The molecular mechanisms through which alternative splicing and histone modifications regulate gene expression are now understood in considerable detail. mechanisms through which DNA methylation and histones modifications modulate alternative splicing patterns. Here we review an emerging theme resulting from these studies: RNA-guided mechanisms integrating chromatin modification and splicing. Several groundbreaking papers reported that small noncoding RNAs affect alternative exon usage by targeting histone methyltransferase complexes to form localized facultative heterochromatin. More recent studies provided evidence that pre-messenger RNA itself can serve as a guide to enable precise alternative splicing regulation via local recruitment of histone-modifying enzymes and emerging evidence points to a similar role for long noncoding RNAs. An exciting challenge for the future is to understand the impact of local modulation of transcription elongation rates on the dynamic interplay between histone modifications alternative splicing and other processes occurring on chromatin. INTRODUCTION Alternative splicing is a versatile mechanism that explains both how the vast complexity of the human proteome is generated from a limited number of genes and serves as a key Tariquidar target for the regulation of gene expression (1-3). The advent of high-throughput technologies paved the way Tariquidar for genome-wide analyses indicating that transcripts from up to 95% of multiple exon-containing human genes undergo alternative splicing (4-6). This review will focus on the most common form of alternative splicing in mammals which involves differential selection of exons within primary RNA transcripts for inclusion in the mature mRNA (1). As the majority of the resulting isoforms are variably expressed at different times in development and/or in different cell and tissue types alternative splicing must be precisely and robustly regulated (4-8). The importance of pre-mRNA splicing in mediating proper temporal and spatial Tariquidar expression of the human genome is underscored by the large number of genetic disorders associated with alterations in this process. Extensive surveys of disease-causing mutations in human genes revealed that the primary effect in up to 50% of Ankrd1 the known examples is to disrupt constitutive splicing or perturb alternative splicing patterns (9-12). Removal of introns from pre-mRNAs is carried out by a large macromolecular machine known as the spliceosome which is comprised of five snRNAs and ～300 proteins (13). Counter to the original view that only the earliest events in spliceosome assembly (formation of the E-complex containing the U1 snRNP and U2AF) are targeted by regulatory mechanisms it is now understood that control over alternative splicing can be exerted at multiple later stages of the process including the transition from the pre-spliceosome containing the U1 and U2 snRNPs to the mature but pre-catalytic spliceosome [for comprehensive reviews see (8 14 Mammalian gene architecture in which exons comprise relatively small islands amidst a sea of intronic sequences necessitates an initial recognition process in which and (22-24). By correlating exon inclusion levels and nucleosome distribution patterns these studies suggested that nucleosome positioning defines exons at the chromatin level. Thus the similarity between the average size of a vertebrate exon 170 nt and a single nucleosome + associated linker DNA may not be coincidental (26). Given that nucleosomes serve as barriers to transcription it is not surprising Tariquidar that RNA polymerase II (Pol II) binding in metazoans is also higher on exons than introns (22 27 Presumably pausing of Pol II at exons allows more time for the splicing machinery to recognize and define exons. Consistent with this idea it has been found that polymerase density is higher on alternative exons than on constitutive exons (28-31). Interestingly for intron-containing genes in fission yeast nucleosomes also appear to be enriched on exons whereas Pol II preferentially accumulates over introns (32). This inverse distribution is nevertheless consistent with a role for polymerase speed in determining the locations.