Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner

Abstract

Recent studies have provided strong evidence for a regulatory link among chromatin structure, histone modification, and splicing regulation. However, it is largely unknown how local histone modification patterns surrounding alternative exons are connected to differential alternative splicing outcomes. Here we show that splicing regulator Hu proteins can induce local histone hyperacetylation by association with their target sequences on the pre-mRNA surrounding alternative exons of two different genes. In both primary and mouse embryonic stem cell-derived neurons, histone hyperacetylation leads to an increased local transcriptional elongation rate and decreased inclusion of these exons. Furthermore, we demonstrate that Hu proteins interact with histone deacetylase 2 and inhibit its deacetylation activity. We propose that splicing regulators may actively modulate chromatin structure when recruited to their target RNA sequences cotranscriptionally. This "reaching back" interaction with chromatin provides a means to ensure accurate and efficient regulation of alternative splicing.histone acetylation | neurofibromatosis type 1 | Fas R ecent genome-wide transcriptome analysis has demonstrated that more than 95% of human genes undergo alternative splicing to produce multiple proteins from one gene (1-4). Most of these alternative splicing events lead to coding differences and occur in a cell type-and/or developmental stage-specific manner (3, 5), underscoring the essential role of alternative splicing in gene expression control. In addition to the well-established role of RNA-binding proteins in the regulation of pre-mRNA alternative splicing (6, 7), recent studies have revealed a role for chromatin-associated proteins and the transcription machinery in splicing regulation (8)(9)(10).A recent study of large human genes demonstrated that premRNA splicing is cotranscriptional and occurs within 5-10 min of synthesis (11). The tight coupling of transcription and splicing predicts cross-talk between chromatin structure and splicing regulation. Indeed, several recent studies have documented a number of interesting links between chromatin features and exon behavior. First, a ChIP analysis indicated that a specific histone modification, trimethylation of lysine 36 of histone H3 (H3K36me3), differentially marks exons (12, 13). Remarkably, this histone mark appears to be associated more significantly with constitutive exons than with alternative exons (13). Second, a genome-wide analysis of nucleosome occupancy showed that nucleosomes are enriched in exons and are depleted in introns, suggesting that nucleosome position helps to distinguish introns from exons (12,(14)(15)(16)(17). Although these studies provide significant evidence for cross-talk between chromatin and splicing, the nature of the cross-talk remains largely unknown. Several studies support a model in which histone marks function to recruit basal spliceosomal factors or splicing regulators to ensure efficient splicing regulation. For example, the histone mark H3K4m...

A recently evolved class of alternative 3′-terminal exons involved in cell cycle regulation by topoisomerase inhibitors

“…5a-c). Consistently, genome-wide mapping of HuR-binding sites revealed its binding to many pre-mRNAs, and HuR can regulate both splicing and polyA site use [37][38][39][40][41][42] . The configuration of HuR-binding sites in CENPN exon 12, with two centrally located strong binding sites and additional (potentially weaker) binding sites along the exon (Supplementary Fig.…”

“…The second factor, HuR/ELAVL1, is an RNA-binding protein that has long been involved in the regulation of cytoplasmic mRNA stability and translation in response to DNA damage (reviewed by Gorospe 36 ) and more recently in pre-mRNA splicing and polyA site use in the nucleus [37][38][39][40][41][42] . As expected from the anti-correlation data, the depletion of HuR using a specific siRNA in MCF-7 cells (Fig.…”

Histone hyperacetylation and exon skipping: a calcium-mediated dynamic regulation in cardiomyocytes

“…21 A previous study from our own laboratory also provided a link between localized histone hyperacetylation and exon skipping, although in this case, the histone hyperacetylation depends on a splicing regulator. 25 Taken together, histone hyperacetylation induced through different mechanisms, and occurring either locally or globally throughout the gene body, can lead to exon skipping.…”

“…Using an antibody that recognizes the elongating RNAPII in this assay, we showed that RNAPII accumulation along the gene body of Nf1 and Ktn1 is approximately 3-fold lower in depolarized than in control cardiomyocytes, consistent with faster RNAPII elongation rate in depolarized cells. 11 Second, using an established procedure, 24,25 we directly measured RNA-PII transcriptional elongation rate on several genes comparing control and depolarized cardiomyocytes. Our results indicate an expected significant increase of transcriptional elongation rate on Nf1 and Ktn1, but not on Capzb, in cardiomyocytes after depolarization.…”

The transcriptional co-activator SND1 is a novel regulator of alternative splicing in prostate cancer cells

“…Labeled pre-mRNA was immunoprecipitated with 1 mg of antiBrdU antibody (Becton Dickinson) and isolated as described. 62 …”