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

Brian T Wilhelm12*, Samuel Marguerat1, Sofia Aligianni13, Sandra Codlin1, Stephen Watt14 and Jürg Bähler1

Author Affiliations

1 Department of Genetics, Evolution and Environment and UCL Cancer Institute, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK

2 Institut de Recherche en Immunologie et en Cancérologie (IRIC), 2900 boulevard Édouard-Montpetit, Montréal, H3C 3J7, Canada

3 Salk Institute for Biological Studies, San Diego, CA 92186-5800, USA

4 Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK

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Genome Biology 2011, 12:R82  doi:10.1186/gb-2011-12-8-r82

Published: 22 August 2011



The generation of mature mRNAs involves interconnected processes, including transcription by RNA polymerase II (Pol II), modification of histones, and processing of pre-mRNAs through capping, intron splicing, and polyadenylation. These processes are thought to be integrated, both spatially and temporally, but it is unclear how these connections manifest at a global level with respect to chromatin patterns and transcription kinetics. We sought to clarify the relationships between chromatin, transcription and splicing using multiple genome-wide approaches 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.