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

  • Author(s): Chen, Liang
  • Chen, Jia-Yu
  • Zhang, Xuan
  • Gu, Ying
  • Xiao, Rui
  • Shao, Changwei
  • Tang, Peng
  • Qian, Hao
  • Luo, Daji
  • Li, Hairi
  • Zhou, Yu
  • Zhang, Dong-Er
  • Fu, Xiang-Dong
  • et al.

Published Web Location

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957070/
No data is associated with this publication.
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.

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