[{"scopus_import":"1","volume":91,"has_accepted_license":"1","doi":"10.1016/j.pbi.2026.102881","day":"01","main_file_link":[{"url":"https://doi.org/10.1016/j.pbi.2026.102881","open_access":"1"}],"oa_version":"Published Version","publisher":"Elsevier","citation":{"chicago":"NAGAI, HIROKI, and Xiaoqi Feng. “Genetic and Epigenetic Mechanisms Underlying Male Reproductive Thermotolerance.” Current Opinion in Plant Biology. Elsevier, 2026. https://doi.org/10.1016/j.pbi.2026.102881.","ama":"NAGAI H, Feng X. Genetic and epigenetic mechanisms underlying male reproductive thermotolerance. Current Opinion in Plant Biology. 2026;91(6). doi:10.1016/j.pbi.2026.102881","short":"H. NAGAI, X. Feng, Current Opinion in Plant Biology 91 (2026).","mla":"NAGAI, HIROKI, and Xiaoqi Feng. “Genetic and Epigenetic Mechanisms Underlying Male Reproductive Thermotolerance.” Current Opinion in Plant Biology, vol. 91, no. 6, 102881, Elsevier, 2026, doi:10.1016/j.pbi.2026.102881.","ista":"NAGAI H, Feng X. 2026. Genetic and epigenetic mechanisms underlying male reproductive thermotolerance. Current Opinion in Plant Biology. 91(6), 102881.","apa":"NAGAI, H., & Feng, X. (2026). Genetic and epigenetic mechanisms underlying male reproductive thermotolerance. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2026.102881","ieee":"H. NAGAI and X. Feng, “Genetic and epigenetic mechanisms underlying male reproductive thermotolerance,” Current Opinion in Plant Biology, vol. 91, no. 6. Elsevier, 2026."},"oa":1,"intvolume":" 91","department":[{"_id":"XiFe"}],"publication_status":"epub_ahead","month":"04","_id":"21716","date_updated":"2026-05-04T11:15:57Z","corr_author":"1","title":"Genetic and epigenetic mechanisms underlying male reproductive thermotolerance","ddc":["580"],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","abstract":[{"text":"Male germline development in plants is highly sensitive to heat stress, with elevated temperatures frequently impairing male fertility and consequently reducing seed production. Indeed, recent global warming has decreased major crop yields, emphasizing the urgent need to elucidate the molecular and cellular mechanisms underlying heat-induced male sterility. This review synthesizes current knowledge on how heat stress disrupts microsporogenesis and microgametogenesis, and how plants counteract these stresses through diverse thermotolerance mechanisms. We emphasize temperature-sensitive processes, including meiotic progression in male germ cells, programmed cell death of somatic tapetal nurse cells, and post-meiotic pollen tube development. We further discuss how epigenetic regulators enhance thermotolerance by reprogramming DNA methylation landscapes and modulating histone variant distribution. Finally, we propose future directions aimed at understanding the mechanisms of reproductive thermotolerance from the epigenetic perspective.","lang":"eng"}],"date_created":"2026-04-12T22:01:50Z","date_published":"2026-04-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","status":"public","OA_place":"publisher","article_type":"original","publication_identifier":{"issn":["1369-5266"],"eissn":["1879-0356"]},"language":[{"iso":"eng"}],"year":"2026","publication":"Current Opinion in Plant Biology","acknowledgement":"This work was supported by JSPS KAKENHI (grant number JP22J01430) and the Osamu Hayaishi Memorial Scholarship for Study Abroad for H.N.","quality_controlled":"1","author":[{"id":"608df3e6-e2ab-11ed-8890-c9318cec7da4","first_name":"Hiroki","full_name":"Nagai, Hiroki","orcid":"0000-0003-1671-9434","last_name":"Nagai"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"}],"issue":"6","article_number":"102881","PlanS_conform":"1"},{"file":[{"content_type":"application/pdf","success":1,"access_level":"open_access","creator":"dernst","file_id":"20270","date_updated":"2025-09-02T07:05:37Z","file_size":10876817,"relation":"main_file","date_created":"2025-09-02T07:05:37Z","checksum":"0f1ae246acc9b075f01bf4afe382c8ba","file_name":"2025_ScienceAdvance_DeJaegerBraet.pdf"}],"page":"eadr5694","OA_type":"gold","abstract":[{"lang":"eng","text":"Stress granules (SG) are biomolecular condensates that represent an adaptive response of cells to various stresses, including heat. However, the cell type–specific function and relevance of SG formation, especially during reproductive development, are largely not understood. Here, we show that the meiotic A-type cyclin TARDY ASYNCHRONOUS MEIOSIS (TAM) is recruited to SGs in male meiocytes of Arabidopsis after exposure to heat. We find that the amino terminus of TAM is necessary and sufficient for the localization of proteins to meiotic SGs. Swapping the amino terminus of TAM with the one of its sister protein CYCA1;1 resulted in a separation-of-function allele of TAM, which prevents the partitioning of TAM to SGs while restoring a wild-type phenotype in a tam mutant background under nonheat stress conditions. Notably, plants expressing this TAM version prematurely terminate meiosis under heat resulting in unreduced gametes. Thus, the formation of TAM-containing SGs is necessary for genome stability under heat stress."}],"article_type":"original","external_id":{"isi":["001549102600016"]},"date_created":"2025-08-24T22:01:30Z","date_published":"2025-08-08T00:00:00Z","article_processing_charge":"Yes","status":"public","OA_place":"publisher","DOAJ_listed":"1","file_date_updated":"2025-09-02T07:05:37Z","acknowledgement":"We thank L. Strader (Duke University, Durham) and A. Holehouse (Washington University, Saint Louis) for discussion and input in LLPS. We thank T. Nakagawa (Shimane University, Matsue) for providing the pGWB604 Gateway vector containing bar gene identified by Meiji Seika Kaisha Ltd. We thank M. Heese (Hamburg University) for the critical reading and comments on this manuscript. We further thank J. Mehrmann (Hamburg University) for technical assistance. We thank the ISTA imaging facility for assistance for microscopy.\r\nThis project has received funding from JST-PRESTO (JPMJPR18H7), JST-CREST (JPMJCR18H4), European Union’s Horizon 2020 under MSCA grant 101034413, and a federal grant from the state of Hamburg (LFF-BiCon).","publication_identifier":{"eissn":["2375-2548"]},"isi":1,"language":[{"iso":"eng"}],"publication":"Science Advances","year":"2025","acknowledged_ssus":[{"_id":"Bio"}],"quality_controlled":"1","author":[{"id":"26bd38d3-c59a-11ee-a1af-d7a988cafcc5","first_name":"Joke G","full_name":"De Jaeger-Braet, Joke G","last_name":"De Jaeger-Braet"},{"first_name":"Merle","full_name":"Hartmann, Merle","last_name":"Hartmann"},{"last_name":"Böttger","first_name":"Lev","full_name":"Böttger, Lev"},{"last_name":"Yang","id":"082e3e6e-8069-11ed-8390-c8cce7b1aaca","first_name":"Chao","full_name":"Yang, Chao"},{"last_name":"Hamada","full_name":"Hamada, Takahiro","first_name":"Takahiro"},{"last_name":"Hoth","first_name":"Stefan","full_name":"Hoth, Stefan"},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"},{"full_name":"Weingartner, Magdalena","first_name":"Magdalena","last_name":"Weingartner"},{"first_name":"Arp","full_name":"Schnittger, Arp","last_name":"Schnittger"}],"issue":"32","doi":"10.1126/sciadv.adr5694","day":"08","oa_version":"Published Version","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"volume":11,"scopus_import":"1","has_accepted_license":"1","intvolume":" 11","department":[{"_id":"XiFe"}],"publication_status":"published","publisher":"AAAS","citation":{"mla":"De Jaeger-Braet, Joke G., et al. “The Recruitment of the A-Type Cyclin TAM to Stress Granules Is Crucial for Meiotic Fidelity under Heat.” Science Advances, vol. 11, no. 32, AAAS, 2025, p. eadr5694, doi:10.1126/sciadv.adr5694.","ista":"De Jaeger-Braet JG, Hartmann M, Böttger L, Yang C, Hamada T, Hoth S, Feng X, Weingartner M, Schnittger A. 2025. The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat. Science Advances. 11(32), eadr5694.","apa":"De Jaeger-Braet, J. G., Hartmann, M., Böttger, L., Yang, C., Hamada, T., Hoth, S., … Schnittger, A. (2025). The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat. Science Advances. AAAS. https://doi.org/10.1126/sciadv.adr5694","ieee":"J. G. De Jaeger-Braet et al., “The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat,” Science Advances, vol. 11, no. 32. AAAS, p. eadr5694, 2025.","chicago":"De Jaeger-Braet, Joke G, Merle Hartmann, Lev Böttger, Chao Yang, Takahiro Hamada, Stefan Hoth, Xiaoqi Feng, Magdalena Weingartner, and Arp Schnittger. “The Recruitment of the A-Type Cyclin TAM to Stress Granules Is Crucial for Meiotic Fidelity under Heat.” Science Advances. AAAS, 2025. https://doi.org/10.1126/sciadv.adr5694.","short":"J.G. De Jaeger-Braet, M. Hartmann, L. Böttger, C. Yang, T. Hamada, S. Hoth, X. Feng, M. Weingartner, A. Schnittger, Science Advances 11 (2025) eadr5694.","ama":"De Jaeger-Braet JG, Hartmann M, Böttger L, et al. The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat. Science Advances. 2025;11(32):eadr5694. doi:10.1126/sciadv.adr5694"},"oa":1,"title":"The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat","ddc":["580"],"month":"08","_id":"20220","date_updated":"2025-09-30T14:24:10Z","ec_funded":1,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"}},{"oa_version":"Published Version","day":"04","doi":"10.1186/s43897-024-00137-9","has_accepted_license":"1","volume":5,"scopus_import":"1","intvolume":" 5","publication_status":"published","department":[{"_id":"XiFe"}],"publisher":"Springer Nature","oa":1,"citation":{"ista":"Zhang J, Wu D, Zhang Y, Feng X, Gao H. 2025. DNA methylation dynamics in male germline development in Brassica Rapa. Molecular Horticulture. 5, 16.","ieee":"J. Zhang, D. Wu, Y. Zhang, X. Feng, and H. Gao, “DNA methylation dynamics in male germline development in Brassica Rapa,” Molecular Horticulture, vol. 5. Springer Nature, 2025.","apa":"Zhang, J., Wu, D., Zhang, Y., Feng, X., & Gao, H. (2025). DNA methylation dynamics in male germline development in Brassica Rapa. Molecular Horticulture. Springer Nature. https://doi.org/10.1186/s43897-024-00137-9","mla":"Zhang, Jun, et al. “DNA Methylation Dynamics in Male Germline Development in Brassica Rapa.” Molecular Horticulture, vol. 5, 16, Springer Nature, 2025, doi:10.1186/s43897-024-00137-9.","chicago":"Zhang, Jun, Di Wu, Yating Zhang, Xiaoqi Feng, and Hongbo Gao. “DNA Methylation Dynamics in Male Germline Development in Brassica Rapa.” Molecular Horticulture. Springer Nature, 2025. https://doi.org/10.1186/s43897-024-00137-9.","short":"J. Zhang, D. Wu, Y. Zhang, X. Feng, H. Gao, Molecular Horticulture 5 (2025).","ama":"Zhang J, Wu D, Zhang Y, Feng X, Gao H. DNA methylation dynamics in male germline development in Brassica Rapa. Molecular Horticulture. 2025;5. doi:10.1186/s43897-024-00137-9"},"corr_author":"1","ddc":["580"],"title":"DNA methylation dynamics in male germline development in Brassica Rapa","month":"03","date_updated":"2025-09-30T11:17:08Z","_id":"19436","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"file":[{"content_type":"application/pdf","success":1,"creator":"dernst","access_level":"open_access","file_id":"19460","date_updated":"2025-03-25T12:15:32Z","file_size":3014980,"relation":"main_file","date_created":"2025-03-25T12:15:32Z","file_name":"2025_MolecularHorticulture_Zhang.pdf","checksum":"6d1e0e9b0e1902e4a711f81c5c17a070"}],"abstract":[{"lang":"eng","text":"Dynamic DNA methylation represses transposable elements (TEs) and regulates gene activity, playing a pivotal role in plant development. Although substantial progress has been made in understanding DNA methylation reprogramming during germline development in Arabidopsis thaliana, whether similar mechanisms exist in other dicot plants remains unclear. Here, we analyzed DNA methylation levels in meiocytes, microspores, and pollens of Brassica Rapa using whole-genome bisulfite sequencing (WGBS). Global DNA methylation analysis revealed similar CHH methylation reprogramming compared to Arabidopsis, while distinct patterns were observed in the dynamics of global CG and CHG methylation in B. rapa. Differentially methylated region (DMR) analysis identified specifically methylated loci in the male sex cells of B. Rapa with a stronger tendency to target genes, similar to observations in Arabidopsis. Additionally, we found that the activity and genomic targeting preference of the small RNA-directed DNA methylation (RdDM) were altered during B. Rapa male germline development. A subset of long terminal repeat (LTR) TEs were activated, possibly due to the dynamic regulation of DNA methylation during male sexual development in B. Rapa. These findings provided new insights into the evolution of epigenetic reprogramming mechanisms in plants."}],"OA_type":"gold","external_id":{"pmid":["40033451"],"isi":["001436233900001"]},"article_type":"original","article_processing_charge":"Yes","date_created":"2025-03-23T23:01:25Z","date_published":"2025-03-04T00:00:00Z","DOAJ_listed":"1","OA_place":"publisher","status":"public","file_date_updated":"2025-03-25T12:15:32Z","acknowledgement":"We thank Prof. Ying Li of Nanjing Agricultural University for her help in providing seeds of K2 materials. This work was carried out with the support of National Natural Science Foundation of China (Grant No. 32070608).","publication_identifier":{"eissn":["2730-9401"]},"publication":"Molecular Horticulture","language":[{"iso":"eng"}],"year":"2025","isi":1,"quality_controlled":"1","article_number":"16","author":[{"last_name":"Zhang","first_name":"Jun","full_name":"Zhang, Jun"},{"last_name":"Wu","first_name":"Di","full_name":"Wu, Di"},{"last_name":"Zhang","first_name":"Yating","full_name":"Zhang, Yating"},{"last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"},{"last_name":"Gao","full_name":"Gao, Hongbo","first_name":"Hongbo","id":"77c2e73a-eabd-11ef-aee9-8093a2ba7a93"}]},{"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.).","file_date_updated":"2025-12-29T13:40:32Z","publication":"Cell","isi":1,"language":[{"iso":"eng"}],"year":"2025","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"PlanS_conform":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"issue":"11","author":[{"last_name":"Walker","first_name":"James","full_name":"Walker, James"},{"last_name":"Zhang","first_name":"Jingyi","full_name":"Zhang, Jingyi"},{"full_name":"Liu, Yalin","first_name":"Yalin","last_name":"Liu"},{"id":"9724dd9d-f591-11ee-bd51-e97ed0652286","first_name":"Shujuan","full_name":"Xu, Shujuan","last_name":"Xu"},{"first_name":"Yiming","id":"318e643b-8b61-11ed-b69e-aafa103ec8dd","full_name":"Yu, Yiming","orcid":"0000-0002-9919-7282","last_name":"Yu"},{"last_name":"Vickers","full_name":"Vickers, Martin","first_name":"Martin"},{"last_name":"Ouyang","first_name":"Weizhi","id":"fec73395-8b60-11ed-b69e-927fda99c743","full_name":"Ouyang, Weizhi"},{"last_name":"Tálas","first_name":"Judit","full_name":"Tálas, Judit"},{"full_name":"Dolan, Liam","first_name":"Liam","last_name":"Dolan"},{"last_name":"Nakajima","full_name":"Nakajima, Keiji","first_name":"Keiji"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"}],"quality_controlled":"1","page":"2890-2906.e14","OA_type":"hybrid","abstract":[{"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.","lang":"eng"}],"file":[{"date_created":"2025-12-29T13:40:32Z","file_name":"2025_Cell_Walker.pdf","checksum":"0dcc2feb368dfe7c4890093366b2dacb","relation":"main_file","file_id":"20871","date_updated":"2025-12-29T13:40:32Z","file_size":11622960,"content_type":"application/pdf","success":1,"access_level":"open_access","creator":"dernst"}],"article_type":"original","external_id":{"pmid":["40209706"],"isi":["001504744800006"]},"related_material":{"link":[{"url":"https://ista.ac.at/en/news/from-bacterial-immunity-to-plant-sex/","relation":"press_release","description":"News on ISTA website"}]},"OA_place":"publisher","status":"public","date_published":"2025-05-29T00:00:00Z","date_created":"2025-04-20T22:01:28Z","article_processing_charge":"Yes (via OA deal)","ddc":["570"],"title":"Extensive N4 cytosine methylation is essential for Marchantia sperm function","corr_author":"1","_id":"19602","date_updated":"2026-04-28T13:36:51Z","month":"05","ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"pmid":1,"type":"journal_article","doi":"10.1016/j.cell.2025.03.014","day":"29","oa_version":"Published Version","has_accepted_license":"1","scopus_import":"1","volume":188,"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"}],"department":[{"_id":"XiFe"}],"publication_status":"published","intvolume":" 188","citation":{"ista":"Walker J, Zhang J, Liu Y, Xu S, Yu Y, Vickers M, Ouyang W, Tálas J, Dolan L, Nakajima K, Feng X. 2025. Extensive N4 cytosine methylation is essential for Marchantia sperm function. Cell. 188(11), 2890–2906.e14.","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. Elsevier. 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. Elsevier, p. 2890–2906.e14, 2025.","mla":"Walker, James, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia Sperm Function.” Cell, vol. 188, no. 11, Elsevier, 2025, p. 2890–2906.e14, doi: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. Elsevier, 2025. https://doi.org/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.","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"},"oa":1,"publisher":"Elsevier"},{"doi":"10.1093/plcell/koae034","oa_version":"Published Version","day":"01","has_accepted_license":"1","volume":36,"scopus_import":"1","department":[{"_id":"XiFe"}],"publication_status":"published","intvolume":" 36","citation":{"mla":"He, Shengbo, et al. “Linker Histone H1 Drives Heterochromatin Condensation via Phase Separation in Arabidopsis.” The Plant Cell, vol. 36, no. 5, Oxford University Press, 2024, pp. 1829–43, doi:10.1093/plcell/koae034.","ieee":"S. He et al., “Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis,” The Plant Cell, vol. 36, no. 5. Oxford University Press, pp. 1829–1843, 2024.","apa":"He, S., Yu, Y., Wang, L., Zhang, J., Bai, Z., Li, G., … Feng, X. (2024). Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koae034","ista":"He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. 2024. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. The Plant Cell. 36(5), 1829–1843.","ama":"He S, Yu Y, Wang L, et al. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. The Plant Cell. 2024;36(5):1829-1843. doi:10.1093/plcell/koae034","short":"S. He, Y. Yu, L. Wang, J. Zhang, Z. Bai, G. Li, P. Li, X. Feng, The Plant Cell 36 (2024) 1829–1843.","chicago":"He, Shengbo, Yiming Yu, Liang Wang, Jingyi Zhang, Zhengyong Bai, Guohong Li, Pilong Li, and Xiaoqi Feng. “Linker Histone H1 Drives Heterochromatin Condensation via Phase Separation in Arabidopsis.” The Plant Cell. Oxford University Press, 2024. https://doi.org/10.1093/plcell/koae034."},"oa":1,"publisher":"Oxford University Press","ddc":["580"],"title":"Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis","corr_author":"1","_id":"15375","date_updated":"2025-09-08T07:21:17Z","month":"05","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","page":"1829-1843","OA_type":"hybrid","abstract":[{"lang":"eng","text":"In the eukaryotic nucleus, heterochromatin forms highly condensed, visible foci known as heterochromatin foci (HF). These HF are enriched with linker histone H1, a key player in heterochromatin condensation and silencing. However, it is unknown how H1 aggregates HF and condenses heterochromatin. In this study, we established that H1 facilitates heterochromatin condensation by enhancing inter- and intrachromosomal interactions between and within heterochromatic regions of the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives HF formation via phase separation, which requires its C-terminal intrinsically disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci or recover HF in the h1 mutant background, whereas C-IDR with a short stretch of the globular domain (18 out of 71 amino acids) is sufficient to rescue both defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome repeat length and DNA methylation in Arabidopsis, indicating that phase separation capability is required for chromatin functions of H1. Our data suggest that bacterial H1-like proteins, which have been shown to condense DNA, are intrinsically disordered and capable of mediating phase separation. Therefore, we propose that phase separation mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing chromatin and DNA."}],"file":[{"file_id":"19611","file_size":50791962,"date_updated":"2025-04-23T07:43:12Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","success":1,"date_created":"2025-04-23T07:43:12Z","file_name":"2024_PlantCell_He.pdf","checksum":"eed76c848fe3d8fe9a53943181aaa53c","relation":"main_file"}],"article_type":"original","external_id":{"pmid":["38309957"],"isi":["001180817000001"]},"OA_place":"publisher","status":"public","date_created":"2024-05-12T22:01:01Z","date_published":"2024-05-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2025-04-23T07:43:12Z","acknowledgement":"This work was funded by ISTA core support (Y.Y. and X.F.) and grants from the National Natural Science Foundation of China (31871443 to L.W. and P.L.; 32100417 to L.W.).\r\nWe thank the ISTA Imaging and Optics Facility for assistance with microscopy and the ISTA Scientific Computing Facility for high-performance computing resources.","language":[{"iso":"eng"}],"isi":1,"publication":"The Plant Cell","year":"2024","publication_identifier":{"eissn":["1532-298X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"issue":"5","author":[{"last_name":"He","first_name":"Shengbo","full_name":"He, Shengbo"},{"last_name":"Yu","first_name":"Yiming","id":"318e643b-8b61-11ed-b69e-aafa103ec8dd","full_name":"Yu, Yiming"},{"first_name":"Liang","full_name":"Wang, Liang","last_name":"Wang"},{"full_name":"Zhang, Jingyi","first_name":"Jingyi","last_name":"Zhang"},{"full_name":"Bai, Zhengyong","first_name":"Zhengyong","last_name":"Bai"},{"last_name":"Li","full_name":"Li, Guohong","first_name":"Guohong"},{"last_name":"Li","full_name":"Li, Pilong","first_name":"Pilong"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"}],"quality_controlled":"1"},{"article_number":"7","author":[{"first_name":"Long","full_name":"Zhao, Long","last_name":"Zhao"},{"full_name":"Yang, Yiman","first_name":"Yiman","last_name":"Yang"},{"last_name":"Chen","full_name":"Chen, Jinchao","first_name":"Jinchao"},{"last_name":"Lin","first_name":"Xuelei","full_name":"Lin, Xuelei"},{"last_name":"Zhang","first_name":"Hao","full_name":"Zhang, Hao"},{"full_name":"Wang, Hao","first_name":"Hao","last_name":"Wang"},{"full_name":"Wang, Hongzhe","first_name":"Hongzhe","last_name":"Wang"},{"last_name":"Bie","full_name":"Bie, Xiaomin","first_name":"Xiaomin"},{"full_name":"Jiang, Jiafu","first_name":"Jiafu","last_name":"Jiang"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"},{"last_name":"Fu","first_name":"Xiangdong","full_name":"Fu, Xiangdong"},{"first_name":"Xiansheng","full_name":"Zhang, Xiansheng","last_name":"Zhang"},{"first_name":"Zhuo","full_name":"Du, Zhuo","last_name":"Du"},{"last_name":"Xiao","first_name":"Jun","full_name":"Xiao, Jun"}],"quality_controlled":"1","language":[{"iso":"eng"}],"year":"2023","publication":"Genome Biology","extern":"1","publication_identifier":{"issn":["1474-760X"]},"external_id":{"pmid":["36639687"]},"article_type":"original","status":"public","article_processing_charge":"No","date_published":"2023-01-13T00:00:00Z","date_created":"2023-02-23T09:13:49Z","abstract":[{"text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.","lang":"eng"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","date_updated":"2023-05-08T10:52:49Z","_id":"12668","month":"01","publication_status":"published","department":[{"_id":"XiFe"}],"intvolume":" 24","oa":1,"citation":{"ieee":"L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7.","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023, doi:10.1186/s13059-022-02844-2.","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.","ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023)."},"publisher":"Springer Nature","day":"13","main_file_link":[{"url":"https://doi.org/10.1186/s13059-022-02844-2","open_access":"1"}],"oa_version":"Published Version","doi":"10.1186/s13059-022-02844-2","scopus_import":"1","volume":24},{"volume":35,"scopus_import":"1","oa_version":"Published Version","day":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/plcell/koac346"}],"doi":"10.1093/plcell/koac346","oa":1,"citation":{"mla":"Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” The Plant Cell, vol. 35, no. 6, koac346, Oxford University Press, 2023, doi:10.1093/plcell/koac346.","ieee":"P. A. Manavella et al., “Beyond transcription: compelling open questions in plant RNA biology,” The Plant Cell, vol. 35, no. 6. Oxford University Press, 2023.","ista":"Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 35(6), koac346.","apa":"Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth, L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac346","short":"P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth, K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J. Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).","ama":"Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 2023;35(6). doi:10.1093/plcell/koac346","chicago":"Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson, Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” The Plant Cell. Oxford University Press, 2023. https://doi.org/10.1093/plcell/koac346."},"publisher":"Oxford University Press","publication_status":"published","department":[{"_id":"XiFe"}],"keyword":["Cell Biology","Plant Science"],"intvolume":" 35","date_updated":"2023-10-04T09:48:43Z","_id":"12669","month":"06","title":"Beyond transcription: compelling open questions in plant RNA biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"type":"journal_article","abstract":[{"lang":"eng","text":"The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader."}],"status":"public","article_processing_charge":"No","date_created":"2023-02-23T09:14:59Z","date_published":"2023-06-01T00:00:00Z","external_id":{"pmid":["36477566"]},"article_type":"original","year":"2023","publication":"The Plant Cell","language":[{"iso":"eng"}],"extern":"1","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"article_number":"koac346","author":[{"full_name":"Manavella, Pablo A","first_name":"Pablo A","last_name":"Manavella"},{"first_name":"Micaela A","full_name":"Godoy Herz, Micaela A","last_name":"Godoy Herz"},{"last_name":"Kornblihtt","first_name":"Alberto R","full_name":"Kornblihtt, Alberto R"},{"last_name":"Sorenson","full_name":"Sorenson, Reed","first_name":"Reed"},{"last_name":"Sieburth","first_name":"Leslie E","full_name":"Sieburth, Leslie E"},{"first_name":"Kentaro","full_name":"Nakaminami, Kentaro","last_name":"Nakaminami"},{"first_name":"Motoaki","full_name":"Seki, Motoaki","last_name":"Seki"},{"first_name":"Yiliang","full_name":"Ding, Yiliang","last_name":"Ding"},{"full_name":"Sun, Qianwen","first_name":"Qianwen","last_name":"Sun"},{"last_name":"Kang","full_name":"Kang, Hunseung","first_name":"Hunseung"},{"full_name":"Ariel, Federico D","first_name":"Federico D","last_name":"Ariel"},{"first_name":"Martin","full_name":"Crespi, Martin","last_name":"Crespi"},{"last_name":"Giudicatti","first_name":"Axel J","full_name":"Giudicatti, Axel J"},{"last_name":"Cai","full_name":"Cai, Qiang","first_name":"Qiang"},{"last_name":"Jin","full_name":"Jin, Hailing","first_name":"Hailing"},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng"},{"last_name":"Qi","full_name":"Qi, Yijun","first_name":"Yijun"},{"full_name":"Pikaard, Craig S","first_name":"Craig S","last_name":"Pikaard"}],"issue":"6","quality_controlled":"1"},{"publication":"Cell Reports","year":"2023","language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"eissn":["2211-1247"]},"acknowledgement":"The authors would like to thank Jasper Rine for advice and mentorship to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from the Helen Hay Whitney Foundation to D.B.L.","file_date_updated":"2023-05-11T10:41:42Z","author":[{"last_name":"Lyons","first_name":"David B.","full_name":"Lyons, David B."},{"last_name":"Briffa","full_name":"Briffa, Amy","first_name":"Amy"},{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"full_name":"Choi, Jaemyung","first_name":"Jaemyung","last_name":"Choi"},{"last_name":"Hollwey","full_name":"Hollwey, Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","first_name":"Elizabeth"},{"last_name":"Colicchio","first_name":"Jack","full_name":"Colicchio, Jack"},{"first_name":"Ian","full_name":"Anderson, Ian","last_name":"Anderson"},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"},{"last_name":"Howard","full_name":"Howard, Martin","first_name":"Martin"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"}],"issue":"3","article_number":"112132","quality_controlled":"1","abstract":[{"lang":"eng","text":"Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation."}],"file":[{"file_name":"2023_CellReports_Lyons.pdf","checksum":"6cbc44fdb18bf18834c9e2a5b9c67123","date_created":"2023-05-11T10:41:42Z","relation":"main_file","file_size":8401261,"date_updated":"2023-05-11T10:41:42Z","file_id":"12941","creator":"kschuh","access_level":"open_access","success":1,"content_type":"application/pdf"}],"status":"public","date_created":"2023-02-23T09:17:44Z","date_published":"2023-03-28T00:00:00Z","article_processing_charge":"Yes","article_type":"original","external_id":{"isi":["000944921600001"]},"_id":"12672","date_updated":"2025-04-14T07:57:43Z","month":"03","ddc":["580"],"title":"Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons","corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","ec_funded":1,"volume":42,"has_accepted_license":"1","scopus_import":"1","project":[{"name":"Quantitative analysis of DNA methylation maintenance with chromatin","grant_number":"725746","_id":"62935a00-2b32-11ec-9570-eff30fa39068","call_identifier":"H2020"}],"doi":"10.1016/j.celrep.2023.112132","oa_version":"Published Version","day":"28","citation":{"apa":"Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman, D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.112132","ista":"Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3), 112132.","ieee":"D. B. Lyons et al., “Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons,” Cell Reports, vol. 42, no. 3. Elsevier, 2023.","mla":"Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports, vol. 42, no. 3, 112132, Elsevier, 2023, doi:10.1016/j.celrep.2023.112132.","chicago":"Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132.","short":"D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).","ama":"Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 2023;42(3). doi:10.1016/j.celrep.2023.112132"},"oa":1,"publisher":"Elsevier","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publication_status":"published","intvolume":" 42"},{"external_id":{"pmid":["36478632"]},"article_type":"review","status":"public","article_processing_charge":"No","date_published":"2022-12-07T00:00:00Z","date_created":"2023-02-23T09:15:57Z","abstract":[{"lang":"eng","text":"DNA methylation plays essential homeostatic functions in eukaryotic genomes. In animals, DNA methylation is also developmentally regulated and, in turn, regulates development. In the past two decades, huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development, especially during sexual reproduction. The power of whole-genome sequencing and cell isolation techniques, as well as bioinformatics tools, have enabled recent studies to reveal dynamic changes in DNA methylation during germline development. Furthermore, the combination of these technological advances with genetics, developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines. In this review, we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants."}],"page":"2240-2251","issue":"12","author":[{"full_name":"He, Shengbo","first_name":"Shengbo","last_name":"He"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng"}],"quality_controlled":"1","year":"2022","language":[{"iso":"eng"}],"publication":"Journal of Integrative Plant Biology","extern":"1","publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"publication_status":"published","department":[{"_id":"XiFe"}],"keyword":["Plant Science","General Biochemistry","Genetics and Molecular Biology","Biochemistry"],"intvolume":" 64","oa":1,"citation":{"ieee":"S. He and X. Feng, “DNA methylation dynamics during germline development,” Journal of Integrative Plant Biology, vol. 64, no. 12. Wiley, pp. 2240–2251, 2022.","apa":"He, S., & Feng, X. (2022). DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13422","ista":"He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 64(12), 2240–2251.","mla":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” Journal of Integrative Plant Biology, vol. 64, no. 12, Wiley, 2022, pp. 2240–51, doi:10.1111/jipb.13422.","chicago":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13422.","short":"S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.","ama":"He S, Feng X. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 2022;64(12):2240-2251. doi:10.1111/jipb.13422"},"publisher":"Wiley","day":"07","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1111/jipb.13422","open_access":"1"}],"doi":"10.1111/jipb.13422","volume":64,"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"type":"journal_article","title":"DNA methylation dynamics during germline development","date_updated":"2024-10-14T12:03:14Z","_id":"12670","month":"12"},{"doi":"10.1038/s41586-022-05386-6","day":"17","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41586-022-05386-6"}],"scopus_import":"1","volume":611,"department":[{"_id":"XiFe"}],"publication_status":"published","intvolume":" 611","citation":{"mla":"Buttress, Toby, et al. “Histone H2B.8 Compacts Flowering Plant Sperm through Chromatin Phase Separation.” Nature, vol. 611, no. 7936, Springer Nature, 2022, pp. 614–22, doi:10.1038/s41586-022-05386-6.","apa":"Buttress, T., He, S., Wang, L., Zhou, S., Saalbach, G., Vickers, M., … Feng, X. (2022). Histone H2B.8 compacts flowering plant sperm through chromatin phase separation. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05386-6","ieee":"T. Buttress et al., “Histone H2B.8 compacts flowering plant sperm through chromatin phase separation,” Nature, vol. 611, no. 7936. Springer Nature, pp. 614–622, 2022.","ista":"Buttress T, He S, Wang L, Zhou S, Saalbach G, Vickers M, Li G, Li P, Feng X. 2022. Histone H2B.8 compacts flowering plant sperm through chromatin phase separation. Nature. 611(7936), 614–622.","chicago":"Buttress, Toby, Shengbo He, Liang Wang, Shaoli Zhou, Gerhard Saalbach, Martin Vickers, Guohong Li, Pilong Li, and Xiaoqi Feng. “Histone H2B.8 Compacts Flowering Plant Sperm through Chromatin Phase Separation.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05386-6.","ama":"Buttress T, He S, Wang L, et al. Histone H2B.8 compacts flowering plant sperm through chromatin phase separation. Nature. 2022;611(7936):614-622. doi:10.1038/s41586-022-05386-6","short":"T. Buttress, S. He, L. Wang, S. Zhou, G. Saalbach, M. Vickers, G. Li, P. Li, X. Feng, Nature 611 (2022) 614–622."},"oa":1,"publisher":"Springer Nature","title":"Histone H2B.8 compacts flowering plant sperm through chromatin phase separation","_id":"12671","date_updated":"2024-10-14T12:03:36Z","month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"type":"journal_article","page":"614-622","abstract":[{"lang":"eng","text":"Sperm chromatin is typically transformed by protamines into a compact and transcriptionally inactive state1,2. Sperm cells of flowering plants lack protamines, yet they have small, transcriptionally active nuclei with chromatin condensed through an unknown mechanism3,4. Here we show that a histone variant, H2B.8, mediates sperm chromatin and nuclear condensation in Arabidopsis thaliana. Loss of H2B.8 causes enlarged sperm nuclei with dispersed chromatin, whereas ectopic expression in somatic cells produces smaller nuclei with aggregated chromatin. This result demonstrates that H2B.8 is sufficient for chromatin condensation. H2B.8 aggregates transcriptionally inactive AT-rich chromatin into phase-separated condensates, which facilitates nuclear compaction without reducing transcription. Reciprocal crosses show that mutation of h2b.8 reduces male transmission, which suggests that H2B.8-mediated sperm compaction is important for fertility. Altogether, our results reveal a new mechanism of nuclear compaction through global aggregation of unexpressed chromatin. We propose that H2B.8 is an evolutionary innovation of flowering plants that achieves nuclear condensation compatible with active transcription."}],"article_type":"original","external_id":{"pmid":["36323776"]},"status":"public","date_published":"2022-11-17T00:00:00Z","date_created":"2023-02-23T09:17:05Z","article_processing_charge":"No","publication":"Nature","language":[{"iso":"eng"}],"year":"2022","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"extern":"1","issue":"7936","author":[{"full_name":"Buttress, Toby","first_name":"Toby","last_name":"Buttress"},{"first_name":"Shengbo","full_name":"He, Shengbo","last_name":"He"},{"full_name":"Wang, Liang","first_name":"Liang","last_name":"Wang"},{"last_name":"Zhou","first_name":"Shaoli","full_name":"Zhou, Shaoli"},{"full_name":"Saalbach, Gerhard","first_name":"Gerhard","last_name":"Saalbach"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"full_name":"Li, Guohong","first_name":"Guohong","last_name":"Li"},{"last_name":"Li","first_name":"Pilong","full_name":"Li, Pilong"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"}],"quality_controlled":"1"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"month":"08","date_updated":"2023-05-08T11:01:18Z","_id":"12186","title":"Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors","publisher":"Oxford University Press","citation":{"short":"P. Ding, T. Sakai, R. Krishna Shrestha, N. Manosalva Perez, W. Guo, B.P.M. Ngou, S. He, C. Liu, X. Feng, R. Zhang, K. Vandepoele, D. MacLean, J.D.G. Jones, Journal of Experimental Botany 72 (2021) 7927–7941.","ama":"Ding P, Sakai T, Krishna Shrestha R, et al. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. 2021;72(22):7927-7941. doi:10.1093/jxb/erab373","chicago":"Ding, Pingtao, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” Journal of Experimental Botany. Oxford University Press, 2021. https://doi.org/10.1093/jxb/erab373.","mla":"Ding, Pingtao, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” Journal of Experimental Botany, vol. 72, no. 22, Oxford University Press, 2021, pp. 7927–41, doi:10.1093/jxb/erab373.","ista":"Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. 2021. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. 72(22), 7927–7941.","ieee":"P. Ding et al., “Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors,” Journal of Experimental Botany, vol. 72, no. 22. Oxford University Press, pp. 7927–7941, 2021.","apa":"Ding, P., Sakai, T., Krishna Shrestha, R., Manosalva Perez, N., Guo, W., Ngou, B. P. M., … Jones, J. D. G. (2021). Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erab373"},"keyword":["Plant Science","Physiology"],"intvolume":" 72","publication_status":"published","department":[{"_id":"XiFe"}],"volume":72,"scopus_import":"1","day":"13","oa_version":"None","doi":"10.1093/jxb/erab373","quality_controlled":"1","issue":"22","author":[{"first_name":"Pingtao","full_name":"Ding, Pingtao","last_name":"Ding"},{"first_name":"Toshiyuki","full_name":"Sakai, Toshiyuki","last_name":"Sakai"},{"last_name":"Krishna Shrestha","first_name":"Ram","full_name":"Krishna Shrestha, Ram"},{"last_name":"Manosalva Perez","first_name":"Nicolas","full_name":"Manosalva Perez, Nicolas"},{"full_name":"Guo, Wenbin","first_name":"Wenbin","last_name":"Guo"},{"last_name":"Ngou","first_name":"Bruno Pok Man","full_name":"Ngou, Bruno Pok Man"},{"first_name":"Shengbo","full_name":"He, Shengbo","last_name":"He"},{"full_name":"Liu, Chang","first_name":"Chang","last_name":"Liu"},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"},{"first_name":"Runxuan","full_name":"Zhang, Runxuan","last_name":"Zhang"},{"full_name":"Vandepoele, Klaas","first_name":"Klaas","last_name":"Vandepoele"},{"last_name":"MacLean","first_name":"Dan","full_name":"MacLean, Dan"},{"last_name":"Jones","first_name":"Jonathan D G","full_name":"Jones, Jonathan D G"}],"extern":"1","publication_identifier":{"issn":["0022-0957","1460-2431"]},"year":"2021","language":[{"iso":"eng"}],"publication":"Journal of Experimental Botany","acknowledgement":"We thank the Gatsby Foundation (UK) for funding to the JDGJ laboratory. PD acknowledges support from the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodowska Curie Actions (grant agreement: 656243) and a Future Leader Fellowship from the Biotechnology and Biological Sciences Research Council (BBSRC) (grant agreement: BB/R012172/1). TS, RKS, DM, and JDGJ were supported by the Gatsby Foundation funding to the\r\nSainsbury Laboratory. NMP and KV were supported by a BOF grant from Ghent University (grant agreement: BOF24Y2019001901). WG and RZ were supported by the Scottish Government Rural and Environment Science and Analytical Services division (RESAS), and RZ also acknowledges the support from a BBSRC Bioinformatics and Biological Resources Fund (grant agreement: BB/S020160/1).BPMN was supported by the Norwich Research Park (NRP) Biosciences Doctoral Training Partnership (DTP) funded by the BBSRC (grant agreement: BB/M011216/1). SH and XF were supported by a BBSRC Responsive Mode grant (grant agreement: BB/S009620/1) and a European Research Council Starting grant ‘SexMeth’ (grant agreement: 804981). CL was supported by Deutsche Forschungsgemeinschaft (grant agreement: LI 2862/4). ","article_processing_charge":"No","date_published":"2021-08-13T00:00:00Z","date_created":"2023-01-16T09:14:35Z","status":"public","external_id":{"pmid":["34387350"]},"article_type":"original","abstract":[{"text":"Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.","lang":"eng"}],"page":"7927-7941"},{"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"extern":"1","language":[{"iso":"eng"}],"year":"2021","publication":"Science","acknowledgement":"We thank the John Innes Centre Bioimaging Facility (S. Lopez, E. Wegel, and K. Findlay) for their assistance with microscopy and the Norwich BioScience Institute Partnership Computing Infrastructure for Science Group for high-performance computing resources. Funding: This work was funded by a European Research Council Starting Grant (“SexMeth” 804981; J.L., J.W., and X.F.), a Sainsbury Charitable Foundation studentship (J.W.), two Biotechnology and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111; W.S., M.V., and X.F.), two John Innes Foundation studentships (B.A. and S.D.), and a BBSRC David Phillips Fellowship (BBL0250431; H.G. and X.F.). Author contributions: J.L., J.W., and X.F. designed the study and wrote the manuscript; J.L., W.S., B.A., H.G., and S.D. performed the experiments; and J.L., J.W., B.A., H.G., S.D., M.V., and X.F. analyzed the data. Competing interests: The authors declare no competing interests. Data and material availability: All sequencing data have been deposited in the Gene Expression Omnibus (GEO) under accession no. GSE161625. Accession nos. of published datasets used in this study are listed in table S6. Published software used in this study include Bowtie v1.2.2 (https://doi.org/10.1002/0471250953.bi1107s32), Bismark v0.22.2 (https://doi.org/10.1093/bioinformatics/btr167), Kallisto v0.43.0 (https://doi.org/10.1038/nbt0816-888d), Shortstack v3.8.5 (https://doi.org/10.1534/g3.116.030452), and Cutadapt v1.15 (https://doi.org/10.1089/cmb.2017.0096). TrimGalore v0.4.1 and MarkDuplicates v1.141 are available from https://github.com/FelixKrueger/TrimGalore and https://github.com/broadinstitute/picard, respectively. All remaining data are in the main paper or the supplementary materials.","quality_controlled":"1","issue":"6550","author":[{"last_name":"Long","first_name":"Jincheng","full_name":"Long, Jincheng"},{"last_name":"Walker","first_name":"James","full_name":"Walker, James"},{"last_name":"She","first_name":"Wenjing","full_name":"She, Wenjing"},{"last_name":"Aldridge","first_name":"Billy","full_name":"Aldridge, Billy"},{"full_name":"Gao, Hongbo","first_name":"Hongbo","last_name":"Gao"},{"full_name":"Deans, Samuel","first_name":"Samuel","last_name":"Deans"},{"last_name":"Vickers","first_name":"Martin","full_name":"Vickers, Martin"},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"}],"OA_type":"green","abstract":[{"lang":"eng","text":"Genomes of germ cells present an existential vulnerability to organisms because germ cell mutations will propagate to future generations. Transposable elements are one source of such mutations. In the small flowering plant Arabidopsis, Long et al. found that genome methylation in the male germline is directed by small interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective by Mosher). These germline siRNAs silence germline transposons and establish inherited methylation patterns in sperm, thus maintaining the integrity of the plant genome across generations."}],"date_created":"2023-01-16T09:15:14Z","date_published":"2021-07-02T00:00:00Z","article_processing_charge":"No","status":"public","OA_place":"repository","article_type":"original","external_id":{"pmid":["34210850"]},"month":"07","_id":"12187","date_updated":"2026-03-19T10:52:21Z","title":"Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"scopus_import":"1","volume":373,"doi":"10.1126/science.abh0556","day":"02","main_file_link":[{"url":"https://doi.org/10.1101/2021.01.25.428150","open_access":"1"}],"oa_version":"Preprint","publisher":"American Association for the Advancement of Science","citation":{"chicago":"Long, Jincheng, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao, Samuel Deans, Martin Vickers, and Xiaoqi Feng. “Nurse Cell-Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” Science. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/science.abh0556.","short":"J. Long, J. Walker, W. She, B. Aldridge, H. Gao, S. Deans, M. Vickers, X. Feng, Science 373 (2021).","ama":"Long J, Walker J, She W, et al. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science. 2021;373(6550). doi:10.1126/science.abh0556","mla":"Long, Jincheng, et al. “Nurse Cell-Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” Science, vol. 373, no. 6550, American Association for the Advancement of Science, 2021, doi:10.1126/science.abh0556.","apa":"Long, J., Walker, J., She, W., Aldridge, B., Gao, H., Deans, S., … Feng, X. (2021). Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abh0556","ieee":"J. Long et al., “Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis,” Science, vol. 373, no. 6550. American Association for the Advancement of Science, 2021.","ista":"Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. 2021. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science. 373(6550)."},"oa":1,"intvolume":" 373","keyword":["Multidisciplinary"],"department":[{"_id":"XiFe"}],"publication_status":"published"},{"article_type":"original","external_id":{"pmid":["32601198"]},"status":"public","date_published":"2020-05-22T00:00:00Z","date_created":"2023-01-16T09:15:44Z","article_processing_charge":"No","page":"16660-16666","abstract":[{"text":"Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states.","lang":"eng"}],"file":[{"relation":"main_file","date_created":"2023-02-07T11:29:55Z","checksum":"cedee184cb12f454f2fba4158ff47db9","file_name":"2020_PNAS_Bloomer.pdf","content_type":"application/pdf","access_level":"open_access","creator":"alisjak","success":1,"file_id":"12526","file_size":1105414,"date_updated":"2023-02-07T11:29:55Z"}],"author":[{"last_name":"Bloomer","full_name":"Bloomer, Rebecca H.","first_name":"Rebecca H."},{"last_name":"Hutchison","full_name":"Hutchison, Claire E.","first_name":"Claire E."},{"full_name":"Bäurle, Isabel","first_name":"Isabel","last_name":"Bäurle"},{"first_name":"James","full_name":"Walker, James","last_name":"Walker"},{"full_name":"Fang, Xiaofeng","first_name":"Xiaofeng","last_name":"Fang"},{"full_name":"Perera, Pumi","first_name":"Pumi","last_name":"Perera"},{"first_name":"Christos N.","full_name":"Velanis, Christos N.","last_name":"Velanis"},{"full_name":"Gümüs, Serin","first_name":"Serin","last_name":"Gümüs"},{"full_name":"Spanos, Christos","first_name":"Christos","last_name":"Spanos"},{"first_name":"Juri","full_name":"Rappsilber, Juri","last_name":"Rappsilber"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng"},{"last_name":"Goodrich","full_name":"Goodrich, Justin","first_name":"Justin"},{"last_name":"Dean","first_name":"Caroline","full_name":"Dean, Caroline"}],"issue":"28","quality_controlled":"1","file_date_updated":"2023-02-07T11:29:55Z","acknowledgement":"We would like to thank Scott Berry for help with ICU-GFP nuclear localization microscopy, Hao Yu and Lisha Shen for assistance with 6mA DNA methylation analysis, Donna Gibson for graphic design assistance, and members of the C.D. and Howard laboratories for helpful discussions. This work was funded by the European Research Council grants to “MEXTIM” (to C.D.) and “SexMeth” (to X. Feng), by the Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programmes GRO (BB/J004588/1), GEN (BB/P013511/1), BBSRC grant (to X. Feng) (BB/S009620/1), and the Marie Sklodowska–Curie Postdoctoral Fellowships “UNRAVEL” (to R.H.B.) and \"WISDOM\" (to X. Fang). Additional funding via the Wellcome Trust through a Senior Research Fellowship (to J.R.) (103139) and a multiuser equipment grant (108504). The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome Trust (203149).","publication":"Proceedings of the National Academy of Sciences","year":"2020","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"extern":"1","department":[{"_id":"XiFe"}],"publication_status":"published","intvolume":" 117","keyword":["Multidisciplinary"],"citation":{"mla":"Bloomer, Rebecca H., et al. “The Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences, vol. 117, no. 28, Proceedings of the National Academy of Sciences, 2020, pp. 16660–66, doi:10.1073/pnas.1920621117.","ista":"Bloomer RH, Hutchison CE, Bäurle I, Walker J, Fang X, Perera P, Velanis CN, Gümüs S, Spanos C, Rappsilber J, Feng X, Goodrich J, Dean C. 2020. The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 117(28), 16660–16666.","ieee":"R. H. Bloomer et al., “The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2,” Proceedings of the National Academy of Sciences, vol. 117, no. 28. Proceedings of the National Academy of Sciences, pp. 16660–16666, 2020.","apa":"Bloomer, R. H., Hutchison, C. E., Bäurle, I., Walker, J., Fang, X., Perera, P., … Dean, C. (2020). The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1920621117","chicago":"Bloomer, Rebecca H., Claire E. Hutchison, Isabel Bäurle, James Walker, Xiaofeng Fang, Pumi Perera, Christos N. Velanis, et al. “The Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1920621117.","ama":"Bloomer RH, Hutchison CE, Bäurle I, et al. The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 2020;117(28):16660-16666. doi:10.1073/pnas.1920621117","short":"R.H. Bloomer, C.E. Hutchison, I. Bäurle, J. Walker, X. Fang, P. Perera, C.N. Velanis, S. Gümüs, C. Spanos, J. Rappsilber, X. Feng, J. Goodrich, C. Dean, Proceedings of the National Academy of Sciences 117 (2020) 16660–16666."},"oa":1,"publisher":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.1920621117","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/"}],"oa_version":"Published Version","day":"22","scopus_import":"1","volume":117,"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","title":"The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2","ddc":["580"],"_id":"12188","date_updated":"2023-05-08T10:53:55Z","month":"05"},{"year":"2020","language":[{"iso":"eng"}],"publication":"PLOS Genetics","extern":"1","publication_identifier":{"issn":["1553-7404"]},"acknowledgement":"The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.","article_number":"e1008894","issue":"6","author":[{"last_name":"Christophorou","full_name":"Christophorou, Nicolas","first_name":"Nicolas"},{"full_name":"She, Wenjing","first_name":"Wenjing","last_name":"She"},{"first_name":"Jincheng","full_name":"Long, Jincheng","last_name":"Long"},{"first_name":"Aurélie","full_name":"Hurel, Aurélie","last_name":"Hurel"},{"first_name":"Sébastien","full_name":"Beaubiat, Sébastien","last_name":"Beaubiat"},{"full_name":"Idir, Yassir","first_name":"Yassir","last_name":"Idir"},{"last_name":"Tagliaro-Jahns","full_name":"Tagliaro-Jahns, Marina","first_name":"Marina"},{"first_name":"Aurélie","full_name":"Chambon, Aurélie","last_name":"Chambon"},{"last_name":"Solier","full_name":"Solier, Victor","first_name":"Victor"},{"full_name":"Vezon, Daniel","first_name":"Daniel","last_name":"Vezon"},{"last_name":"Grelon","first_name":"Mathilde","full_name":"Grelon, Mathilde"},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"},{"full_name":"Bouché, Nicolas","first_name":"Nicolas","last_name":"Bouché"},{"last_name":"Mézard","first_name":"Christine","full_name":"Mézard, Christine"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells."}],"status":"public","article_processing_charge":"No","date_created":"2023-01-16T09:16:10Z","date_published":"2020-06-29T00:00:00Z","external_id":{"pmid":["32598340"]},"article_type":"original","date_updated":"2023-05-08T10:54:39Z","_id":"12189","month":"06","title":"AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":16,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/"}],"day":"29","oa_version":"Published Version","doi":"10.1371/journal.pgen.1008894","oa":1,"citation":{"mla":"Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics, vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:10.1371/journal.pgen.1008894.","ista":"Christophorou N, She W, Long J, Hurel A, Beaubiat S, Idir Y, Tagliaro-Jahns M, Chambon A, Solier V, Vezon D, Grelon M, Feng X, Bouché N, Mézard C. 2020. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 16(6), e1008894.","ieee":"N. Christophorou et al., “AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization,” PLOS Genetics, vol. 16, no. 6. Public Library of Science (PLoS), 2020.","apa":"Christophorou, N., She, W., Long, J., Hurel, A., Beaubiat, S., Idir, Y., … Mézard, C. (2020). AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1008894","ama":"Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 2020;16(6). doi:10.1371/journal.pgen.1008894","short":"N. Christophorou, W. She, J. Long, A. Hurel, S. Beaubiat, Y. Idir, M. Tagliaro-Jahns, A. Chambon, V. Solier, D. Vezon, M. Grelon, X. Feng, N. Bouché, C. Mézard, PLOS Genetics 16 (2020).","chicago":"Christophorou, Nicolas, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics. Public Library of Science (PLoS), 2020. https://doi.org/10.1371/journal.pgen.1008894."},"publisher":"Public Library of Science (PLoS)","publication_status":"published","department":[{"_id":"XiFe"}],"keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"intvolume":" 16"},{"date_updated":"2025-01-14T14:31:02Z","_id":"12190","month":"08","title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"type":"journal_article","scopus_import":"1","volume":29,"oa_version":"None","day":"19","doi":"10.1016/j.cub.2019.06.084","citation":{"short":"E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3.","ama":"Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084","chicago":"Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.06.084.","mla":"Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.","apa":"Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.06.084","ista":"Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.","ieee":"E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier, p. 2676–2686.e3, 2019."},"publisher":"Elsevier","publication_status":"published","department":[{"_id":"XiFe"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"intvolume":" 29","publication":"Current Biology","year":"2019","language":[{"iso":"eng"}],"extern":"1","publication_identifier":{"issn":["0960-9822"]},"acknowledgement":"We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.).","author":[{"first_name":"Emma J.","full_name":"Lawrence, Emma J.","last_name":"Lawrence"},{"last_name":"Gao","full_name":"Gao, Hongbo","first_name":"Hongbo"},{"full_name":"Tock, Andrew J.","first_name":"Andrew J.","last_name":"Tock"},{"last_name":"Lambing","first_name":"Christophe","full_name":"Lambing, Christophe"},{"first_name":"Alexander R.","full_name":"Blackwell, Alexander R.","last_name":"Blackwell"},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"},{"last_name":"Henderson","first_name":"Ian R.","full_name":"Henderson, Ian R."}],"issue":"16","quality_controlled":"1","abstract":[{"lang":"eng","text":"Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor."}],"page":"2676-2686.e3","status":"public","article_processing_charge":"No","date_published":"2019-08-19T00:00:00Z","date_created":"2023-01-16T09:16:33Z","external_id":{"pmid":["31378616"]},"article_type":"original"},{"has_accepted_license":"1","scopus_import":"1","volume":8,"oa_version":"Published Version","day":"28","doi":"10.7554/elife.42530","oa":1,"citation":{"chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.42530.","short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).","ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530","mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, 2019, doi:10.7554/elife.42530.","ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, 2019.","ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","apa":"He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.42530"},"publisher":"eLife Sciences Publications","publication_status":"published","department":[{"_id":"XiFe"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"intvolume":" 8","date_updated":"2025-01-14T14:31:41Z","_id":"12192","month":"05","ddc":["580"],"title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","abstract":[{"lang":"eng","text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation."}],"file":[{"date_updated":"2023-02-07T09:42:46Z","file_size":2493837,"file_id":"12525","success":1,"creator":"alisjak","access_level":"open_access","content_type":"application/pdf","file_name":"2019_elife_He.pdf","checksum":"ea6b89c20d59e5eb3646916fe5d568ad","date_created":"2023-02-07T09:42:46Z","relation":"main_file"}],"status":"public","article_processing_charge":"No","date_created":"2023-01-16T09:17:21Z","date_published":"2019-05-28T00:00:00Z","external_id":{"unknown":["31135340"]},"article_type":"original","language":[{"iso":"eng"}],"publication":"eLife","year":"2019","extern":"1","publication_identifier":{"issn":["2050-084X"]},"acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","file_date_updated":"2023-02-07T09:42:46Z","article_number":"42530","author":[{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"last_name":"Vickers","first_name":"Martin","full_name":"Vickers, Martin"},{"last_name":"Zhang","full_name":"Zhang, Jingyi","first_name":"Jingyi"},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"}],"quality_controlled":"1"},{"language":[{"iso":"eng"}],"publication":"Nature Genetics","year":"2017","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"extern":"1","acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","issue":"1","author":[{"last_name":"Walker","first_name":"James","full_name":"Walker, James"},{"last_name":"Gao","full_name":"Gao, Hongbo","first_name":"Hongbo"},{"first_name":"Jingyi","full_name":"Zhang, Jingyi","last_name":"Zhang"},{"last_name":"Aldridge","full_name":"Aldridge, Billy","first_name":"Billy"},{"last_name":"Vickers","first_name":"Martin","full_name":"Vickers, Martin"},{"last_name":"Higgins","full_name":"Higgins, James D.","first_name":"James D."},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"}],"quality_controlled":"1","page":"130-137","OA_type":"green","abstract":[{"lang":"eng","text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants."}],"status":"public","OA_place":"repository","date_published":"2017-12-18T00:00:00Z","date_created":"2023-01-16T09:18:05Z","article_processing_charge":"No","article_type":"original","external_id":{"pmid":["29255257"]},"_id":"12193","date_updated":"2026-03-19T10:51:18Z","month":"12","title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"type":"journal_article","scopus_import":"1","volume":50,"doi":"10.1038/s41588-017-0008-5","day":"18","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/","open_access":"1"}],"oa_version":"Submitted Version","citation":{"short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 2017;50(1):130-137. doi:10.1038/s41588-017-0008-5","chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” Nature Genetics. Nature Research, 2017. https://doi.org/10.1038/s41588-017-0008-5.","ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137.","ieee":"J. Walker et al., “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” Nature Genetics, vol. 50, no. 1. Nature Research, pp. 130–137, 2017.","apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., & Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. Nature Research. https://doi.org/10.1038/s41588-017-0008-5","mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” Nature Genetics, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:10.1038/s41588-017-0008-5."},"oa":1,"publisher":"Nature Research","department":[{"_id":"XiFe"}],"publication_status":"published","intvolume":" 50","keyword":["Genetics"]},{"abstract":[{"text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations.","lang":"eng"}],"page":"15132-15137","article_processing_charge":"No","date_created":"2021-06-07T06:21:39Z","date_published":"2016-12-27T00:00:00Z","status":"public","external_id":{"pmid":["27956643"]},"article_type":"original","extern":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"year":"2016","publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","author":[{"full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung","last_name":"Hsieh"},{"last_name":"He","first_name":"Shengbo","full_name":"He, Shengbo"},{"last_name":"Buttress","full_name":"Buttress, Toby","first_name":"Toby"},{"last_name":"Gao","full_name":"Gao, Hongbo","first_name":"Hongbo"},{"last_name":"Couchman","first_name":"Matthew","full_name":"Couchman, Matthew"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"}],"issue":"52","scopus_import":"1","volume":113,"oa_version":"Published Version","day":"27","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619074114"}],"doi":"10.1073/pnas.1619074114","publisher":"National Academy of Sciences","oa":1,"citation":{"short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619074114.","ieee":"P.-H. Hsieh et al., “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” Proceedings of the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016.","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619074114","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:10.1073/pnas.1619074114."},"intvolume":" 113","publication_status":"published","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"month":"12","date_updated":"2023-05-08T11:00:40Z","_id":"9473","title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","type":"journal_article","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_type":"original","external_id":{"pmid":["27956642"]},"status":"public","date_created":"2021-06-07T07:10:59Z","date_published":"2016-12-27T00:00:00Z","article_processing_charge":"No","page":"15138-15143","abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"issue":"52","author":[{"full_name":"Park, Kyunghyuk","first_name":"Kyunghyuk","last_name":"Park"},{"last_name":"Kim","full_name":"Kim, M. Yvonne","first_name":"M. Yvonne"},{"last_name":"Vickers","first_name":"Martin","full_name":"Vickers, Martin"},{"last_name":"Park","full_name":"Park, Jin-Sup","first_name":"Jin-Sup"},{"last_name":"Hyun","full_name":"Hyun, Youbong","first_name":"Youbong"},{"first_name":"Takashi","full_name":"Okamoto, Takashi","last_name":"Okamoto"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"},{"last_name":"Choi","first_name":"Yeonhee","full_name":"Choi, Yeonhee"},{"last_name":"Scholten","first_name":"Stefan","full_name":"Scholten, Stefan"}],"quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","year":"2016","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"extern":"1","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publication_status":"published","intvolume":" 113","keyword":["Multidisciplinary"],"citation":{"chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.","short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.","ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 2016;113(52):15138-15143. doi:10.1073/pnas.1619047114","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619047114","ieee":"K. Park et al., “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” Proceedings of the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016."},"oa":1,"publisher":"National Academy of Sciences","doi":"10.1073/pnas.1619047114","day":"27","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619047114"}],"oa_version":"Published Version","volume":113,"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"type":"journal_article","title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","_id":"9477","date_updated":"2023-05-08T11:00:07Z","month":"12"},{"abstract":[{"lang":"eng","text":"SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity."}],"page":"1616-1623","status":"public","article_processing_charge":"No","date_published":"2015-08-01T00:00:00Z","date_created":"2023-01-16T09:20:22Z","external_id":{"pmid":["26063389"]},"article_type":"original","publication":"Plant and Cell Physiology","year":"2015","language":[{"iso":"eng"}],"extern":"1","publication_identifier":{"issn":["0032-0781","1471-9053"]},"acknowledgement":"This work was supported by the National Sciences and Engineering Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles Copeland for critical reading of the manuscript.","author":[{"last_name":"Johnson","first_name":"Kaeli C.M.","full_name":"Johnson, Kaeli C.M."},{"last_name":"Xia","first_name":"Shitou","full_name":"Xia, Shitou"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"},{"full_name":"Li, Xin","first_name":"Xin","last_name":"Li"}],"issue":"8","quality_controlled":"1","scopus_import":"1","volume":56,"oa_version":"None","doi":"10.1093/pcp/pcv087","citation":{"mla":"Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology, vol. 56, no. 8, Oxford University Press, 2015, pp. 1616–23, doi:10.1093/pcp/pcv087.","apa":"Johnson, K. C. M., Xia, S., Feng, X., & Li, X. (2015). The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcv087","ista":"Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.","ieee":"K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity,” Plant and Cell Physiology, vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.","chicago":"Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology. Oxford University Press, 2015. https://doi.org/10.1093/pcp/pcv087.","ama":"Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 2015;56(8):1616-1623. doi:10.1093/pcp/pcv087","short":"K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015) 1616–1623."},"publisher":"Oxford University Press","publication_status":"published","department":[{"_id":"XiFe"}],"keyword":["Cell Biology","Plant Science","Physiology","General Medicine"],"intvolume":" 56","date_updated":"2023-05-08T11:03:23Z","_id":"12196","month":"08","title":"The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article"}]