The Cornelia de Lange Syndrome-associated factor NIPBL interacts with BRD4 ET domain for transcription control of a common set of genes

Abstract

Mutations in NIPBL are the major cause of Cornelia de Lange Syndrome (CdLS). NIPBL is the cohesin-loading factor and has recently been associated with the BET (bromodomains and extra-terminal (ET) domain) proteins BRD2 and BRD4. Related to this, a CdLS-like phenotype has been described associated to BRD4 mutations. Here, we show direct interaction of NIPBL with different BET members in yeast, and selective interaction with BRD4 in cells, being the ET domain involved in the interaction. To understand the relationship between NIPBL and BET proteins, we have performed RNA-Seq expression analysis following depletion of the different proteins. Results indicate that genes regulated by NIPBL largely overlap with those regulated by BRD4 but not with those regulated by BRD2. ChIP-Seq analysis indicates preferential NIPBL occupancy at promoters, and knockdown experiments show mutual stabilization of NIPBL and BRD4 on co-regulated promoters. Moreover, human fibroblasts from CdLS probands with mutations in NIPBL show reduced BRD4 at co-occupied promoters. Functional analysis in vivo, using mutants of Drosophila melanogaster , confirmed the genetic interaction between Nipped-B and fs(1)h , the orthologs of human NIPBL and BRD4 , respectively. Thus, we provide evidence for NIPBL and BRD4 cooperation in transcriptional regulation, which should contribute to explain the recently observed CdLS-like phenotype associated with BRD4 mutations.

Dicer promotes genome stability via the bromodomain transcriptional co-activator Brd4

“…We further detected a substantial reduction of RAD21 at both the major and minor satellite loci in Brd4 BD2-/- Dicer1 -/- double mutants (Fig. S9C) consistent with recent findings that BRD4 interacts directly with RAD21 in human cells (53) and in D. melanogaster (54) as well as with NIPBL in humans (53, 55) . RAD21 encodes cohesin, while NIPBL encodes the cohesin loading complex, which is responsible for proper chromosome cohesion and subsequent segregation at mitosis.…”

BETting on a Transcriptional Deficit as the Main Cause for Cornelia de Lange Syndrome

“…Since SMC1A, SMC3 and RAD21 are core components of the cohesin complex and NIPBL best known facet was to function as a regulatory component involved in its loading (Dorsett, 2009), it was assumed that genetic variants accounted for an altered cohesin function, which justified the original designation of CdLS as a "cohesinopathy". Some of the newly identified mutations affect genes coding for proteins that can also be related to cohesin function: HDAC8 mediates the regulatory deacetylation of SMC3 (Deardorff et al, 2012a); BRD4 interacts with NIPBL (Olley et al, 2018;Luna-Peláez et al, 2019) and cohesin (Wong et al, 2014); MAU2 is a partner of NIPBL and EP300 interacts with cohesin and is required for its proper loading after mitosis (Wong et al, 2014). However, for most of the recently identified new variants, no functional relation with cohesin can be established so far, but all of them can be somehow related to a transcriptional function.…”

Chromatinopathies: A focus on Cornelia de Lange syndrome

“…Recently, BRD4 variants have been reported in patients with clinical features of CdLS . Recently, a study reported overlap of gene‐expression regulation between NIPBL and BRD4, consequence of promoters co‐occupancy . Both BRD4 and cohesin are known to bind super‐enhancer regions, controlling cell fate decision, hence a role of super‐enhancers function has been postulated in the pathogenesis of CdLS.…”