Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm.

Genome Biology
Jordi Moreno-RomeroClaudia Köhler

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...Continue Reading

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Citations

Jan 4, 2020·Genes & Development·Rita A Batista, Claudia Köhler
Jun 11, 2020·Cold Spring Harbor Symposia on Quantitative Biology·Jean-Sébastien ParentRobert A Martienssen
May 22, 2020·Frontiers in Plant Science·Linhao Xu, Hua Jiang
Mar 22, 2021·Nucleic Acids Research·Vikash Kumar YadavClaudia Köhler
Apr 30, 2021·Plant Reproduction·Sean A Montgomery, Frédéric Berger
Jul 18, 2021·Proceedings of the National Academy of Sciences of the United States of America·Jessica A RodriguesDaniel Zilberman
Jul 27, 2021·Trends in Genetics : TIG·Maximilian W D RaasHendrik Marks
Jul 9, 2021·Plant Reproduction·Jérômine Vigneau, Michael Borg

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Methods Mentioned

BETA
transgenic
RNAseq
PCR
ChIP-seq
ChIP
confocal microscopy

Software Mentioned

INTACT
Zeiss ZEN

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