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

Abstract

How steroid hormone receptors (SHRs) orchestrate transcriptional activity remains only partly understood. Upon activation, SHRs bind the genome and recruit their co-regulators, crucial to induce gene expression. However, it remains unknown which components of the SHR-recruited co-regulator complex are essential to drive transcription following hormonal stimuli. Through a FACS-based genome-wide CRISPR screen, we comprehensively dissected the Glucocorticoid Receptor (GR) co-regulatory complex involved in gene-target regulation. We describe a novel functional cross-talk between PAXIP1 and the cohesin subunit STAG2 that is critical for regulation of gene expression by GR. Without altering the GR cistrome, PAXIP1 and STAG2 depletion alter the GR transcriptome, by impairing the recruitment of 3D-genome organization proteins to the GR complex. Importantly, we demonstrate that PAXIP1 is required for stability of cohesin on the genome, its localization to GR-occupied sites, and maintenance of enhancer-promoter interactions. Moreover, in lung cancer, where GR acts as tumor suppressor, PAXIP1/STAG2 loss enhances GR-mediated tumor suppressor activity by modifying local chromatin interactions. All together, we introduce PAXIP1 and STAG2 as novel co-regulators of GR, required to maintain 3D-genome architecture and drive the GR transcriptional programme following hormonal stimuli.

CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin

“…Thus, PAXIP1-PAGR1 may act as a direct chromatin acceptor for the cohesin loading reaction, as has been suggested for several other chromatin binding proteins 29,30,35,[75][76][77] , or stabilize cohesin on chromatin. This is further supported by FRAP analysis of SMC1-EGFP, which revealed reduced cohesin stability on chromatin in PAXIP1-KO cells 74 . This may involve the FDF motif that we identified in PAGR1, which may antagonize WAPL similar as has been shown for CTCF 28 and MCM3 61 .…”

“…Since PAXIP1 binding is also enriched at promoters and enhancers and is necessary for long-range enhancer-promotor contacts 45, 65, 71 , a function that is shared with cohesin 36, 72, 73 , PAXIP1 may facilitate enhancer-promotor contacts by cohesin mediated loop formation. In line with this model, cohesin binding to glucocorticoid receptor (GR) binding sites depends on PAXIP1, resulting in a joint regulation of hormone-induced transcriptional activity via chromosome folding, described in the accompanying paper 74 . Together, a picture emerges in which PAXIP1 facilitates chromatin binding of cohesin to regulate enhancer-promoter interactions, to control cell-type specific and context-responsive gene expression patterns.…”

“…Our findings suggest that human KMT2C and KMT2D are not involved in promoting cohesin occupancy on chromatin, although we cannot exclude that incomplete depletions preclude a detectable effect. Of note, PAXIP1 functions together with cohesin in glucocorticoid receptor activity apparently independent from KMT2D/C 74 , indeed pointing at a function of PAXIP1-PAGR1 separate from KMT2C/D in cohesin regulation. Nevertheless, two PAXIP1 mutants previously described to abrogate KMT2C/D binding 46, 55 were unable to restore chromatin-bound cohesin, suggesting that BRCT5-6 has roles other than KMT2C/D binding.…”

Inhibiting the Glucocorticoid Receptor to Enhance Chemotherapy Response

“…3 These sites, frequently situated distal to their associated genes, effectively determine the target gene repertoire of GR. 4 Assisted by proteins that shape genome structure, glucocorticoid response element-bound GR is directed toward target genes where it recruits various cofactors, thereby finely regulating gene transcription 5 (Fig 1). This process is crucial for the influence of glucocorticoids on various cellular functions, including cell proliferation, differentiation, apoptosis, and angiogenesis, which have an integral role in cancer biology.…”