气候变化领域集成服务门户(CCPortal): Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting

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DOI	10.1073/pnas.2104445118
	Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting
	Rodrigues J.A.; Hsieh P.-H.; Ruan D.; Nishimura T.; Sharma M.K.; Sharma R.; Ye X.; Nguyen N.D.; Nijjar S.; Ronald P.C.; Fischer R.L.; Zilberman D.
发表日期	2021
ISSN	0027-8424
卷号	118 期号:29
英文摘要	Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	Chromatin modification \| epigenome \| transcriptome \| bisulfite sequencing \| siren loci
语种	英语
scopus关键词	histone; lysine; polycomb group protein; RNA directed DNA polymerase; plant protein; angiosperm; Arabidopsis thaliana; Article; bisulfite sequencing; differential gene expression; DNA methylation; DNA sequence; DNA transposition; endosperm; epigenetic modification; epigenetics; gene deletion; gene expression; gene insertion; genetic variability; genetic variation; genome imprinting; homeobox; Indian rice; Japonica rice; long terminal repeat; promoter region; RNA sequencing; Sanger sequencing; sequence analysis; single nucleotide polymorphism; transposon; classification; gene expression regulation; genetics; metabolism; molecular evolution; mutation; Oryza; DNA Methylation; DNA Transposable Elements; Endosperm; Epigenomics; Evolution, Molecular; Gene Expression Regulation, Plant; Genomic Imprinting; Mutation; Oryza; Plant Proteins
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/251116
作者单位	Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States; Department of Plant Pathology, University of California, Davis, CA 95616, United States; Genome Center, University of California, Davis, CA 95616, United States; Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
推荐引用方式 GB/T 7714	Rodrigues J.A.,Hsieh P.-H.,Ruan D.,et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting[J],2021,118(29).
APA	Rodrigues J.A..,Hsieh P.-H..,Ruan D..,Nishimura T..,Sharma M.K..,...&Zilberman D..(2021).Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting.Proceedings of the National Academy of Sciences of the United States of America,118(29).
MLA	Rodrigues J.A.,et al."Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting".Proceedings of the National Academy of Sciences of the United States of America 118.29(2021).