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Cohesin-mediated loop anchors confine the location of human replication origins

ABSTRACT: DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability. It is currently unknown how the location of replication origins is determined in the human genome. Here, we dissect the role for topologically associating domains (TADs), subTADs, and loops in the positioning of replication initiation zones (IZs). We stratify TADs/subTADs by the presence of corner-dots indicative of loops and the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently-oriented CTCF motifs. By contrast, low-efficiency IZs localize to weak boundaries devoid of CTCF and corner-dots. Upon ablation of cohesin-mediated loop extrusion in G1, high-efficiency IZs become diffuse and de-localized specifically at boundaries with complex CTCF motif orientation. Moreover, G1 knock-down of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with loss and gain of IZs, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically-encoded TAD/subTAD boundaries is an essential determinant of the precise location of replication initiation in human S phase.

ORGANISM(S): Homo sapiens

PROVIDER: GSE190117 | GEO | 2021/12/05

REPOSITORIES: GEO

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