Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders

Genome Biol. 2016 Aug 31;17(1):182. doi: 10.1186/s13059-016-1043-8.

Abstract

Background: Type II DNA topoisomerases (TOP2) regulate DNA topology by generating transient double stranded breaks during replication and transcription. Topoisomerase II beta (TOP2B) facilitates rapid gene expression and functions at the later stages of development and differentiation. To gain new insight into the genome biology of TOP2B, we used proteomics (BioID), chromatin immunoprecipitation, and high-throughput chromosome conformation capture (Hi-C) to identify novel proximal TOP2B protein interactions and characterize the genomic landscape of TOP2B binding at base pair resolution.

Results: Our human TOP2B proximal protein interaction network included members of the cohesin complex and nucleolar proteins associated with rDNA biology. TOP2B associates with DNase I hypersensitivity sites, allele-specific transcription factor (TF) binding, and evolutionarily conserved TF binding sites on the mouse genome. Approximately half of all CTCF/cohesion-bound regions coincided with TOP2B binding. Base pair resolution ChIP-exo mapping of TOP2B, CTCF, and cohesin sites revealed a striking structural ordering of these proteins along the genome relative to the CTCF motif. These ordered TOP2B-CTCF-cohesin sites flank the boundaries of topologically associating domains (TADs) with TOP2B positioned externally and cohesin internally to the domain loop.

Conclusions: TOP2B is positioned to solve topological problems at diverse cis-regulatory elements and its occupancy is a highly ordered and prevalent feature of CTCF/cohesin binding sites that flank TADs.

Keywords: BioID; CTCF; ChIP-exo; ChIP-seq; Cohesin; Comparative genomics; DNA supercoiling; Genome organization; Hi-C; Proteomics; Topoisomerase II beta; Topological associated domains.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Binding Sites
  • CCCTC-Binding Factor
  • Cell Cycle Proteins / genetics*
  • Cell Cycle Proteins / metabolism
  • Chromatin / genetics
  • Chromatin Immunoprecipitation
  • Chromosomal Proteins, Non-Histone / genetics*
  • Chromosomal Proteins, Non-Histone / metabolism
  • Chromosomes
  • DNA Topoisomerases, Type II / genetics*
  • DNA Topoisomerases, Type II / metabolism
  • DNA, Ribosomal / genetics
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism
  • Genome
  • Humans
  • Mice
  • Poly-ADP-Ribose Binding Proteins
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Interaction Maps / genetics*
  • Proteomics
  • Repressor Proteins / genetics*
  • Repressor Proteins / metabolism
  • Transcription, Genetic*

Substances

  • CCCTC-Binding Factor
  • CTCF protein, human
  • Cell Cycle Proteins
  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • Ctcf protein, mouse
  • DNA, Ribosomal
  • DNA-Binding Proteins
  • Poly-ADP-Ribose Binding Proteins
  • Repressor Proteins
  • cohesins
  • DNA Topoisomerases, Type II
  • TOP2B protein, human
  • Top2b protein, mouse