Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast

To investigate these functional interdependencies, we determined Pol II occupancy across all genes using high-density tiling arrays. We also performed ChIP-chip on the same array platform to globally map histone H3 and its H3K36me3 modification, complemented by formaldehyde-assisted isolation of regulatory elements (FAIRE). Surprisingly, Pol II occupancy was higher in introns than in exons, and this difference was inversely correlated with gene expression levels at a global level. Moreover, introns showed distinct distributions of histone H3, H3K36me3 and FAIRE signals, similar to those at promoters and terminators. These distinct transcription and chromatin patterns of intronic regions were most pronounced in poorly expressed genes.Our findings suggest that Pol II accumulates at the 3' ends of introns, leading to substantial transcriptional delays in weakly transcribed genes. We propose that the global relationship between transcription, chromatin remodeling, and splicing may reflect differences in local nuclear environments, with highly expressed genes being associated with abundant processing factors that promote effective intron splicing and transcriptional elongation.Generation of mature mRNA transcripts requires complex and interconnected processes that involve opening of the local chromatin structure around the DNA region to be transcribed, binding and transcription by RNA polymerase II (Pol II), and processing of the pre-mRNAs, including the splicing of the non-coding introns [1,2]. Protein production is streamlined at several levels of gene expression, including coordinated transcription and translation [3]. Moreover, there is some evidence for functional coupling between transcription and pre-mRNA processing [4-6].We have previously reported that, in fission yeast (Schizosaccharomyces pombe), highly transcribed genes tend to be most efficiently spliced while lowly transcribed genes are less efficiently spliced [7]. The reason for this unexpected global coo