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 across dividing cells in metazoans. It is currently unknown how the location of replication origins and the timing of their activation is determined in the human genome. Here, we dissect the role for G1 phase topologically associating domains (TADs), subTADs, and loops in the activation of replication initiation zones (IZs). We identify twelve subtypes of self-interacting chromatin domains distinguished by their degree of nesting, the presence of corner dot structures indicative of loops, and their co-localization with A/B compartments. Early replicating IZs localize to boundaries of nested corner-dot TAD/subTADs anchored by high density arrays of co-occupied CTCF+cohesin binding sites with divergently oriented motifs. By contrast, late replicating IZs localize to weak TADs/subTAD boundaries devoid of corner dots and most often anchored by singlet CTCF+cohesin sites. Upon global knock-down of cohesin-mediated loops in G1, early wave focal IZs replicate later in S phase and convert to diffuse placement along the genome. Moreover, IZs in mid-late S phase are delayed to the final minutes before entry into G2 when cohesin-mediated dot-less boundaries are ablated. We also delete a specific loop anchor and observe a sharp local delay of an early wave IZ to replication in late S phase. Our data demonstrate that cohesin-mediated loops at genetically-encoded TAD/subTAD boundaries in G1 phase are an essential determinant of the precise genomic placement of human replication origins in S phase.

The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation

“…7F ). Nuclear confined regions have been proposed to arise from highly interacting DNA loops, such as TADs, where a high concentration of TFs promotes dynamic transcriptional events and chromatin intermingling ( 3 , 39 ). By the formation of these confined regions through their IDRs, TFs could amplify transcriptional output, perhaps by increasing the local concentration of transcriptional regulators at specific chromatin sites ( 36 ).…”

Mammalian DNA Replication Timing

“…One hint at how this could occur comes from recent evidence suggesting that the replicative helicase MCM2-7 complex, which designates sites of initiation (discussed below), can impede cohesin extrusion (Dequeker et al 2020) and could thus influence the positions of boundaries. Other evidence suggests that cohesin extrusion confines the replicative helicase to domain boundaries (Emerson et al 2021). Clearly there is much work to be done to understand the mechanisms linking replication and genome architecture but new tools to manipulate the replication program (Klein et al 2019;Sima et al 2019) should reveal new insights in the near future.…”

Remodeling and compaction of the inactive X is regulated byXistduring female B cell activation

“…Replicates for each condition were merged. We balanced the merged contact matrices using Knight-Ruiz balancing as previously described 79,80 80,82,83 . As previously described, we filtered sparse regions 83 .…”

“…Replicates for each condition were merged. We balanced the merged contact matrices using Knight-Ruiz balancing as previously described 79,80…”

“…For each balanced matrix, we performed simple scalar normalization, where a simple scalar size factor for each pixel was calculated based on the genomic distance between pairs of bins81 . Mb overlap between adjacent regions and 3 Mb regions with 2 Mb overlap80,82,83 . As previously described, we filtered sparse regions83 .…”