Chromatin organization marks exon-intron structure
Abstract
An increasing body of evidence indicates that transcription and splicing are coupled, and it is accepted that chromatin organization regulates transcription. Little is known about the cross-talk between chromatin structure and exon-intron architecture. By analysis of genome-wide nucleosome-positioning data sets from humans, flies and worms, we found that exons show increased nucleosome-occupancy levels with respect to introns, a finding that we link to differential GC content and nucleosome-disfavoring elements between exons and introns. Analysis of genome-wide chromatin immunoprecipitation data in humans and mice revealed four specific post-translational histone modifications enriched in exons. Our findings indicate that previously described enrichment of H3K36me3 modifications in exons reflects a more fundamental phenomenon, namely increased nucleosome occupancy along exons. Our results suggest an RNA polymerase II-mediated cross-talk between chromatin structure and exon-intron architecture, implying that exon selection may be modulated by chromatin structure.
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RNA Pol II ChIP on chip and ChIP-seq data showed that RNA Pol II accumulates on exons in yeast and human, suggesting that RNA Pol II pauses over exons.
“Indeed, RNA Pol II ChIP on chip and ChIP‐seq data showed that RNA Pol II accumulates on exons in yeast and human, suggesting that RNA Pol II pauses over exons (Brodsky et al, 2005; Schwartz et al, 2009; Alexander et al, 2010; Carrillo Oesterreich et al, 2010; Kwak et al, 2013; Mayer et al, 2015; Nojima et al, 2015; Harlen et al, 2016).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Schwartz et al, 2009
Increased nucleosome occupancy occurs on exons with respect to introns.
“First, increased nucleosome occupancy occurs on exons with respect to introns (Andersson et al, 2009; Nahkuri et al, 2009; Schwartz et al, 2009; Spies et al, 2009; Tilgner et al, 2009; Chodavarapu et al, 2010).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Schwartz et al, 2009
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- Authors
- Schwartz, S., Meshorer, E., & Ast, G.
- Affiliations
- Tel Aviv University (IL)
- Hebrew University of Jerusalem (IL)
- Corresponding author
- Ast, Gil
- Venue
- Nature Structural & Molecular Biology
- Published
- 2009-08-16
- Volume
- 16
- Issue
- 9
- Pages
- 990-995
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- OpenAlex
- W2155453721
- Cited by
- 638
- References
- 57
- Citations by year
- 2026: 10 · 2025: 16 · 2024: 18 · 2023: 25 · 2022: 21 · 2021: 31 · 2020: 32 · 2019: 33 · 2018: 32 · 2017: 32 · 2016: 35 · 2015: 45 · 2014: 48 · 2013: 57 · 2012: 62
- FWCI
- 27.08
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- exon-intron structure, nucleosome occupancy, chromatin organization, transcription-splicing coupling, histone modifications, H3K36me3, GC content, exon selection, RNA polymerase II, chromatin immunoprecipitation, nucleosome positioning
- MeSH terms
- Animals, Base Composition, Chromatin, Exons, Histones, Humans, Introns, Methylation, Protein Processing, Post-Translational, RNA Polymerase II, RNA Splicing, Genome
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