Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm
Moreno-Romero, Jordi (Centre de Recerca en Agrigenòmica)
Del Toro-De León, Gerardo (Swedish University of Agricultural Sciences and Linnean Center for Plant Biology. Department of Plant Biology)
Yadav, Vikash Kumar (Swedish University of Agricultural Sciences and Linnean Center for Plant Biology. Department of Plant Biology)
Santos-González, Juan (Swedish University of Agricultural Sciences and Linnean Center for Plant Biology. Department of Plant Biology)
Köhler, Claudia (Swedish University of Agricultural Sciences and Linnean Center for Plant Biology. Department of Plant Biology)

Date:	2019
Abstract:	Imprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression. In this study, we show that imprinted paternally expressed genes (PEGs) in the Arabidopsis endosperm are marked by an epigenetic signature of Polycomb Repressive Complex2 (PRC2)-mediated H3K27me3 together with heterochromatic H3K9me2 and CHG methylation, which specifically mark the silenced maternal alleles of PEGs. The co-occurrence of H3K27me3 and H3K9me2 on defined loci in the endosperm drastically differs from the strict separation of both pathways in vegetative tissues, revealing tissue-specific employment of repressive epigenetic pathways in plants. Based on the presence of this epigenetic signature on maternal alleles, we are able to predict known PEGs at high accuracy and identify several new PEGs that we confirm using INTACT-based transcriptomes generated in this study. The presence of the three repressive epigenetic marks, H3K27me3, H3K9me2, and CHG methylation on the maternal alleles in the endosperm serves as a specific epigenetic signature that allows prediction of genes with parental-specific gene expression. Our study reveals that there are substantially more PEGs than previously identified, indicating that paternal-specific gene expression is of higher functional relevance than currently estimated. The combined activity of PRC2-mediated H3K27me3 together with the heterochromatic H3K9me3 has also been reported to silence the maternal Xist locus in mammalian preimplantation embryos, suggesting convergent employment of both pathways during the evolution of genomic imprinting. The online version of this article (10. 1186/s13059-019-1652-0) contains supplementary material, which is available to authorized users.
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	H3K9me2 ; H3K27me3 ; CHG methylation ; Endosperm ; Genomic imprinting ; Paternally expressed genes
Published in:	Genome biology, Vol. 20 (February 2019) , ISSN 1474-760X
Related work:	Moreno Romero, Jordi; Del Toro-De León, Gerardo; Yadav, Vikash Kumar; [et al.]. «Correction to : Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm». Genome biology, Vol. 20 (September 2019), art. 182 https://doi.org/10.1186/s13059-019-1803-3

Correcció de l'article: https://ddd.uab.cat/record/253333
DOI: 10.1186/s13059-019-1652-0
PMID: 30791924

11 p, 1.9 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles