Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica.
While previous studies have shown that histone modifications could influence plant growth and development 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 (ChIP-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 analyzing 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.
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
Zhou
Z
Du
Hui
H
Li
Qiang
Q
Wei
Xin
X
Zhao
Chunchao
C
Wang
Qilin
Q
Zhu
Xin
X
Yi
Wenying
W
Xu
X Shirley
XS
Liu
Weiwei
W
Jin
Zhen
Z
Su
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D003851:Deoxyribonucleases / Q000378:metabolism; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D006657:Histones / Q000378:metabolism*; D008239:Lysine / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics / Q000378:metabolism*; D011499:Protein Processing, Post-Translational; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
D004251:DNA Transposable Elements; D006657:Histones; D014157:Transcription Factors; D003851:Deoxyribonucleases; D008239:Lysine
bioinformatics; chromatin structure and remodeling; epigenetics; gene regulation; genomics; rice.