Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice.
Document Type
Article
Publication Date
8-1-2019
Department
College of Forest Resources and Environmental Science
Abstract
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.
Publication Title
Genome research
Recommended Citation
Fang, Y.,
Chen, L.,
Lin, K.,
Feng, Y.,
Zhang, P.,
Pan, X.,
Sanders, J.,
Wu, Y.,
Wang, X.,
Su, Z.,
Chen, C.,
Wei, H.,
&
Zhang, W.
(2019).
Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice..
Genome research,
29(8), 1287-1297.
http://doi.org/10.1101/gr.246009.118
Retrieved from: https://digitalcommons.mtu.edu/michigantech-p/1468
Creative Commons License
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Publisher's Statement
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. Publisher’s version of record: https://doi.org/10.1101/gr.246009.118