Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus

Abstract

Cohesin-mediated sister chromatid cohesion is essential for chromosome segregation and post-replicative DNA repair1,2. In addition, evidence from model organisms3-6 and from human genetics7 suggests that cohesin plays a role in the control of gene expression8,9. This non-canonical role has recently been rationalized by the findings that mammalian cohesin complexes are recruited to a subset of DNase I hypersensitive sites (HSS) and to conserved non-coding sequences by the DNA binding protein CTCF10-13. CTCF functions at insulators (which control interactions between enhancers and promoters) and at boundary elements (which demarcate regions of distinct chromatin structure)14, and cohesin contributes to CTCF’s enhancer blocking activity10,11. The underlying mechanisms remain unknown, and the full spectrum of cohesin functions remains to be elucidated. Here we show that cohesin forms the topological and mechanistic basis for cell type-specific long-range chromosomal interactions in cis at the developmentally regulated cytokine locus IFNG. Hence, cohesin’s ability to constrain chromosome topology is utilized not only for the purpose of sister chromatid cohesion1,2, but also to dynamically define the spatial conformation of specific loci. This novel aspect of cohesin function is likely of importance to normal development3-6 and to disease7.

Cell type specificity of chromatin organization mediated by CTCF and cohesin

“…Thus, our data suggest the importance of both cohesin and CTCF to long-range interactions between and among CTCF sites. In contrast, two CTCF/cohesin site looping interactions at the IFNG cytokine locus were reduced after Rad21 protein reduction even though CTCF remained bound (9).…”

“…Similarly, CTCF binding and chromatin organization is necessary for activation of IFNG during T-cell differentiation (9). However, in the mouse β-globin locus, CTCF binding at the flanking HS5 and 3′ HS1 sites results in loop formation, but the loop does not appear to be required for normal globin gene regulation in erythroid progenitor cells (10).…”

CTCF: the protein, the binding partners, the binding sites and their chromatin loops

“…Indeed, at the H19-Igf2 locus, cohesin was shown to be important for CTCF-mediated chromatin loop formation and proper regulation of Igf2 transcription [44]. Similarly, at the interferon gamma (IFNG) locus, depletion of cohesin was found to disrupt chromatin loops between regulatory DNA sequences and cause a reduction in IFNG expression [45]. Also at the b-globin locus cohesin has been implicated in chromatin looping, not only between the flanking CTCF sites but also between the LCR enhancer region and the downstream b-globin target genes [46].…”

DNA entry, exit and second DNA capture by cohesin: insights from biochemical experiments

“…Bacterial SMC complexes also ensure proper chromosome distribution to daughter cells during rapid cell proliferation. In addition to its mitotic roles, cohesin contributes to interphase chromosome organization and is thought to modulate the interaction of promoters with cognate enhancer elements [8,9]. At the molecular level, cohesin is thought to establish DNA-DNA interactions between sister chromatids and/or different stretches of DNA segments on the same chromosome.…”

“…Two, non-mutually exclusive models have been proposed: cohesin stochastically tethers different DNA segments on the same chromosome (stochastic pairwise interactions) or the ring generates a chromatin loop by extruding a chromatin fiber via a passive or active mechanism (loop extrusions) [76,77]. Cohesin often establishes chromatin loops between enhancers and promoters [8]. Recent high resolution Hi-C studies have also found that cohesin makes contributions to interactions between enhancers and along gene bodies [78,79].…”