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...