State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
Mol Plant. 2013 Sep;6(5):1463-72. doi: 10.1093/mp/sst018. Epub 2013 Jan 25.
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.
虽然先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，但关于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结合高通量测序（ChIP-Seq）技术，研究了四种组蛋白修饰（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）在籼稻中的全基因组分布。通过分析已发表的 DNase-Seq 数据，本研究探索了水稻基因组上的 DNase 超敏（DH）位点。组蛋白标记主要出现在通用区域，并在基因转录起始位点（TSS）周围富集。该分析表明，这四种组蛋白修饰和 DH 位点都与活跃的转录相关。此外，这四种组蛋白修饰与转录区域高度一致——这一有前景的特征被用于预测水稻基因注释中缺失的基因。通过实验证实两个预测的缺失基因的转录，进一步验证了预测结果。此外，还构建了序列基序分析，以识别 DH 位点和许多假定的转录因子结合位点。
