Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice
Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice
复制标题
水稻 R 环与基因转录和表观遗传修饰功能关系的表征
DOI：
10.1101/gr.246009.118
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发表时间：
2019-08-01
期刊：
影响因子：
7
通讯作者：
Zhang, Wenli
中科院分区：
文献类型：
--
作者：
Fang, Yuan;Chen, Lifen;Zhang, Wenli
我们进行了全基因组范围内的R-环鉴定，随后对水稻基因组中与基因表达和表观遗传标记相关的R-环进行了综合分析。我们发现，基因表达水平和R-loop峰值水平之间的相关性取决于基因结构中R-loop的位置（以下称为“基因位置”）。反义（阿索）-R-环和正义/反义（S /AS）-R-环都在转录起始位点（TSS）附近达到峰值，这些峰值水平与重叠基因的转录水平呈正相关。相反，正义（SO）-R-环通常分布在编码区，其峰值水平与重叠基因的转录水平呈反比。此外，R环数据与现有的RNA-seq，染色质免疫沉淀测序（ChIP-seq），DNase I超敏位点测序（DNase-seq）和全基因组亚硫酸氢盐测序（WGBS或BS-seq）数据的综合分析揭示了R环，基因表达和表观遗传特征之间的相互关系和复杂联系。实验验证提供了DNA和组蛋白标记的去甲基化可以在全基因组范围内影响R环峰水平的证据。这是第一个在植物中的研究，揭示了新的功能方面的R-环，它们与表观遗传甲基化的相互关系，以及在转录调控中的作用。
We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expression and epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-loop peak levels was dependent on the positions of R-loops within gene structures (hereafter named "genic position"). Both antisense only (ASO)-R-loops and sense/ antisense (S /AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peak levels corresponded positively with transcript levels of overlapping genes. In contrast, sense only (SO)-R-loops were generally spread over the coding regions, and their peak levels corresponded inversely to transcript levels of overlapping genes. In addition, integrative analyses of R-loop data with existing RNA-seq, chromatin immunoprecipitation sequencing (ChIP-seq), DNase I hypersensitive sites sequencing (DNase-seq), and whole-genome bisulfite sequencing (WGBS or BS-seq) data revealed interrelationships and intricate connections among R-loops, gene expression, and epigenetic signatures. Experimental validation provided evidence that the demethylation of both DNA and histone marks can influence R-loop peak levels on a genome-wide scale. This is the first study in plants that reveals novel functional aspects of R-loops, their interrelations with epigenetic methylation, and roles in transcriptional regulation.