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

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.

journal_name

Genome Biol

journal_title

Genome biology

authors

Uusküla-Reimand L,Hou H,Samavarchi-Tehrani P,Rudan MV,Liang M,Medina-Rivera A,Mohammed H,Schmidt D,Schwalie P,Young EJ,Reimand J,Hadjur S,Gingras AC,Wilson MD

doi

10.1186/s13059-016-1043-8

subject

Has Abstract

pub_date

2016-08-31 00:00:00

pages

182

issue

1

eissn

1474-7596

issn

1474-760X

pii

10.1186/s13059-016-1043-8

journal_volume

17

pub_type

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