RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF

Abstract

Given our previous demonstration that RBPJ binds a methylated repressor element and regulates smooth muscle cell (SMC)-specific gene expression, we used genome-wide approaches to identify RBPJ binding regions in human aortic SMC and to assess RBPJ’s effects on chromatin structure and gene expression. RBPJ bound to consensus cis elements, but also to TCmGGGA sequences within Alu repeats that were less transcriptionally active as assessed by DNAse hypersensitivity, H3K9 acetylation, and Notch3 and RNA Pol II binding. Interestingly, RBPJ binding was frequently detected at the borders of open chromatin, and a large fraction of genes induced or repressed by RBPJ depletion were associated with this cluster of RBPJ binding sites. RBPJ binding dramatically co-localized with serum response factor (SRF) and RNA seq experiments in RBPJ- and SRF-depleted SMC demonstrated that these factors interact functionally to regulate the contraction and inflammatory gene programs that help define SMC phenotype. Finally, we showed that RBPJ bound preferentially to phased nucleosomes independent of active chromatin marks and to cis elements positioned at the beginning and middle of the nucleosome dyad. These novel findings add important insight into RBPJ’s role in chromatin structure and gene expression in SMC.

Distinct p63 and p73 Protein Interactions Predict Specific Functions in mRNA Splicing and Polyploidy Control in Epithelia

“…It is widely accepted that transcription is regulated by the interplay of the multiprotein complexes [ 61 , 62 , 63 , 64 , 65 ]. Moreover, due to the presence of dominant activators or repressors co-occupying DNA regulatory sites, functions of a particular transcription factor might be limited to a subset of its binding sites [ 61 , 64 , 66 , 67 , 68 ].…”

“…It is widely accepted that transcription is regulated by the interplay of the multiprotein complexes [ 61 , 62 , 63 , 64 , 65 ]. Moreover, due to the presence of dominant activators or repressors co-occupying DNA regulatory sites, functions of a particular transcription factor might be limited to a subset of its binding sites [ 61 , 64 , 66 , 67 , 68 ]. For the p53 transcription factors family, interactions with distinct proteins may skew the binding of p53, p63 and p73 isoforms towards different sites in the genome and determine their specific activities [ 14 , 21 , 43 , 63 , 69 , 70 , 71 ].…”

Synergistic Effects of Hyperandrogenemia and Obesogenic Western-style Diet on Transcription and DNA Methylation in Visceral Adipose Tissue of Nonhuman Primates

“…Moreover, our computational analysis showed that DMRs from the T + WSD group were enriched in TF binding motifs, supporting the regulatory role of DNA methylation in modulating TF binding affinities 78 . As an example, RBPJ has been shown to control the expression of notch signaling genes 79 and to bind chromatin in a methylation-dependent fashion 80,81 .…”

Transcriptional and posttranscriptional regulation of the SMC-selective blood pressure-associated gene, ARHGAP42

“…This binding interaction not only displaces transcriptional repressors that are bound to RBPJ in the absence of active Notch but also facilitates the recruitment of transcription activators such as mastermind-like transcriptional coactivator (MAML) and histone acetyl transferases. We and others have shown that RBPJ binds to a number of SMC-specific promoters (8,38,39,44), and in vivo evidence suggests that Notch/RBPJ signaling is required for SMC differentiation from multiple precursors (5,8,15,21). We also identified a consensus motif (CATTCC) for the TEAD factors that have been implicated in muscle-selective gene expression and are transcriptional mediators of the Hippo signaling pathway [see Fu et al (12) for review].…”