Abstract
BackgroundType 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.ResultsOur 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.ConclusionsTOP2B 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1043-8) contains supplementary material, which is available to authorized users.
Highlights
Type II DNA topoisomerases (TOP2) regulate DNA topology by generating transient double stranded breaks during replication and transcription
Using ChIP-seq and ChIP-exo in combination with high-throughput chromosome conformation capture (Hi-C) data, we find that TOP2B interacts with CTCF and the cohesin complex with a distinct spatial organization at the borders of long-range chromosomal domain structures
We performed BioID in HeLa cells with a TOP2B bait protein tagged with a N-terminal BirA*-FLAG tag (n = 6)
Summary
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. The type II topoisomerase (TOP2) enzymes resolve DNA topology problems in core biological processes such as transcription, replication, recombination, DNA repair, chromatin remodeling, chromosome condensation, and segregation [1,2,3]. TOP2 enzymes catalyze and rejoin transient DNA double-stranded breaks (DSB) by allowing one of the duplex DNA strands to pass through the other [1,2,3]. TOP2A and TOP2B are not functionally redundant despite their structural and catalytic similarities [6]. TOP2B is ubiquitously expressed and is upregulated during cellular differentiation [7]
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