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

Abstract

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.

Photosynthetic Genes and Genes Associated with the C4 Trait in Maize Are Characterized by a Unique Class of Highly Regulated Histone Acetylation Peaks on Upstream Promoters

“…The highest number of these upstream acetylation peaks was found around position 21,000 bp relative to the TIS. Whereas H3K9ac and H3K4me3 peaks in the TIS region and downstream region were already described in different species (Wang et al, 2009;Roudier et al, 2011;Du et al, 2013;He et al, 2013;Hussey et al, 2015), our observation of regulated upstream H3K9ac peaks on an genome-wide basis was, to our knowledge, unique. We first wanted to test whether regulated upstream acetylation was simply caused by false annotations of TIS.…”

Relationship between histone modifications and transcription factor binding is protein family specific

“…H3K4me2, as an activating mark, was significantly different in regions surrounding BSs of TFs from the bHLH and ETS families. The same histone mark, however, showed lesser importance in the three cell types, implying co-occurrence with other activating marks such as H3K4me3 or H3K27ac (Peach et al 2012;Du et al 2013). …”

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

“…[8][9][10][11][12][13] In plants, recent advances in high throughput sequencing technology have enabled the large-scale profiling of histone acetylation marks and have greatly improved our understanding of the function of histone acetylation and its relationship with transcription. [14][15][16][17][18] Besides its role in gene expression, plant histone acetylation plays crucial roles in the crosstalk between genomes and the environment during plant responses to diverse stresses at the cellular and organismal levels. [19][20][21][22][23][24] Acetylation occurs at many histone lysine residues and regulates chromatin activity by at least 2 different mechanisms.…”