title: Expansion and Functional Divergence of Jumonji C-Containing Histone Demethylases: Significance of Duplications in Ancestral Angiosperms and Vertebrates.
abstract: Histone modifications, such as methylation and demethylation, are crucial mechanisms altering chromatin structure and gene expression. Recent biochemical and molecular studies have uncovered a group of histone demethylases called Jumonji C (JmjC) domain proteins. However, their evolutionary history and patterns have not been examined systematically. Here, we report extensive analyses of eukaryotic JmjC genes and define 14 subfamilies, including the Lysine-Specific Demethylase3 (KDM3), KDM5, JMJD6, Putative-Lysine-Specific Demethylase11 (PKDM11), and PKDM13 subfamilies, shared by plants, animals, and fungi. Other subfamilies are detected in plants and animals but not in fungi (PKDM12) or in animals and fungi but not in plants (KDM2 and KDM4). PKDM7, PKDM8, and PKDM9 are plant-specific groups, whereas Jumonji, AT-Rich Interactive Domain2, KDM6, and PKDM10 are animal specific. In addition to known domains, most subfamilies have characteristic conserved amino acid motifs. Whole-genome duplication (WGD) was likely an important mechanism for JmjC duplications, with four pairs from an angiosperm-wide WGD and others from subsequent WGDs. Vertebrates also experienced JmjC duplications associated with the vertebrate ancestral WGDs, with additional mammalian paralogs from tandem duplication and possible transposition. The sequences of paralogs have diverged in both known functional domains and other regions, showing evidence of selection pressure. The increases of JmjC copy number and the divergences in sequence and expression might have contributed to the divergent functions of JmjC genes, allowing the angiosperms and vertebrates to adapt to a great number of ecological niches and contributing to their evolutionary successes.
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China (S.Q., Y.W., H.M.);Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China (H.M.); andDepartment of Bioinformatics, School of Life Sciences and Technology, and Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China (L.Z.).
authors.forename: Shengzhan
authors.initials: S
authors.lastname: Qian
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China (S.Q., Y.W., H.M.);Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China (H.M.); andDepartment of Bioinformatics, School of Life Sciences and Technology, and Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China (L.Z.).
authors.forename: Yingxiang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China (S.Q., Y.W., H.M.);Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China (H.M.); andDepartment of Bioinformatics, School of Life Sciences and Technology, and Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China (L.Z.) hongma@fudan.edu.cn zls@tongji.edu.cn.
authors.forename: Hong
authors.identifier: http://orcid.org/0000-0001-8717-4422
authors.initials: H
authors.lastname: Ma
authors.affiliation: State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China (S.Q., Y.W., H.M.);Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China (H.M.); andDepartment of Bioinformatics, School of Life Sciences and Technology, and Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China (L.Z.) hongma@fudan.edu.cn zls@tongji.edu.cn.
authors.forename: Liangsheng
authors.identifier: http://orcid.org/0000-0003-1919-3677
authors.initials: L
authors.lastname: Zhang
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D005075:Biological Evolution; D002843:Chromatin / Q000235:genetics*; D020440:Gene Duplication; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics* / Q000378:metabolism; D019684:Magnoliopsida / Q000201:enzymology* / Q000235:genetics; D008745:Methylation; D010802:Phylogeny; D016415:Sequence Alignment; D026801:Synteny; D014714:Vertebrates / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D006657:Histones; D056484:Jumonji Domain-Containing Histone Demethylases