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R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters.

Abstract：

:R-loop, a three-stranded RNA/DNA structure, has been linked to induced genome instability and regulated gene expression. To enable precision analysis of R-loops in vivo, we develop an RNase-H-based approach; this reveals predominant R-loop formation near gene promoters with strong G/C skew and propensity to form G-quadruplex in non-template DNA, corroborating with all biochemically established properties of R-loops. Transcription perturbation experiments further indicate that R-loop induction correlates to transcriptional pausing. Interestingly, we note that most mapped R-loops are each linked to a nearby free RNA end; by using a ribozyme to co-transcriptionally cleave nascent RNA, we demonstrate that such a free RNA end coupled with a G/C-skewed sequence is necessary and sufficient to induce R-loop. These findings provide a topological solution for RNA invasion into duplex DNA and suggest an order for R-loop initiation and elongation in an opposite direction to that previously proposed.

journal_name

Mol Cell

journal_title

Molecular cell

authors

Chen L,Chen JY,Zhang X,Gu Y,Xiao R,Shao C,Tang P,Qian H,Luo D,Li H,Zhou Y,Zhang DE,Fu XD

doi

10.1016/j.molcel.2017.10.008

subject

Has Abstract

pub_date

2017-11-16 00:00:00

pages

745-757.e5

issue

4

eissn

1097-2765

issn

1097-4164

pii

S1097-2765(17)30757-8

journal_volume

68

pub_type

杂志文章

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