RT Journal
A1 Fang, Yuan
A1 Chen, Lifen
A1 Lin, Kande
A1 Feng, Yilong
A1 Zhang, Pengyue
A1 Pan, Xiucai
A1 Sanders, Jennifer
A1 Wu, Yufeng
A1 Wang, Xiu-e
A1 Su, Zhen
A1 Chen, Caiyan
A1 Wei, Hairong
A1 Zhang, Wenli
T1 Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice
JF Genome Research 
JO Genome Research 
YR 2019 
FD August 01 
VO 29 
IS 8 
SP 1287 
OP 1297 
DO 10.1101/gr.246009.118 
UL http://genome.cshlp.org/content/29/8/1287.abstract 
AB 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.