--- _id: '11703' abstract: - lang: eng text: Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism. acknowledgement: "JRP was supported by the Swiss National Science Foundation (https://www.snf.ch/en), Sinergia grant 26073998. BV was supported by the European Research Council (https://erc.europa.eu/) under the European Union’s Horizon 2020 research and innovation program, grant number 715257. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\r\nPlants were grown in Lausanne by Aline Revel, and RNA extraction and library preparation were performed by Dessislava Savova Bianchi. All sequencing and the IsoSeq3 analysis were carried out by Center for Integrative Genomics at the University of Lausanne. All other computational analyses were performed on the server at IST Austria." article_number: e1010226 article_processing_charge: No article_type: original author: - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: John R. full_name: Pannell, John R. last_name: Pannell citation: ama: Toups MA, Vicoso B, Pannell JR. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genetics. 2022;18(7). doi:10.1371/journal.pgen.1010226 apa: Toups, M. A., Vicoso, B., & Pannell, J. R. (2022). Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1010226 chicago: Toups, Melissa A, Beatriz Vicoso, and John R. Pannell. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” PLoS Genetics. Public Library of Science, 2022. https://doi.org/10.1371/journal.pgen.1010226. ieee: M. A. Toups, B. Vicoso, and J. R. Pannell, “Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis,” PLoS Genetics, vol. 18, no. 7. Public Library of Science, 2022. ista: Toups MA, Vicoso B, Pannell JR. 2022. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genetics. 18(7), e1010226. mla: Toups, Melissa A., et al. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” PLoS Genetics, vol. 18, no. 7, e1010226, Public Library of Science, 2022, doi:10.1371/journal.pgen.1010226. short: M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022). date_created: 2022-07-31T22:01:48Z date_published: 2022-07-06T00:00:00Z date_updated: 2023-08-03T12:17:12Z day: '06' ddc: - '570' department: - _id: BeVi doi: 10.1371/journal.pgen.1010226 ec_funded: 1 external_id: isi: - '000886643100006' pmid: - '35793353' file: - access_level: open_access checksum: aa4c137f82635e700856c359dccfaa0a content_type: application/pdf creator: dernst date_created: 2022-08-01T07:49:25Z date_updated: 2022-08-01T07:49:25Z file_id: '11708' file_name: 2022_PLoSGenetics_Toups.pdf file_size: 1620272 relation: main_file success: 1 file_date_updated: 2022-08-01T07:49:25Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 18 year: '2022' ... --- _id: '9497' abstract: - lang: eng text: The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes. article_number: e1002988 article_processing_charge: No article_type: original author: - first_name: Devin full_name: Coleman-Derr, Devin last_name: Coleman-Derr - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988 apa: Coleman-Derr, D., & Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002988 chicago: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988. ieee: D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10. Public Library of Science, 2012. ista: Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988. mla: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002988. short: D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012). date_created: 2021-06-07T10:55:27Z date_published: 2012-10-11T00:00:00Z date_updated: 2021-12-14T08:29:57Z day: '11' department: - _id: DaZi doi: 10.1371/journal.pgen.1002988 extern: '1' external_id: pmid: - '23071449' intvolume: ' 8' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pgen.1002988 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 issn: - 1553-7390 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Deposition of histone variant H2A.Z within gene bodies regulates responsive genes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 8 year: '2012' ... --- _id: '9499' abstract: - lang: eng text: EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism. article_number: e1002512 article_processing_charge: No article_type: original author: - first_name: Sang Yeol full_name: Kim, Sang Yeol last_name: Kim - first_name: Jungeun full_name: Lee, Jungeun last_name: Lee - first_name: Leor full_name: Eshed-Williams, Leor last_name: Eshed-Williams - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Z. Renee full_name: Sung, Z. Renee last_name: Sung citation: ama: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3). doi:10.1371/journal.pgen.1002512 apa: Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., & Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002512 chicago: Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512. ieee: S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development,” PLoS Genetics, vol. 8, no. 3. Public Library of Science, 2012. ista: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 8(3), e1002512. mla: Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002512. short: S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012). date_created: 2021-06-07T11:07:56Z date_published: 2012-03-22T00:00:00Z date_updated: 2021-12-14T08:31:14Z day: '22' department: - _id: DaZi doi: 10.1371/journal.pgen.1002512 extern: '1' external_id: pmid: - '22457632' intvolume: ' 8' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pgen.1002512 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: eissn: - 1553-7404 issn: - 1553-7390 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 8 year: '2012' ...