RBFox2 Binds Nascent RNA to Globally Regulate Polycomb Complex 2 Targeting in Mammalian Genomes

Abstract

SUMMARY Increasing evidence suggests that diverse RNA binding proteins (RBPs) interact with regulatory RNAs to regulate transcription. RBFox2 is a well-characterized pre-mRNA splicing regulator, but we now encounter an unexpected paradigm where depletion of this RBP induces widespread increase in nascent RNA production in diverse cell types. Chromatin immunoprecipitation sequencing (ChIP-seq) reveals extensive interaction of RBFox2 with chromatin in a nascent RNA-dependent manner. Bayesian network analysis connects RBFox2 to Polycomb complex 2 (PRC2) and H3K27me3, and biochemical experiments demonstrate the ability of RBFox2 to directly interact with PRC2. Strikingly, RBFox2 inactivation eradicates PRC2 targeting on the majority of bivalent gene promoters and leads to transcriptional de-repression. Together, these findings uncover a mechanism underlying the enigmatic association of PRC2 with numerous active genes, highlight the importance of gene body sequences to gauge transcriptional output, and suggest nascent RNAs as critical signals for transcriptional feedback control to maintain homeostatic gene expression in mammalian genomes.

A Large-Scale Binding and Functional Map of Human RNA Binding Proteins

“…Collectively, even this moderately sized set of RBPs occupied ~30% of all DNase 1 3 hypersensitive or open chromatin regions and ~70% of annotated gene promoters, which was similar between the two cell types, suggesting broad involvement of RBPs in chromatin activities in the human genome. These data provide a foundation for future investigation of direct roles of specific RBPs in transcriptional control, exemplified by recent studies on SR proteins 21 and RBFOX2 36 .…”

Splicing Activation by Rbfox Requires Self-Aggregation through Its Tyrosine-Rich Domain

“…This is in keeping with the finding that the tyrosine-rich domain causes the enrichment of the protein in nuclear speckles. The Rbfox2 CTD was also found to bind the Polycomb Repressive Complex 2 and to affect transcriptional changes in cardiomyocytes (Wei et al, 2016). We have not found PRC2 in Rbfox/LASR complexes.…”

Emerging roles of RNA‐binding proteins in diabetes and their therapeutic potential in diabetic complications

“…RBFOX2 belongs to a family of RBPs that include RBFOX1 and RBFOX3. Rbfox proteins bind the (U)GCAUG motif in RNA and regulate AS (Jangi, Boutz, Paul, & Sharp, ; Lovci et al, ; Singh et al, ; Wei et al, , ; Weyn‐Vanhentenryck et al, ; Yeo et al, ). While RBFOX1 and RBFOX2 are widely expressed in different tissues, RBFOX3 is neuron specific.…”

“…Recent studies defined new functions for RBFOX2 in regulating transcription via interactions with the polycomb complex (Wei et al, ) and in microRNA processing (Chen et al, ). Owing to its importance, genome‐wide RNA targets of RBFOX2 have been identified using cross‐linking immunoprecipitation (CLIP)‐sequencing in several different cell types (Jangi et al, ; Lovci et al, ; Singh et al, ; Wei et al, , ; Weyn‐Vanhentenryck et al, ; Yeo et al, ). RBFOX2 is a master regulator of posttranscriptional gene expression as it controls expression levels of other RBPs via AS‐dependent nonsense‐mediated mRNA decay (Jangi et al, ; Lovci et al, ; Yeo et al, ).…”