A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation

Abstract

Histone H3 Lys4 (H3K4) methylation is a chromatin feature enriched at gene -regulatory sequences such as promoters and enhancers. Here we identify an evolutionarily conserved factor, BRWD2/PHIP, which colocalizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Biochemical analysis of BRWD2 demonstrated an association with the Cullin-4-RING ubiquitin E3 ligase-4 (CRL4) complex, nucleosomes, and chromatin remodelers. BRWD2/PHIP binds directly to H3K4 methylation through a previously unidentified chromatin-binding module related to Royal Family Tudor domains, which we named the CryptoTudor domain. Using CRISPR-Cas9 genetic knockouts, we demonstrate that COMPASS H3K4 methyltransferase family members differentially regulate BRWD2/PHIP chromatin occupancy. Finally, we demonstrate that depletion of the single homolog dBRWD3 results in altered gene expression and aberrant patterns of histone H3 Lys27 acetylation at enhancers and promoters, suggesting a cross-talk between these chromatin modifications and transcription through the BRWD protein family.

Epigenetic control of transcriptional regulation in pluripotency and early differentiation

“…Thus, MLL1-dependent H3K4 methylation appears to be required for maintenance of the EpiSC state. Another recent study found that MLL2 and MLL4 deletion in ESCs results in loss of H3K4me1 at partially overlapping sets of distal regulatory elements, suggesting redundant and non-redundant functions of these MLL proteins (Morgan et al, 2017). A careful dissection of the relative contributions of MLL proteins to H3K4me1 and target gene transcription at different classes of enhancers and promoters in well-defined pluripotency conditions is necessary to clarify the role of MLL proteins and H3K4me1 in ESC transcriptional regulation.…”

PHIP as a therapeutic target for driver-negative subtypes of melanoma, breast, and lung cancer

“…The PHIP bromodomains do not share significant sequence homology with that of BRD2-4 (18,26), suggesting that novel small molecule inhibitors will need to be identified to most effectively target PHIP. Although a recent study has described a domain in the PHIP protein important for interacting with methylated histones (27), whether the PHIP bromodomains are functional has not been conclusively demonstrated. Our studies, using immunofluorescence, confocal microscopy, and coimmunoprecipitation, showed not only a colocalization but also a physical interaction between PHIP and H4K91ac, thereby indicating a role for the PHIP protein in chromatin remodeling.…”

Enhancer-associated H3K4 methylation safeguards in vitro germline competence

“…6f), which could perhaps be attributed to the compensatory activity of other histone methyltransferases (e.g. MLL1/KMT2A 72 , MLL2/KMT2B 73,74 ). Additionally, and consistent with previous work 32 , RNA-seq experiments performed in ESC, EpiLC and EpiSC revealed minor gene expression changes in dCD cells, with PGCLC genes being slightly down or upregulated in dCD ESC and EpiLC, respectively ( Supplementary Fig.…”