title: Evolution and Coevolution of PRC2 Genes in Vertebrates and Mammals.
abstract: Recruited by noncoding RNAs (ncRNAs) to specific genomic sites, polycomb repressive complexes 2 (PRC2) modify chromatin states in nearly all eukaryotes. The limited ncRNAs in Drosophila but abundant in mammals should have made PRC2 genes evolved significantly in Deuterostomia to adapt to the much increased ncRNAs. This study analyzes the evolution and coevolution of seven PRC2 genes in 29 Deuterostomia. These genes, previously assumed highly conserved, are found to have obtained multiple insertions in vertebrates and mammals and undergone significant positive selections in marsupials and prosimians, indicating adaptions to substantially increased lncRNAs (long noncoding RNAs) in mammals and in primates. Some insertions occur notably in homologous sequences of human nonsense-mediated decay (NMD) transcripts. Moreover, positive selections and signals of convergent evolution imply the independent increase of lncRNAs in mammals and in primates. Coevolutionary analysis reveals that patterns of interaction between PRC2 proteins have also much evolved from vertebrates to mammals, indicating adaptation at the protein complex level. The potential functions of mammalian-specific insertions and NMD transcripts deserve further experimental examination.
authors.affiliation: Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
authors.forename: Xi
authors.initials: X
authors.lastname: Liu
authors.affiliation: Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
authors.forename: Jingwen
authors.initials: J
authors.lastname: Yang
authors.affiliation: Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Wu
authors.affiliation: Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
authors.forename: Ruixian
authors.initials: R
authors.lastname: Song
authors.affiliation: Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. Electronic address: zhuhao@smu.edu.cn.
authors.forename: Hao
authors.initials: H
authors.lastname: Zhu
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D006801:Humans; D008322:Mammals / Q000235:genetics; D010802:Phylogeny; D063151:Polycomb Repressive Complex 2 / Q000145:classification / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D014714:Vertebrates / Q000235:genetics
chemical_list: D062085:RNA, Long Noncoding; D063151:Polycomb Repressive Complex 2
keywords: Coevolution; Epigenome; Evolution; LncRNAs; Nonsense-mediated decay transcript; PRC2; Polycomb repressive complexes 2