The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries

Abstract

Summary BET (bromodomain and extraterminal motif) proteins are pharmacologic targets for the treatment of diverse diseases, yet the roles of individual BET family members remain unclear. We find that BRD2 but not BRD4 colocalizes with the architectural/insulator protein CCCTC-binding factor (CTCF) genome-wide. CTCF recruits BRD2 to co-bound sites, whereas BRD2 is dispensable for CTCF occupancy. Disruption of a CTCF/BRD2-occupied element positioned between two unrelated genes enables regulatory influence to spread from one gene to another, suggesting that CTCF and BRD2 form a transcriptional boundary. Accordingly, single molecule mRNA FISH reveals that upon site-specific CTCF disruption or BRD2 depletion, expression of the two genes becomes increasingly correlated. HiC shows that BRD2 depletion weakens boundaries co-occupied by CTCF and BRD2, but not those that lack BRD2. These findings indicate that BRD2 supports boundary activity and raise the possibility that pharmacologic BET inhibitors can influence gene expression in part by perturbing domain boundary function.

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

“…On the other hand, YY1-, ELK1- and E2F-binding motifs were enriched in H4K5acK8ac peaks with BRD2 binding (Figure 6(C), right). Consistent with previous reports that BRD2 colocalizes with CTCF [34,35], our HOMER motif enrichment analysis shows higher enrichment of CTCF motif with BRD2 peaks (Fig. S10A).…”

“…Since ZNF281 is involved in inducing epithelial–mesenchymal transition (EMT) and promotes metastatis [52], anti-oncogenic effects of JQ1 on H23 cells may partly be due to downregulation of ZNF281, presumably through dissociation of BRD2, which may lead to disrupted EMT in lung cancer. Interestingly, a recent study showed that BRD2 activates expression of genes involved in EMT induction, whereas BRD3 and BRD4 exert opposite functions [53], supporting distinct roles of BRD2 among the somatic BET proteins [34,35,54,55]. Other TFs identified by MARA but not discussed here may be involved in the BRD2-associated transcriptional regulation.…”

The Role of Bromodomain and Extraterminal Motif (BET) Proteins in Chromatin Structure

“…In mammalian cells we recently observed that the BET protein BRD2 occupies sites bound by the architectural/ insulator protein CTCF in erythroid cells (Hsu et al 2017). This is in line with findings from another recent study showing significant overlap between BRD2 and CTCF binding in Th17 cells (Cheung et al 2017) and in the Kaposi's sarcoma-associated herpesvirus genome , indicating that the relationship between BRD2 and CTCF is a widespread phenomenon.…”

“…We observed that BRD3 also binds to CTCF sites, consistent with previous work from our laboratory demonstrating partial functional redundancy between BRD2 and BRD3 in erythroid maturation (Stonestrom et al 2015). BRD4 did not similarly localize to CTCF sites in either erythroid (Hsu et al 2017) or Th17 (Cheung et al 2017) cells, providing evidence for distinct roles of BET family members. We showed that mutation of a specific CTCF site using genome editing led to loss of both CTCF and BRD2 binding, whereas depletion of BRD2 appeared to have little effect on CTCF occupancy, indicating that CTCF recruits BRD2 to co-bound sites.…”

“…This is consistent with CTCF-dependent and -independent mechanisms of boundary formation. Notably, sustained BRD2 depletion in erythroid cells also led to increased contacts across chromatin domain boundaries, specifically at those boundaries occupied by BRD2 (Hsu et al 2017), suggesting that BRD2 may potentiate CTCF's ability to maintain domain border integrity. The effects of BRD2 depletion may be less pronounced compared to those observed upon CTCF depletion in other contexts, which might be due to compensatory mechanisms, perhaps mediated by BRD3, or reflect that CTCF likely functions with multiple cofactors to form or reinforce boundaries.…”