_name":"M. Yvonne","last_name":"Kim"},{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"last_name":"Coleman-Derr","first_name":"Devin","full_name":"Coleman-Derr, Devin"},{"full_name":"Eshed-Williams, Leor","first_name":"Leor","last_name":"Eshed-Williams"},{"full_name":"Thao, Ka","last_name":"Thao","first_name":"Ka"},{"full_name":"Harmer, Stacey L.","last_name":"Harmer","first_name":"Stacey L."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman"}],"publication":"Cell","date_updated":"2021-12-14T08:25:35Z","department":[{"_id":"DaZi"}],"intvolume":"       153","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","article_type":"original","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.02.033","open_access":"1"}],"doi":"10.1016/j.cell.2013.02.033","scopus_import":"1","_id":"9459","date_created":"2021-06-04T12:23:28Z","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."}],"year":"2013","citation":{"ama":"Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. 2013;153(1):193-205. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>","ieee":"A. Zemach <i>et al.</i>, “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” <i>Cell</i>, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.","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.” <i>Cell</i>, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>.","apa":"Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>","chicago":"Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>.","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_published":"2013-03-28T00:00:00Z","external_id":{"pmid":["23540698"]},"type":"journal_article","publisher":"Elsevier","pmid":1,"status":"public","month":"03","extern":"1","language":[{"iso":"eng"}],"quality_controlled":"1","day":"28","page":"193-205","issue":"1"}]