Replisome bypass of transcription complexes and R-loops

Nucleic Acids Res. 2020 Oct 9;48(18):10353-10367. doi: 10.1093/nar/gkaa741.

Abstract

The vast majority of the genome is transcribed by RNA polymerases. G+C-rich regions of the chromosomes and negative superhelicity can promote the invasion of the DNA by RNA to form R-loops, which have been shown to block DNA replication and promote genome instability. However, it is unclear whether the R-loops themselves are sufficient to cause this instability or if additional factors are required. We have investigated replisome collisions with transcription complexes and R-loops using a reconstituted bacterial DNA replication system. RNA polymerase transcription complexes co-directionally oriented with the replication fork were transient blockages, whereas those oriented head-on were severe, stable blockages. On the other hand, replisomes easily bypassed R-loops on either template strand. Replication encounters with R-loops on the leading-strand template (co-directional) resulted in gaps in the nascent leading strand, whereas lagging-strand template R-loops (head-on) had little impact on replication fork progression. We conclude that whereas R-loops alone can act as transient replication blocks, most genome-destabilizing replication fork stalling likely occurs because of proteins bound to the R-loops.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Composition / genetics
  • Chromosome Structures / genetics
  • Chromosomes / genetics
  • DNA Helicases / genetics
  • DNA Repair / genetics
  • DNA Replication / genetics*
  • DNA-Binding Proteins / genetics*
  • Escherichia coli / genetics
  • Genomic Instability / genetics
  • R-Loop Structures / genetics*
  • Transcription, Genetic*

Substances

  • DNA-Binding Proteins
  • DNA Helicases