DNA Topoisomerase I differentially modulates R-loops across the human genome

Genome Biol. 2018 Jul 30;19(1):100. doi: 10.1186/s13059-018-1478-1.


Background: Co-transcriptional R-loops are abundant non-B DNA structures in mammalian genomes. DNA Topoisomerase I (Top1) is often thought to regulate R-loop formation owing to its ability to resolve both positive and negative supercoils. How Top1 regulates R-loop structures at a global level is unknown.

Results: Here, we perform high-resolution strand-specific R-loop mapping in human cells depleted for Top1 and find that Top1 depletion results in both R-loop gains and losses at thousands of transcribed loci, delineating two distinct gene classes. R-loop gains are characteristic for long, highly transcribed, genes located in gene-poor regions anchored to Lamin B1 domains and in proximity to H3K9me3-marked heterochromatic patches. R-loop losses, by contrast, occur in gene-rich regions overlapping H3K27me3-marked active replication initiation regions. Interestingly, Top1 depletion coincides with a block of the cell cycle in G0/G1 phase and a trend towards replication delay.

Conclusions: Our findings reveal new properties of Top1 in regulating R-loop homeostasis in a context-dependent manner and suggest a potential role for Top1 in modulating the replication process via R-loop formation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin Immunoprecipitation
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism
  • DNA Replication
  • DNA Topoisomerases, Type I / genetics*
  • DNA Topoisomerases, Type I / metabolism
  • G1 Phase Cell Cycle Checkpoints
  • Gene Silencing
  • Genome, Human*
  • HEK293 Cells
  • Heterochromatin / chemistry*
  • Heterochromatin / metabolism
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • Lamin Type B / genetics
  • Lamin Type B / metabolism
  • Nucleic Acid Conformation
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism
  • Resting Phase, Cell Cycle
  • Transcription, Genetic*


  • Heterochromatin
  • Histones
  • Lamin Type B
  • RNA, Small Interfering
  • lamin B1
  • DNA
  • RNA Polymerase II
  • DNA Topoisomerases, Type I
  • TOP1 protein, human