生物
表观遗传学
遗传学
基因
染色质
基因组
基因表达
DNA甲基化
计算生物学
作者
Yuan Fang,Lifen Chen,Kande Lin,Yilong Feng,Pengyue Zhang,Xiucai Pan,J. L. Sanders,Yufeng Wu,Xiue Wang,Zhen Su,Caiyan Chen,Hairong Wei,Wenli Zhang
出处
期刊:Genome Research
[Cold Spring Harbor Laboratory]
日期:2019-07-01
卷期号:29 (8): 1287-1297
被引量:40
标识
DOI:10.1101/gr.246009.118
摘要
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.
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