[{"type":"journal_article","date_updated":"2023-05-08T10:52:49Z","_id":"12668","publisher":"Springer Nature","doi":"10.1186/s13059-022-02844-2","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"external_id":{"pmid":["36639687"]},"year":"2023","date_published":"2023-01-13T00:00:00Z","pmid":1,"publication":"Genome Biology","status":"public","extern":"1","article_type":"original","date_created":"2023-02-23T09:13:49Z","volume":24,"title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","oa_version":"Published Version","author":[{"last_name":"Zhao","full_name":"Zhao, Long","first_name":"Long"},{"last_name":"Yang","full_name":"Yang, Yiman","first_name":"Yiman"},{"first_name":"Jinchao","last_name":"Chen","full_name":"Chen, Jinchao"},{"first_name":"Xuelei","last_name":"Lin","full_name":"Lin, Xuelei"},{"full_name":"Zhang, Hao","last_name":"Zhang","first_name":"Hao"},{"first_name":"Hao","last_name":"Wang","full_name":"Wang, Hao"},{"first_name":"Hongzhe","full_name":"Wang, Hongzhe","last_name":"Wang"},{"first_name":"Xiaomin","full_name":"Bie, Xiaomin","last_name":"Bie"},{"full_name":"Jiang, Jiafu","last_name":"Jiang","first_name":"Jiafu"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"first_name":"Xiangdong","full_name":"Fu, Xiangdong","last_name":"Fu"},{"first_name":"Xiansheng","last_name":"Zhang","full_name":"Zhang, Xiansheng"},{"last_name":"Du","full_name":"Du, Zhuo","first_name":"Zhuo"},{"last_name":"Xiao","full_name":"Xiao, Jun","first_name":"Jun"}],"scopus_import":"1","day":"13","publication_identifier":{"issn":["1474-760X"]},"publication_status":"published","abstract":[{"lang":"eng","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."}],"intvolume":" 24","article_number":"7","department":[{"_id":"XiFe"}],"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","ieee":"L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.","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).","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.","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.","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","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."},"language":[{"iso":"eng"}],"oa":1},{"department":[{"_id":"XiFe"}],"article_number":"koac346","month":"06","issue":"6","citation":{"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","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.","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.","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.","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.","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":35,"article_type":"original","date_created":"2023-02-23T09:14:59Z","author":[{"first_name":"Pablo A","last_name":"Manavella","full_name":"Manavella, Pablo A"},{"last_name":"Godoy Herz","full_name":"Godoy Herz, Micaela A","first_name":"Micaela A"},{"full_name":"Kornblihtt, Alberto R","last_name":"Kornblihtt","first_name":"Alberto R"},{"first_name":"Reed","full_name":"Sorenson, Reed","last_name":"Sorenson"},{"last_name":"Sieburth","full_name":"Sieburth, Leslie E","first_name":"Leslie E"},{"first_name":"Kentaro","full_name":"Nakaminami, Kentaro","last_name":"Nakaminami"},{"full_name":"Seki, Motoaki","last_name":"Seki","first_name":"Motoaki"},{"last_name":"Ding","full_name":"Ding, Yiliang","first_name":"Yiliang"},{"first_name":"Qianwen","full_name":"Sun, Qianwen","last_name":"Sun"},{"first_name":"Hunseung","last_name":"Kang","full_name":"Kang, Hunseung"},{"full_name":"Ariel, Federico D","last_name":"Ariel","first_name":"Federico D"},{"full_name":"Crespi, Martin","last_name":"Crespi","first_name":"Martin"},{"first_name":"Axel J","full_name":"Giudicatti, Axel J","last_name":"Giudicatti"},{"first_name":"Qiang","full_name":"Cai, Qiang","last_name":"Cai"},{"last_name":"Jin","full_name":"Jin, Hailing","first_name":"Hailing"},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"},{"full_name":"Qi, Yijun","last_name":"Qi","first_name":"Yijun"},{"first_name":"Craig S","full_name":"Pikaard, Craig S","last_name":"Pikaard"}],"scopus_import":"1","day":"01","oa_version":"Published Version","title":"Beyond transcription: compelling open questions in plant RNA biology","publication_status":"published","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"abstract":[{"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.","lang":"eng"}],"intvolume":" 35","keyword":["Cell Biology","Plant Science"],"year":"2023","external_id":{"pmid":["36477566"]},"pmid":1,"date_published":"2023-06-01T00:00:00Z","status":"public","publication":"The Plant Cell","extern":"1","date_updated":"2023-10-04T09:48:43Z","_id":"12669","type":"journal_article","doi":"10.1093/plcell/koac346","article_processing_charge":"No","publisher":"Oxford University Press","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/plcell/koac346"}],"quality_controlled":"1"},{"month":"03","article_number":"112132","file":[{"date_updated":"2023-05-11T10:41:42Z","creator":"kschuh","date_created":"2023-05-11T10:41:42Z","file_size":8401261,"file_id":"12941","content_type":"application/pdf","access_level":"open_access","file_name":"2023_CellReports_Lyons.pdf","success":1,"checksum":"6cbc44fdb18bf18834c9e2a5b9c67123","relation":"main_file"}],"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"3","citation":{"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","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).","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.","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.","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.","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.","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"},"title":"Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons","oa_version":"Published Version","author":[{"full_name":"Lyons, David B.","last_name":"Lyons","first_name":"David B."},{"first_name":"Amy","last_name":"Briffa","full_name":"Briffa, Amy"},{"first_name":"Shengbo","full_name":"He, Shengbo","last_name":"He"},{"first_name":"Jaemyung","last_name":"Choi","full_name":"Choi, Jaemyung"},{"first_name":"Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","full_name":"Hollwey, Elizabeth","last_name":"Hollwey"},{"last_name":"Colicchio","full_name":"Colicchio, Jack","first_name":"Jack"},{"full_name":"Anderson, Ian","last_name":"Anderson","first_name":"Ian"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"first_name":"Martin","full_name":"Howard, Martin","last_name":"Howard"},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"day":"28","scopus_import":"1","article_type":"original","date_created":"2023-02-23T09:17:44Z","volume":42,"abstract":[{"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.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 42","has_accepted_license":"1","publication_identifier":{"eissn":["2211-1247"]},"publication_status":"published","file_date_updated":"2023-05-11T10:41:42Z","external_id":{"isi":["000944921600001"]},"year":"2023","isi":1,"project":[{"call_identifier":"H2020","name":"Quantitative analysis of DNA methylation maintenance with chromatin","grant_number":"725746","_id":"62935a00-2b32-11ec-9570-eff30fa39068"}],"publication":"Cell Reports","status":"public","date_published":"2023-03-28T00:00:00Z","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.","ec_funded":1,"publisher":"Elsevier","doi":"10.1016/j.celrep.2023.112132","article_processing_charge":"Yes","type":"journal_article","date_updated":"2023-11-02T12:23:45Z","_id":"12672","ddc":["580"],"quality_controlled":"1"},{"page":"2240-2251","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.13422"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1111/jipb.13422","publisher":"Wiley","_id":"12670","date_updated":"2023-05-08T10:59:00Z","type":"journal_article","status":"public","extern":"1","publication":"Journal of Integrative Plant Biology","pmid":1,"date_published":"2022-12-07T00:00:00Z","year":"2022","external_id":{"pmid":["36478632"]},"keyword":["Plant Science","General Biochemistry","Genetics and Molecular Biology","Biochemistry"],"intvolume":" 64","abstract":[{"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.","lang":"eng"}],"publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"publication_status":"published","day":"07","scopus_import":"1","author":[{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"}],"oa_version":"Published Version","title":"DNA methylation dynamics during germline development","volume":64,"date_created":"2023-02-23T09:15:57Z","article_type":"review","oa":1,"language":[{"iso":"eng"}],"citation":{"ista":"He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 64(12), 2240–2251.","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.","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.","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","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","short":"S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.","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."},"issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","department":[{"_id":"XiFe"}]},{"date_updated":"2023-05-08T10:59:22Z","_id":"12671","type":"journal_article","doi":"10.1038/s41586-022-05386-6","article_processing_charge":"No","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41586-022-05386-6"}],"quality_controlled":"1","page":"614-622","year":"2022","external_id":{"pmid":["36323776"]},"pmid":1,"date_published":"2022-11-17T00:00:00Z","publication":"Nature","extern":"1","status":"public","volume":611,"article_type":"original","date_created":"2023-02-23T09:17:05Z","author":[{"full_name":"Buttress, Toby","last_name":"Buttress","first_name":"Toby"},{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"last_name":"Wang","full_name":"Wang, Liang","first_name":"Liang"},{"last_name":"Zhou","full_name":"Zhou, Shaoli","first_name":"Shaoli"},{"last_name":"Saalbach","full_name":"Saalbach, Gerhard","first_name":"Gerhard"},{"last_name":"Vickers","full_name":"Vickers, Martin","first_name":"Martin"},{"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","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"}],"day":"17","scopus_import":"1","oa_version":"Published Version","title":"Histone H2B.8 compacts flowering plant sperm through chromatin phase separation","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication_status":"published","intvolume":" 611","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"XiFe"}],"month":"11","issue":"7936","citation":{"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","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.","short":"T. Buttress, S. He, L. Wang, S. Zhou, G. Saalbach, M. Vickers, G. Li, P. Li, X. Feng, Nature 611 (2022) 614–622.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}]},{"status":"public","publication":"Journal of Experimental Botany","extern":"1","date_published":"2021-08-13T00:00:00Z","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). ","pmid":1,"external_id":{"pmid":["34387350"]},"year":"2021","keyword":["Plant Science","Physiology"],"page":"7927-7941","quality_controlled":"1","publisher":"Oxford University Press","doi":"10.1093/jxb/erab373","article_processing_charge":"No","type":"journal_article","date_updated":"2023-05-08T11:01:18Z","_id":"12186","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"22","citation":{"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","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.","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.","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.","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.","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"},"month":"08","department":[{"_id":"XiFe"}],"abstract":[{"lang":"eng","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."}],"intvolume":" 72","publication_status":"published","publication_identifier":{"issn":["0022-0957","1460-2431"]},"title":"Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors","oa_version":"None","author":[{"first_name":"Pingtao","last_name":"Ding","full_name":"Ding, Pingtao"},{"first_name":"Toshiyuki","last_name":"Sakai","full_name":"Sakai, Toshiyuki"},{"last_name":"Krishna Shrestha","full_name":"Krishna Shrestha, Ram","first_name":"Ram"},{"first_name":"Nicolas","last_name":"Manosalva Perez","full_name":"Manosalva Perez, Nicolas"},{"full_name":"Guo, Wenbin","last_name":"Guo","first_name":"Wenbin"},{"first_name":"Bruno Pok Man","full_name":"Ngou, Bruno Pok Man","last_name":"Ngou"},{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"first_name":"Chang","full_name":"Liu, Chang","last_name":"Liu"},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"},{"full_name":"Zhang, Runxuan","last_name":"Zhang","first_name":"Runxuan"},{"first_name":"Klaas","full_name":"Vandepoele, Klaas","last_name":"Vandepoele"},{"full_name":"MacLean, Dan","last_name":"MacLean","first_name":"Dan"},{"last_name":"Jones","full_name":"Jones, Jonathan D G","first_name":"Jonathan D G"}],"day":"13","scopus_import":"1","article_type":"original","date_created":"2023-01-16T09:14:35Z","volume":72},{"language":[{"iso":"eng"}],"issue":"6550","citation":{"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","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 (AAAS), 2021.","short":"J. Long, J. Walker, W. She, B. Aldridge, H. Gao, S. Deans, M. Vickers, X. Feng, Science 373 (2021).","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 (AAAS), 2021. https://doi.org/10.1126/science.abh0556.","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).","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 (AAAS). https://doi.org/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 (AAAS), 2021, doi:10.1126/science.abh0556."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","department":[{"_id":"XiFe"}],"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."}],"intvolume":" 373","publication_status":"published","publication_identifier":{"issn":["0036-8075","1095-9203"]},"author":[{"full_name":"Long, Jincheng","last_name":"Long","first_name":"Jincheng"},{"first_name":"James","full_name":"Walker, James","last_name":"Walker"},{"first_name":"Wenjing","last_name":"She","full_name":"She, Wenjing"},{"first_name":"Billy","last_name":"Aldridge","full_name":"Aldridge, Billy"},{"first_name":"Hongbo","last_name":"Gao","full_name":"Gao, Hongbo"},{"last_name":"Deans","full_name":"Deans, Samuel","first_name":"Samuel"},{"full_name":"Vickers, Martin","last_name":"Vickers","first_name":"Martin"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"}],"scopus_import":"1","day":"02","title":"Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis","oa_version":"None","volume":373,"article_type":"original","date_created":"2023-01-16T09:15:14Z","extern":"1","publication":"Science","status":"public","pmid":1,"date_published":"2021-07-02T00:00:00Z","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.","year":"2021","external_id":{"pmid":["34210850"]},"keyword":["Multidisciplinary"],"quality_controlled":"1","doi":"10.1126/science.abh0556","article_processing_charge":"No","publisher":"American Association for the Advancement of Science (AAAS)","date_updated":"2023-05-08T10:56:39Z","_id":"12187","type":"journal_article"},{"ddc":["580"],"page":"16660-16666","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/"}],"publisher":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","doi":"10.1073/pnas.1920621117","type":"journal_article","_id":"12188","date_updated":"2023-05-08T10:53:55Z","status":"public","extern":"1","publication":"Proceedings of the National Academy of Sciences","date_published":"2020-05-22T00:00:00Z","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).","pmid":1,"external_id":{"pmid":["32601198"]},"year":"2020","keyword":["Multidisciplinary"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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"}],"intvolume":" 117","has_accepted_license":"1","file_date_updated":"2023-02-07T11:29:55Z","publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"oa_version":"Published Version","title":"The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2","day":"22","scopus_import":"1","author":[{"first_name":"Rebecca H.","last_name":"Bloomer","full_name":"Bloomer, Rebecca H."},{"full_name":"Hutchison, Claire E.","last_name":"Hutchison","first_name":"Claire E."},{"last_name":"Bäurle","full_name":"Bäurle, Isabel","first_name":"Isabel"},{"first_name":"James","full_name":"Walker, James","last_name":"Walker"},{"last_name":"Fang","full_name":"Fang, Xiaofeng","first_name":"Xiaofeng"},{"full_name":"Perera, Pumi","last_name":"Perera","first_name":"Pumi"},{"first_name":"Christos N.","full_name":"Velanis, Christos N.","last_name":"Velanis"},{"full_name":"Gümüs, Serin","last_name":"Gümüs","first_name":"Serin"},{"first_name":"Christos","full_name":"Spanos, Christos","last_name":"Spanos"},{"full_name":"Rappsilber, Juri","last_name":"Rappsilber","first_name":"Juri"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"},{"last_name":"Goodrich","full_name":"Goodrich, Justin","first_name":"Justin"},{"first_name":"Caroline","last_name":"Dean","full_name":"Dean, Caroline"}],"date_created":"2023-01-16T09:15:44Z","article_type":"original","volume":117,"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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.","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."},"issue":"28","month":"05","file":[{"date_updated":"2023-02-07T11:29:55Z","creator":"alisjak","date_created":"2023-02-07T11:29:55Z","file_size":1105414,"file_id":"12526","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2020_PNAS_Bloomer.pdf","checksum":"cedee184cb12f454f2fba4158ff47db9","relation":"main_file"}],"department":[{"_id":"XiFe"}]},{"month":"06","department":[{"_id":"XiFe"}],"article_number":"e1008894","oa":1,"language":[{"iso":"eng"}],"issue":"6","citation":{"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","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.","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.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Nicolas","last_name":"Christophorou","full_name":"Christophorou, Nicolas"},{"full_name":"She, Wenjing","last_name":"She","first_name":"Wenjing"},{"first_name":"Jincheng","full_name":"Long, Jincheng","last_name":"Long"},{"last_name":"Hurel","full_name":"Hurel, Aurélie","first_name":"Aurélie"},{"first_name":"Sébastien","last_name":"Beaubiat","full_name":"Beaubiat, Sébastien"},{"first_name":"Yassir","full_name":"Idir, Yassir","last_name":"Idir"},{"first_name":"Marina","last_name":"Tagliaro-Jahns","full_name":"Tagliaro-Jahns, Marina"},{"last_name":"Chambon","full_name":"Chambon, Aurélie","first_name":"Aurélie"},{"full_name":"Solier, Victor","last_name":"Solier","first_name":"Victor"},{"full_name":"Vezon, Daniel","last_name":"Vezon","first_name":"Daniel"},{"last_name":"Grelon","full_name":"Grelon, Mathilde","first_name":"Mathilde"},{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"last_name":"Bouché","full_name":"Bouché, Nicolas","first_name":"Nicolas"},{"full_name":"Mézard, Christine","last_name":"Mézard","first_name":"Christine"}],"scopus_import":"1","day":"29","title":"AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization","oa_version":"Published Version","volume":16,"article_type":"original","date_created":"2023-01-16T09:16:10Z","intvolume":" 16","abstract":[{"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.","lang":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1553-7404"]},"year":"2020","external_id":{"pmid":["32598340"]},"keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"publication":"PLOS Genetics","status":"public","extern":"1","pmid":1,"date_published":"2020-06-29T00:00:00Z","acknowledgement":"The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.","doi":"10.1371/journal.pgen.1008894","article_processing_charge":"No","publisher":"Public Library of Science (PLoS)","date_updated":"2023-05-08T10:54:39Z","_id":"12189","type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/","open_access":"1"}],"quality_controlled":"1"},{"page":"2676-2686.e3","quality_controlled":"1","publisher":"Elsevier BV","doi":"10.1016/j.cub.2019.06.084","article_processing_charge":"No","type":"journal_article","date_updated":"2023-05-08T10:54:54Z","_id":"12190","publication":"Current Biology","extern":"1","status":"public","date_published":"2019-08-19T00:00:00Z","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.).","pmid":1,"external_id":{"pmid":["31378616"]},"year":"2019","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"abstract":[{"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.","lang":"eng"}],"intvolume":" 29","publication_identifier":{"issn":["0960-9822"]},"publication_status":"published","title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","oa_version":"None","author":[{"first_name":"Emma J.","full_name":"Lawrence, Emma J.","last_name":"Lawrence"},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"last_name":"Tock","full_name":"Tock, Andrew J.","first_name":"Andrew J."},{"last_name":"Lambing","full_name":"Lambing, Christophe","first_name":"Christophe"},{"first_name":"Alexander R.","full_name":"Blackwell, Alexander R.","last_name":"Blackwell"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"first_name":"Ian R.","last_name":"Henderson","full_name":"Henderson, Ian R."}],"scopus_import":"1","day":"19","article_type":"original","date_created":"2023-01-16T09:16:33Z","volume":29,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"16","citation":{"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 BV, 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 BV. https://doi.org/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 BV, 2019. 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.","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.","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 BV, p. 2676–2686.e3, 2019.","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"},"month":"08","department":[{"_id":"XiFe"}]},{"file":[{"file_id":"12525","date_updated":"2023-02-07T09:42:46Z","creator":"alisjak","file_size":2493837,"date_created":"2023-02-07T09:42:46Z","checksum":"ea6b89c20d59e5eb3646916fe5d568ad","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2019_elife_He.pdf"}],"article_number":"42530","department":[{"_id":"XiFe"}],"month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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, Ltd, 2019.","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","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, Ltd. https://doi.org/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, Ltd, 2019, doi:10.7554/elife.42530.","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, Ltd, 2019. https://doi.org/10.7554/elife.42530.","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."},"language":[{"iso":"eng"}],"oa":1,"article_type":"original","date_created":"2023-01-16T09:17:21Z","volume":8,"oa_version":"Published Version","title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","author":[{"first_name":"Shengbo","last_name":"He","full_name":"He, Shengbo"},{"full_name":"Vickers, Martin","last_name":"Vickers","first_name":"Martin"},{"first_name":"Jingyi","last_name":"Zhang","full_name":"Zhang, Jingyi"},{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng"}],"scopus_import":"1","day":"28","publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","file_date_updated":"2023-02-07T09:42:46Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 8","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."}],"has_accepted_license":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"external_id":{"unknown":["31135340"]},"year":"2019","date_published":"2019-05-28T00:00:00Z","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).","publication":"eLife","status":"public","extern":"1","type":"journal_article","date_updated":"2023-05-08T10:54:12Z","_id":"12192","publisher":"eLife Sciences Publications, Ltd","doi":"10.7554/elife.42530","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/"}],"ddc":["580"]},{"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","citation":{"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.","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","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.","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.","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."},"month":"12","department":[{"_id":"XiFe"}],"intvolume":" 50","abstract":[{"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.","lang":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","oa_version":"None","author":[{"full_name":"Walker, James","last_name":"Walker","first_name":"James"},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"first_name":"Jingyi","full_name":"Zhang, Jingyi","last_name":"Zhang"},{"full_name":"Aldridge, Billy","last_name":"Aldridge","first_name":"Billy"},{"full_name":"Vickers, Martin","last_name":"Vickers","first_name":"Martin"},{"first_name":"James D.","full_name":"Higgins, James D.","last_name":"Higgins"},{"orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi"}],"scopus_import":"1","day":"18","article_type":"original","date_created":"2023-01-16T09:18:05Z","volume":50,"publication":"Nature Genetics","status":"public","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.","date_published":"2017-12-18T00:00:00Z","pmid":1,"external_id":{"pmid":["29255257"]},"year":"2017","keyword":["Genetics"],"page":"130-137","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/"}],"publisher":"Nature Research","doi":"10.1038/s41588-017-0008-5","article_processing_charge":"No","type":"journal_article","date_updated":"2023-10-18T07:21:53Z","_id":"12193"},{"type":"journal_article","date_updated":"2023-05-08T11:00:40Z","_id":"9473","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1619074114","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619074114"}],"page":"15132-15137","external_id":{"pmid":["27956643"]},"year":"2016","date_published":"2016-12-27T00:00:00Z","pmid":1,"publication":"Proceedings of the National Academy of Sciences","status":"public","extern":"1","article_type":"original","date_created":"2021-06-07T06:21:39Z","volume":113,"oa_version":"Published Version","title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","author":[{"first_name":"Ping-Hung","full_name":"Hsieh, Ping-Hung","last_name":"Hsieh"},{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"first_name":"Toby","last_name":"Buttress","full_name":"Buttress, Toby"},{"last_name":"Gao","full_name":"Gao, Hongbo","first_name":"Hongbo"},{"first_name":"Matthew","last_name":"Couchman","full_name":"Couchman, Matthew"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"}],"day":"27","scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","abstract":[{"lang":"eng","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."}],"intvolume":" 113","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"52","citation":{"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","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.","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.","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.","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.","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"},"language":[{"iso":"eng"}],"oa":1},{"type":"journal_article","date_updated":"2023-05-08T11:00:07Z","_id":"9477","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1619047114","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619047114","open_access":"1"}],"page":"15138-15143","keyword":["Multidisciplinary"],"external_id":{"pmid":["27956642"]},"year":"2016","date_published":"2016-12-27T00:00:00Z","pmid":1,"publication":"Proceedings of the National Academy of Sciences","status":"public","extern":"1","article_type":"original","date_created":"2021-06-07T07:10:59Z","volume":113,"oa_version":"Published Version","title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","author":[{"first_name":"Kyunghyuk","full_name":"Park, Kyunghyuk","last_name":"Park"},{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"first_name":"Martin","full_name":"Vickers, Martin","last_name":"Vickers"},{"first_name":"Jin-Sup","last_name":"Park","full_name":"Park, Jin-Sup"},{"full_name":"Hyun, Youbong","last_name":"Hyun","first_name":"Youbong"},{"first_name":"Takashi","last_name":"Okamoto","full_name":"Okamoto, Takashi"},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."},{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"},{"first_name":"Yeonhee","full_name":"Choi, Yeonhee","last_name":"Choi"},{"last_name":"Scholten","full_name":"Scholten, Stefan","first_name":"Stefan"}],"scopus_import":"1","day":"27","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"intvolume":" 113","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."}],"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"52","citation":{"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.","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.","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","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.","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","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.","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."},"language":[{"iso":"eng"}],"oa":1},{"abstract":[{"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.","lang":"eng"}],"intvolume":" 56","publication_status":"published","publication_identifier":{"issn":["0032-0781","1471-9053"]},"scopus_import":"1","author":[{"last_name":"Johnson","full_name":"Johnson, Kaeli C.M.","first_name":"Kaeli C.M."},{"last_name":"Xia","full_name":"Xia, Shitou","first_name":"Shitou"},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"last_name":"Li","full_name":"Li, Xin","first_name":"Xin"}],"oa_version":"None","title":"The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity","volume":56,"date_created":"2023-01-16T09:20:22Z","article_type":"original","language":[{"iso":"eng"}],"citation":{"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.","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.","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","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.","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."},"issue":"8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","department":[{"_id":"XiFe"}],"page":"1616-1623","quality_controlled":"1","article_processing_charge":"No","doi":"10.1093/pcp/pcv087","publisher":"Oxford University Press","_id":"12196","date_updated":"2023-05-08T11:03:23Z","type":"journal_article","publication":"Plant and Cell Physiology","status":"public","extern":"1","pmid":1,"date_published":"2015-08-01T00:00:00Z","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.","year":"2015","external_id":{"pmid":["26063389"]},"keyword":["Cell Biology","Plant Science","Physiology","General Medicine"]},{"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.","ama":"Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014","apa":"Feng, X., Zilberman, D., & Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2013.01.014","mla":"Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell, vol. 24, no. 3, Elsevier, 2013, pp. 215–25, doi:10.1016/j.devcel.2013.01.014.","chicago":"Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier, 2013. https://doi.org/10.1016/j.devcel.2013.01.014.","ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225."},"issue":"3","language":[{"iso":"eng"}],"oa":1,"date_created":"2021-06-08T06:14:50Z","article_type":"review","volume":24,"title":"A conversation across generations: Soma-germ cell crosstalk in plants","oa_version":"Published Version","day":"11","scopus_import":"1","author":[{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng"},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"first_name":"Hugh","full_name":"Dickinson, Hugh","last_name":"Dickinson"}],"publication_status":"published","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"abstract":[{"lang":"eng","text":"Plants undergo alternation of generation in which reproductive cells develop in the plant body (\"sporophytic generation\") and then differentiate into a multicellular gamete-forming \"gametophytic generation.\" Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes."}],"intvolume":" 24","external_id":{"pmid":["23410937"]},"year":"2013","date_published":"2013-02-11T00:00:00Z","pmid":1,"status":"public","publication":"Developmental Cell","extern":"1","type":"journal_article","_id":"9520","date_updated":"2023-05-08T11:00:59Z","publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.devcel.2013.01.014","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2013.01.014","open_access":"1"}],"page":"215-225"},{"publication":"Science","status":"public","pmid":1,"acknowledgement":"We thank S. Harmer for assistance with the analysis of histone modifications, the BioOptics team at the Vienna Biocenter Campus for sorting sperm and vegetative cell nuclei, K. Slotkin for the LAT52p-amiRNA=GFP plasmid, and G. Drews for the DD45p-GFP transgenic line. This work was partially funded by an NIH grant (GM69415) to R.L.F., NSF grants (MCB-0918821 and IOS-1025890) to R.L.F. and D.Z., a Young Investigator Grant from the Arnold and Mabel Beckman Foundation to D.Z., an Austrian Science Fund (FWF) grant P21389-B03 to H.T., a Ruth L. Kirschstein NIH Predoctoral Fellowship (GM093633) to C.A.I., a Fulbright Scholarship to J.A.R., a fellowship from the Jane Coffin Childs Memorial Fund to A.Z., and a Robert and Colleen Haas Scholarship to D.R. Sequencing data are deposited in GEO (GSE38935).","date_published":"2012-09-14T00:00:00Z","year":"2012","external_id":{"pmid":["22984074"]},"keyword":["Multidisciplinary"],"page":"1360-1364","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/","open_access":"1"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1126/science.1224839","publisher":"American Association for the Advancement of Science","_id":"12198","date_updated":"2023-10-16T09:27:26Z","type":"journal_article","oa":1,"language":[{"iso":"eng"}],"citation":{"mla":"Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839.","apa":"Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224839","chicago":"Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.","ista":"Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364.","short":"C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.","ieee":"C. A. Ibarra et al., “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012.","ama":"Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364. doi:10.1126/science.1224839"},"issue":"6100","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","department":[{"_id":"XiFe"}],"abstract":[{"lang":"eng","text":"The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations."}],"intvolume":" 337","publication_status":"published","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"day":"14","scopus_import":"1","author":[{"first_name":"Christian A.","full_name":"Ibarra, Christian A.","last_name":"Ibarra"},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh","first_name":"Tzung-Fu"},{"last_name":"Uzawa","full_name":"Uzawa, Rie","first_name":"Rie"},{"first_name":"Jessica A.","full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues"},{"last_name":"Zemach","full_name":"Zemach, Assaf","first_name":"Assaf"},{"first_name":"Nina","full_name":"Chumak, Nina","last_name":"Chumak"},{"full_name":"Machlicova, Adriana","last_name":"Machlicova","first_name":"Adriana"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"last_name":"Rojas","full_name":"Rojas, Denisse","first_name":"Denisse"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"full_name":"Tamaru, Hisashi","last_name":"Tamaru","first_name":"Hisashi"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel"}],"oa_version":"Published Version","title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","volume":337,"date_created":"2023-01-16T09:21:24Z","article_type":"original"},{"article_processing_charge":"No","doi":"10.1242/dev.049320","publisher":"The Company of Biologists","_id":"12199","date_updated":"2023-05-08T10:57:11Z","type":"journal_article","page":"2409-2416","quality_controlled":"1","year":"2010","external_id":{"pmid":["20570940"]},"keyword":["Developmental Biology","Molecular Biology","Anther Tapetum","Arabidopsis","Cell Fate Establishment","EMS1","Reproductive Cell Lineage"],"publication":"Development","extern":"1","status":"public","pmid":1,"date_published":"2010-07-15T00:00:00Z","acknowledgement":"We thank the following for providing mutant lines and reagents: Hong Ma, De Ye, Sacco De Vries, and Rod Scott for providing the pA9::Barnase lines and information on A9 expression patterns. Carla Galinha and Paolo Piazza gave valuable help with in situ hybridisation and qRT-PCR, respectively, and we acknowledge Qing Zhang, Helen Prescott and Matthew Dicks for providing excellent technical assistance. We are indebted to Miltos Tsiantis and Angela Hay for helpful discussion, and the research was funded by Oxford University through a Clarendon Scholarship to X.F., with additional financial support from Magdalen College (Oxford).","day":"15","scopus_import":"1","author":[{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"last_name":"Dickinson","full_name":"Dickinson, Hugh G.","first_name":"Hugh G."}],"oa_version":"None","title":"Tapetal cell fate, lineage and proliferation in the Arabidopsis anther","volume":137,"date_created":"2023-01-16T09:21:54Z","article_type":"original","abstract":[{"text":"The four microsporangia of the flowering plant anther develop from archesporial cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes are surrounded by concentric monolayers of tapetal, middle layer and endothecial cells. How this intricate array of tissues, each containing relatively few cells, is established in an organ possessing no formal meristems is poorly understood. We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES 1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually for plants, tapetal cells are specified very early in development, and are subsequently stimulated to proliferate by a receptor-like kinase (RLK) complex that includes EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly, these cells continue to develop, isolated at the locular periphery. Mutant and wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the periphery of mutant locules becomes occupied by microsporocytes. However, induction of late expression of EMS1 in the few tapetal initials in ems1 plants results in their proliferation to generate a functional tapetum, and this proliferation suppresses microsporocyte number. Our experiments also show that integrity of the tapetal monolayer is crucial for the maintenance of the polarity of divisions within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the context of tissue development in complex plant organs, where constancy in size, shape and cell number is crucial.","lang":"eng"}],"intvolume":" 137","publication_status":"published","publication_identifier":{"issn":["1477-9129","0950-1991"]},"month":"07","department":[{"_id":"XiFe"}],"language":[{"iso":"eng"}],"citation":{"short":"X. Feng, H.G. Dickinson, Development 137 (2010) 2409–2416.","ieee":"X. Feng and H. G. Dickinson, “Tapetal cell fate, lineage and proliferation in the Arabidopsis anther,” Development, vol. 137, no. 14. The Company of Biologists, pp. 2409–2416, 2010.","ama":"Feng X, Dickinson HG. Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. Development. 2010;137(14):2409-2416. doi:10.1242/dev.049320","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation in the Arabidopsis Anther.” Development, vol. 137, no. 14, The Company of Biologists, 2010, pp. 2409–16, doi:10.1242/dev.049320.","apa":"Feng, X., & Dickinson, H. G. (2010). Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. Development. The Company of Biologists. https://doi.org/10.1242/dev.049320","ista":"Feng X, Dickinson HG. 2010. Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. Development. 137(14), 2409–2416.","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation in the Arabidopsis Anther.” Development. The Company of Biologists, 2010. https://doi.org/10.1242/dev.049320."},"issue":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","publication_identifier":{"issn":["0300-5127","1470-8752"]},"intvolume":" 38","abstract":[{"lang":"eng","text":"Key steps in the evolution of the angiosperm anther include the patterning of the concentrically organized microsporangium and the incorporation of four such microsporangia into a leaf-like structure. Mutant studies in the model plant Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the cell lineages culminating in the different cell types present in the microsporangium (the microsporocytes, the tapetum, and the middle and endothecial layers), and (ii) some of the genes responsible for specifying their fates. However, the processes that confer polarity on the developing anther and position the microsporangia within it remain unclear. Certainly, data from a range of experimental strategies suggest that hormones play a central role in establishing polarity and the patterning of the anther initial, and may be responsible for locating the microsporangia. But the fact that microsporangia were originally positioned externally suggests that their development is likely to be autonomous, perhaps with the reproductive cells generating signals controlling the growth and division of the investing anther epidermis. These possibilities are discussed in the context of the expression of genes which initiate and maintain male and female reproductive development, and in the perspective of our current views of anther evolution."}],"article_type":"original","date_created":"2023-01-16T09:22:18Z","volume":38,"title":"Cell–cell interactions during patterning of the Arabidopsis anther","oa_version":"None","author":[{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"},{"last_name":"Dickinson","full_name":"Dickinson, Hugh G.","first_name":"Hugh G."}],"scopus_import":"1","day":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","citation":{"ama":"Feng X, Dickinson HG. Cell–cell interactions during patterning of the Arabidopsis anther. Biochemical Society Transactions. 2010;38(2):571-576. doi:10.1042/bst0380571","ieee":"X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of the Arabidopsis anther,” Biochemical Society Transactions, vol. 38, no. 2. Portland Press Ltd., pp. 571–576, 2010.","short":"X. Feng, H.G. Dickinson, Biochemical Society Transactions 38 (2010) 571–576.","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the Arabidopsis Anther.” Biochemical Society Transactions. Portland Press Ltd., 2010. https://doi.org/10.1042/bst0380571.","ista":"Feng X, Dickinson HG. 2010. Cell–cell interactions during patterning of the Arabidopsis anther. Biochemical Society Transactions. 38(2), 571–576.","apa":"Feng, X., & Dickinson, H. G. (2010). Cell–cell interactions during patterning of the Arabidopsis anther. Biochemical Society Transactions. Portland Press Ltd. https://doi.org/10.1042/bst0380571","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the Arabidopsis Anther.” Biochemical Society Transactions, vol. 38, no. 2, Portland Press Ltd., 2010, pp. 571–76, doi:10.1042/bst0380571."},"language":[{"iso":"eng"}],"department":[{"_id":"XiFe"}],"month":"03","quality_controlled":"1","page":"571-576","type":"journal_article","date_updated":"2023-05-08T10:57:59Z","_id":"12200","publisher":"Portland Press Ltd.","doi":"10.1042/bst0380571","article_processing_charge":"No","date_published":"2010-03-22T00:00:00Z","pmid":1,"publication":"Biochemical Society Transactions","status":"public","extern":"1","keyword":["Biochemistry","Anther Development","Arabidopsis","Cell Fate","Microsporangium","Polarity","Receptor Kinase"],"external_id":{"pmid":["20298223"]},"year":"2010"},{"type":"journal_article","_id":"12201","date_updated":"2023-05-08T10:58:47Z","publisher":"Elsevier BV","article_processing_charge":"No","doi":"10.1016/j.tig.2007.08.005","quality_controlled":"1","page":"503-510","keyword":["Genetics"],"external_id":{"pmid":["17825943"]},"year":"2007","acknowledgement":"X.F. holds a Clarendon Scholarship from the University of Oxford. We thank Angela Hay and Jill Harrison for helpful advice and discussion.","date_published":"2007-10-01T00:00:00Z","pmid":1,"publication":"Trends in Genetics","extern":"1","status":"public","date_created":"2023-01-16T09:22:44Z","article_type":"original","volume":23,"title":"Packaging the male germline in plants","oa_version":"None","scopus_import":"1","author":[{"last_name":"Feng","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"full_name":"Dickinson, Hugh G.","last_name":"Dickinson","first_name":"Hugh G."}],"publication_status":"published","publication_identifier":{"issn":["0168-9525"]},"abstract":[{"lang":"eng","text":"The development of plant lateral organs is interesting because, although many of the same genes seem to be involved in the early growth of primordia, completely different gene combinations are required for the complete development of organs such as leaves and stamens. Thus, the genes common to the development of most organs, which generally form and polarize the primordial ‘envelope’, must at some stage interact with those that ‘install’ the functional content of the organ – in the case of the stamen, the four microsporangia. Although distinct genetic pathways of organ initiation, polarity establishment and setting up the reproductive cell line can readily be recognized, they do not occur sequentially. Rather, they are activated early and run in parallel. There is evidence for continuing crosstalk between these pathways."}],"intvolume":" 23","department":[{"_id":"XiFe"}],"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.” Trends in Genetics. Elsevier BV, 2007. https://doi.org/10.1016/j.tig.2007.08.005.","ista":"Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends in Genetics. 23(10), 503–510.","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.” Trends in Genetics, vol. 23, no. 10, Elsevier BV, 2007, pp. 503–10, doi:10.1016/j.tig.2007.08.005.","apa":"Feng, X., & Dickinson, H. G. (2007). Packaging the male germline in plants. Trends in Genetics. Elsevier BV. https://doi.org/10.1016/j.tig.2007.08.005","ama":"Feng X, Dickinson HG. Packaging the male germline in plants. Trends in Genetics. 2007;23(10):503-510. doi:10.1016/j.tig.2007.08.005","short":"X. Feng, H.G. Dickinson, Trends in Genetics 23 (2007) 503–510.","ieee":"X. Feng and H. G. Dickinson, “Packaging the male germline in plants,” Trends in Genetics, vol. 23, no. 10. Elsevier BV, pp. 503–510, 2007."},"issue":"10","language":[{"iso":"eng"}]}]