Chromatin remodeller SMARCA4 recruits topoisomerase 1 and suppresses transcription-associated genomic instability

Nat Commun. 2016 Feb 4;7:10549. doi: 10.1038/ncomms10549.

Abstract

Topoisomerase 1, an enzyme that relieves superhelical tension, is implicated in transcription-associated mutagenesis and genome instability-associated with neurodegenerative diseases as well as activation-induced cytidine deaminase. From proteomic analysis of TOP1-associated proteins, we identify SMARCA4, an ATP-dependent chromatin remodeller; FACT, a histone chaperone; and H3K4me3, a transcriptionally active chromatin marker. Here we show that SMARCA4 knockdown in a B-cell line decreases TOP1 recruitment to chromatin, and leads to increases in Igh/c-Myc chromosomal translocations, variable and switch region mutations and negative superhelicity, all of which are also observed in response to TOP1 knockdown. In contrast, FACT knockdown inhibits association of TOP1 with H3K4me3, and severely reduces DNA cleavage and Igh/c-Myc translocations, without significant effect on TOP1 recruitment to chromatin. We thus propose that SMARCA4 is involved in the TOP1 recruitment to general chromatin, whereas FACT is required for TOP1 binding to H3K4me3 at non-B DNA containing chromatin for the site-specific cleavage.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • B-Lymphocytes
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism
  • Cell Line, Tumor
  • Cell Proliferation / genetics
  • Chromatin / metabolism*
  • Chromatin Assembly and Disassembly / genetics
  • Chromatin Immunoprecipitation
  • DNA Breaks, Double-Stranded
  • DNA Cleavage
  • DNA Helicases / genetics*
  • DNA Helicases / metabolism
  • DNA Topoisomerases, Type I / genetics*
  • DNA Topoisomerases, Type I / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Flow Cytometry
  • Gene Knockdown Techniques
  • Genes, Immunoglobulin Heavy Chain
  • Genes, myc
  • Genomic Instability / genetics*
  • High Mobility Group Proteins / genetics
  • High Mobility Group Proteins / metabolism
  • Histone Chaperones / genetics*
  • Histone Chaperones / metabolism
  • Humans
  • Immunoprecipitation
  • Mice
  • Nuclear Proteins / genetics*
  • Nuclear Proteins / metabolism
  • Proteome
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Transcription, Genetic
  • Transcriptional Elongation Factors / genetics
  • Transcriptional Elongation Factors / metabolism
  • Translocation, Genetic

Substances

  • Cell Cycle Proteins
  • Chromatin
  • DNA-Binding Proteins
  • High Mobility Group Proteins
  • Histone Chaperones
  • Nuclear Proteins
  • Proteome
  • SSRP1 protein, human
  • SUPT16H protein, human
  • Supt16 protein, mouse
  • Transcription Factors
  • Transcriptional Elongation Factors
  • Ssrp1 protein, mouse
  • SMARCA4 protein, human
  • Smarca4 protein, mouse
  • DNA Helicases
  • DNA Topoisomerases, Type I