Formation of Chromosomal Domains by Loop Extrusion

Abstract

Summary Topologically Associating Domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes, yet mechanisms of TAD formation remain unclear. Here we propose that loop extrusion underlies TAD formation. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops, but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. Using polymer simulations, we show that this model produces TADs and other fine features of Hi-C data. Contrary to typical illustrations, each TAD consists of multiple loops dynamically formed through extrusion, rather than a single static loop. Loop extrusion both explains diverse experimental observations, including the preferential orientation of CTCF motifs, enrichments of architectural proteins at TAD boundaries, and boundary deletion experiments, and makes specific predictions for depletion of CTCF versus cohesin. Finally, loop extrusion has additional, potentially far-ranging, consequences for processes including enhancer-promoter interactions, orientation-specific chromosomal looping, and compaction of mitotic chromosomes.

Two independent modes of chromatin organization revealed by cohesin removal

“…Insulation and directionality of the contact footprint of CTCF sites also disappear upon Nipbl deletion (Extended Data Figure 6). However, we observe no effect of Nipbl deletion on CTCF occupancy, demonstrating that the loss of TADs and CTCF contact in ΔNipbl is not due to loss or changes in CTCF occupancy (Extended Data Figure 3), This further strengthens the very distinct roles of CTCF and cohesin in shaping chromosome architecture 14,18 .…”

“…Cohesin and CTCF co-localize at TAD boundaries and the bases of Hi-C peaks 7,12 , but their roles are not fully defined. The recently proposed loop extrusion model 14,15 yields predictions that are consistent with experiments. In this model, TADs emerge from the progressive extrusion of chromatin loops by a protein complex (e.g.…”

“…2h). Together, these analyses and the observed effects of Nipbl deletion indicate that cohesin plays a central role in the local compaction of chromosomes, and support that this effect is mediated by the production of dynamic populations of extruded chromatin loops between boundary elements, which forms TAD and corner peak patterns in interphase Hi-C maps 14,15 .…”

“…This major reorganization of chromatin architecture is also reflected in the curves of contact frequency P(s) as a function of genomic distance s 3,29 . In control samples, like in other mammalian cells 14,15 , P(s) curve has two regimes: a more shallow decay for s<200Kb ( P(s)~s −0.7 ), and a steeper scaling for 200Kb < s < 3Mb ( P(s)~s −1.2 ). Loss of chromatin-associated cohesin leads to disappearance of the first regime, producing a single decay of contact probability across the whole range (Fig.…”

“…To investigate the impact of NIPBL depletion on TADs and associated peaks in the context of loop extrusion, we performed simulations that couple the 1D dynamics of loop extrusion by LEFs with 3D polymer dynamics, as previously 14 . We then generated contact maps and calculated P(s), also as previously described.…”