Genome-Wide Analysis of Histone Modifications： H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica

• Published in: Molecular plant Vol. 6; no. 5; pp. 1463 - 1472
• Main Authors: Du, Zhou, Li, Hui, Wei, Qiang, Zhao, Xin, Wang, Chunchao, Zhu, Qilin, Yi, Xin, Xu, Wenying, Liu, X. Shirley, Jin, Weiwei, Su, Zhen
• Format: Journal Article
• Language: English
• Published: England Elsevier Inc 01.09.2013; Cell Press; Oxford University Press
• Subjects: acylation; Base Sequence; binding sites; Binding Sites - genetics; bioinformatics; Chromatin; chromatin structure and remodeling; Deoxyribonucleases - metabolism; DNA Transposable Elements - genetics; epigenetics; Gene expression; gene regulation; genes; Genes, Plant - genetics; Genome, Plant - genetics; Genomes; genomics; growth and development; high-throughput nucleotide sequencing; histones; Histones - metabolism; Lysine - metabolism; Molecular Sequence Annotation; Molecular Sequence Data; Oryza - genetics; Oryza - metabolism; Oryza sativa; Plant growth; precipitin tests; prediction; Protein Processing, Post-Translational; Reproducibility of Results; Rice; Sequence Analysis, DNA; Studies; transcription (genetics); Transcription factors; Transcription Factors - metabolism; Transcription Initiation Site; Transcription, Genetic; 基因组分析; 基因转录; 染色质免疫沉淀; 水稻基因组; 粳稻; 组蛋白修饰; 转录因子结合位点; 转录起始位点; genomics; chromatin structure and remodeling; rice; gene regulation; epigenetics; bioinformatics
• ISSN: 1674-2052; 1752-9867; 1752-9867
• DOI: 10.1093/mp/sst018

While previous studies have shown that histone modifications could influence plant growth and devel- opment by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing （ChlP-Seq）, to investigate the genome-wide distribution of four histone modifications： di and trimethylation of H3K4 （H3K4me2 and H3K4me3） and acylation of H3K9 and H3K27 （H3K9ac and H3K27ac） in Oryza sativa L. japonica. By analyz- ing published DNase-Seq data, this study explored DNase-Hypersensitive （DH） sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites （TSSs） of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites.