Genome-Wide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica
Genome-Wide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica
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DOI：
10.1093/mp/sst018
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发表时间：
2013-09-01
期刊：
影响因子：
27.5
通讯作者：
Su, Zhen
中科院分区：
文献类型：
--
作者：
Du, Zhou;Li, Hui;Su, Zhen
ChIP-Seq 研究的 H3K4me2/3、H3K9ac 和 H3K27ac 显示出通用区域和转录起始位点的富集，并且与水稻中的活性转录相关。它们被用来发现未注释的基因，并与 DNase-Seq 数据一起预测转录因子结合位点。虽然之前的研究表明组蛋白修饰可以通过调节基因转录来影响植物的生长和发育，但有关这些修饰与基因表达之间关系的知识仍然有限。本研究使用染色质免疫沉淀和高通量测序 (ChIP-Seq)，研究了水稻中四种组蛋白修饰的全基因组分布：H3K4 的二甲基化和三甲基化（H3K4me2 和 H3K4me3）以及 H3K9 和 H3K27 的酰化（H3K9ac 和 H3K27ac）。 粳稻。通过分析已发表的 DNase-Seq 数据，本研究探索了水稻基因组中的 DNase-Hypersensitive (DH) 位点。组蛋白标记主要出现在通用区域，并在基因的转录起始位点（TSS）周围富集。该分析表明，四个组蛋白修饰和 DH 位点均与活性转录相关。此外，这四种组蛋白修饰与转录区域高度一致，该区域有希望用于预测水稻基因注释中缺失的基因。通过实验确认两个预测缺失基因的转录，进一步验证了预测。此外，构建了序列基序分析以鉴定DH位点和许多假定的转录因子结合位点。
H3K4me2/3, H3K9ac, and H3K27ac investigated by ChIP-Seq showed enrichment in generic regions and transcription start sites, and associated with active transcription in rice. They were used to discover unannotated genes and to predict transcription factor binding sites together with DNase-Seq data.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 regionsua 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.