Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans

Abstract

Condensins are molecular motors that compact DNA for chromosome segregation and gene regulation. In vitro experiments have begun to elucidate the mechanics of condensin function but how condensin loading and translocation along DNA controls eukaryotic chromosome structure in vivo remains poorly understood. To address this question, we took advantage of a specialized condensin, which organizes the 3D conformation of X chromosomes to mediate dosage compensation (DC) in C. elegans. Condensin DC is recruited and spreads from a small number of recruitment elements on the X chromosome (rex). We found that ectopic insertion of rex sites on an autosome leads to bidirectional spreading of the complex over hundreds of kilobases. On the X chromosome, strong rex sites contain multiple copies of a 12-bp sequence motif and act as TAD borders. Inserting a strong rex and ectopically recruiting the complex on the X chromosome or an autosome creates a loop-anchored TAD. Unlike the CTCF system, which controls TAD formation by cohesin, direction of the 12-bp motif does not control the specificity of loops. In an X;V fusion chromosome, condensin DC linearly spreads into V and increases 3D DNA contacts, but fails to form TADs in the absence of rex sites. Finally, we provide in vivo evidence for the loop extrusion hypothesis by targeting multiple dCas9-Suntag complexes to an X chromosome repeat region. Consistent with linear translocation along DNA, condensin DC accumulates at the block site. Together, our results support a model whereby strong rex sites act as insulation elements through recruitment and bidirectional spreading of condensin DC molecules and form loop-anchored TADs.

Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells

“…These data support a model in which multiple condensins bind L-CID boundaries and extrude loops in opposite directions, possibly through a version of the handcuff model in which an anti-parallel dimer of condensins is loaded at boundaries (Banigan and Mirny, 2020b). Alternately, multiple condensin monomers may be loaded at boundaries in random orientation, resulting in bi-directional extrusion, particularly when viewed at the cell population level (Banigan et al, 2020;Sebastian Jimenez et al, 2021). Further, although the CTCF-dependent mechanism of loop domain boundary formation present in mammalian cells is not conserved in yeast, stripes can be observed extending across multiple L-CID boundaries in yeast just as they do in mammals (Vian et al, 2018).…”

Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not

“…5). Interestingly, this diffusivity is observed for loops that form by extrusion, such as loops in human 2,24-27 and C. elegans 20,22,23 , but is not observed for loops that are believed to form by compartmentalization, such as the numerous Pc-associated loops observed in Drosophila 14,21,29,30 . Intriguingly, variations in diffusivity between different loops could explain differences in domains signal (See Supplemental Discussion, Fig.…”

“…S4H), and form by cohesin-mediated extrusion [24][25][26][27] . Similarly, the loops in C. elegans are bound by the SMC complex condensin and we previously suggested that they are formed by condensin-mediated loop extrusion 20,22,23 . Indeed, the interactions between loop-adjacent sequences are in further support of loop formation by extrusion in C. elegans.…”

“…Finally, we examined loops previously identified in C. elegans 20,22,23 . The loop decay was slower (c.a.…”

The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding

“…From there, the complex spreads linearly along chromatin, accumulating at active promoters, enhancers, and other accessible regulatory sites [12,13]. Condensin DC recruitment and spreading regulate the compaction of the 3D structure of the X chromosomes [14][15][16][17][18].…”