H3K4me2 functions as a repressive epigenetic mark in plants

Epigenetics & Chromatin

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[1] 0000 0001 0125 2443, grid.8547.e, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China;0000 0001 0125 2443, grid.8547.e, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS–Fudan–HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China;0000 0001 0125 2443, grid.8547.e, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS–Fudan–HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China;0000 0001 2157 9291, grid.11843.3f, Universite de Strasbourg, CNRS, IBMP UPR 2357, 67000, Strasbourg, France;0000 0001 2297 5165, grid.94365.3d, Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, 20892, Bethesda, MD, USA;0000000119573309, grid.9227.e, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China;0000 0004 1797 8419, grid.410726.6, University of the Chinese Academy of Sciences, 100049, Beijing, China;

关键词: H3K4me2;    ChIP-seq;    RNA-seq;    Gene expression;    Epigenetic mark;    Rice;   

DOI  :  10.1186/s13072-019-0285-6

来源: publisher

【 摘 要 】

BackgroundIn animals, H3K4me2 and H3K4me3 are enriched at the transcription start site (TSS) and function as epigenetic marks that regulate gene transcription, but their functions in plants have not been fully characterized.ResultsWe used chromatin immunoprecipitation sequencing to analyze the rice genome-wide changes to H3K4me1/H3K4me2/H3K4me3 following the loss of an H3K4-specific methyltransferase, SDG701. The knockdown of SDG701 resulted in a global decrease in H3K4me2/H3K4me3 levels throughout the rice genome. An RNA-sequencing analysis revealed that many genes related to diverse developmental processes were misregulated in the SDG701 knockdown mutant. In rice, H3K4me3 and H3K36me3 are positively correlated with gene transcription; however, surprisingly, the H3K4me2 level was negatively associated with gene transcription levels. Furthermore, the H3K4me3 level at the TSS region decreased significantly in the genes that exhibited down-regulated expression in the SDG701 knockdown mutant. In contrast, the genes with up-regulated expression in the mutant were associated with a considerable decrease in H3K4me2 levels over the gene body region.ConclusionA comparison of the genome-wide distributions of H3K4me2 in eukaryotes indicated that the H3K4me2 level is not correlated with the gene transcription level in yeast, but is positively and negatively correlated with gene expression in animals and plants, respectively. Our results uncovered H3K4me2 as a novel repressive mark in plants.

【 授权许可】

CC BY