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

Abstract

The cohesin complex is central to chromatin looping, but mechanisms by which these long-range chromatin interactions are formed and persist remain unclear. We demonstrate that interactions between a transcription factor (TF) and the cohesin loader NIPBL regulate enhancer-dependent gene activity. Using mass spectrometry, genome mapping, and single-molecule tracking methods, we demonstrate that the glucocorticoid (GC) receptor (GR) interacts with NIPBL and the cohesin complex at the chromatin level, promoting loop extrusion and long-range gene regulation. Real-time single-molecule experiments show that loss of cohesin markedly diminishes the concentration of TF molecules at specific nuclear confinement sites, increasing TF local concentration and promoting gene regulation. Last, patient-derived acute myeloid leukemia cells harboring cohesin mutations exhibit a reduced response to GCs, suggesting that the GR-NIPBL-cohesin interaction is defective in these patients, resulting in poor response to GC treatment.

Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1

“…6 ). Surprisingly, we found that cohesin depletion, but not CTCF depletion, significantly reduces YY1 chromatin binding and slows down its target search time from 28 s to 61 s. A similar effect was also observed in SOX2 and KLF4 in the present study, as well as independently in glucocorticoid receptors by another group 91 . Furthermore, a study using high-throughput ChIP-seq analysis suggested that cohesin is critical to promote TF rebinding after mitosis 92 .…”

Enhancer-promoter contact formation requires RNAPII and antagonizes loop extrusion

“…Now, we document a comparable reduction in interphase nuclei upon RNAPII depletion, which is most apparent at enhancers-promoter loops. This is in line with the binding of cohesin loaders at gene promoters (Busslinger et al, 2017, although the specificity of some of this data is now debated; Preprint: Banigan et al, 2022); with the fact that the loader NIPBL and unloader WAPL co-purify with RNAPII complexes (Zhang et al, 2021); as well as with recent work pointing to enhancers as cohesin-loading sites for the formation of 3D interactions (Liu et al, 2021a;Zhu et al, 2021;Rinaldi et al, 2022;Rinzema et al, 2022). Moreover, we should reconsider studies where pioneer transcription factors (like OCT4 and SOX2; Liu et al, 2021a) and chromatin remodelers (like SNF2h; Hakimi et al, 2002) affected the loading/unloading cycles of cohesin onto chromatin.…”

“…Notably, this accumulation is less if we consider an "alternative wt" model where cohesin can to bind all beads with equal probability, has a weak affinity with RNAPII, but is not allowed to co-bind promoters with it. This skews loading in favor of enhancers (Figure 4C and as suggested by recent studies; Zhu et al, 2021;Rinaldi et al, 2022;Rinzema et al, 2022). In this "wt-alt" model (Table S2), we also see increased cohesin presence and loop formation at the intragenic CTCF (Figure 4B; contact map not shown), which does not agree with our Micro-C data.…”

PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription

“…Moreover, GR activation increases both the number and intensity of enhancer-promoter interactions of their target genes upon hormonal stimulation 20 . GR was recently described to interact with NIBL, which is responsible for cohesin loading onto DNA, localization of cohesin to GR-bound sites, and promotion of long-range genomic interactions 18 .…”

“…Once SHRs occupy their cognate regulatory elements, a coordinated recruitment of co-regulators occurs, including chromatin remodeling factors, mediator complex, histone modifiers including histone lysine (de)-methyl transferases (KMT/KMDs), histone acetyltransferases (HATs) and ultimately RNA polymerase II (RNAPII) to drive gene transcription [11][12][13][14][15][16][17] . Altogether, SHR activation ultimately results in a large-scale transcriptional complex that loops towards targeting promoters to regulate gene expression, relying on 3D genome architectural proteins, such as the cohesin complex [18][19][20] . As a result, SHR and their interactors, together with the transcriptional machinery and 3D-genome organization proteins converge to either induce or repress specific target genes 12,17,21,22 .…”