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Global Profiling of RNA-chromatin Interactions Reveals Co-regulatory Gene Expression Networks in Arabidopsis

Overview
Journal Nat Plants
Specialties Biology
Genetics
Date 2021 Oct 15
PMID 34650265
Citations 8
Authors
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Abstract

It is increasingly evident that various RNAs can bind chromatin to regulate gene expression and genome organization. Here we adapted a sequencing-based technique to profile RNA-chromatin interactions at a genome-wide scale in Arabidopsis seedlings. We identified more than 10,000 RNA-chromatin interactions mediated by protein-coding RNAs and non-coding RNAs. Cis and intra-chromosomal interactions are mainly mediated by protein-coding RNAs, whereas inter-chromosomal interactions are primarily mediated by non-coding RNAs. Many RNA-chromatin interactions tend to positively correlate with DNA-DNA interactions, suggesting their mutual influence and reinforcement. We further show that some RNA-chromatin interactions undergo alterations in response to biotic and abiotic stresses and that altered RNA-chromatin interactions form co-regulatory networks. Our study provides a global view on RNA-chromatin interactions in Arabidopsis and a rich resource for future investigations of regulatory roles of RNAs in gene expression and genome organization.

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References
1.
Fu X . Non-coding RNA: a new frontier in regulatory biology. Natl Sci Rev. 2015; 1(2):190-204. PMC: 4374487. DOI: 10.1093/nsr/nwu008. View

2.
Engreitz J, Ollikainen N, Guttman M . Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol. 2016; 17(12):756-770. DOI: 10.1038/nrm.2016.126. View

3.
Rinn J, Chang H . Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012; 81:145-66. PMC: 3858397. DOI: 10.1146/annurev-biochem-051410-092902. View

4.
Chen L, Chen J, Zhang X, Gu Y, Xiao R, Shao C . R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters. Mol Cell. 2017; 68(4):745-757.e5. PMC: 5957070. DOI: 10.1016/j.molcel.2017.10.008. View

5.
Xiao R, Chen J, Liang Z, Luo D, Chen G, Lu Z . Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. Cell. 2019; 178(1):107-121.e18. PMC: 6760001. DOI: 10.1016/j.cell.2019.06.001. View