Nucleosomes are well positioned in exons and carry characteristic histone modifications
Open accessAbstract
The genomes of higher organisms are packaged in nucleosomes with functional histone modifications. Until now, genome-wide nucleosome and histone modification studies have focused on transcription start sites (TSSs) where nucleosomes in RNA polymerase II (RNAPII) occupied genes are well positioned and have histone modifications that are characteristic of expression status. Using public data, we here show that there is a higher nucleosome-positioning signal in internal human exons and that this positioning is independent of expression. We observed a similarly strong nucleosome-positioning signal in internal exons of Caenorhabditis elegans . Among the 38 histone modifications analyzed in man, H3K36me3, H3K79me1, H2BK5me1, H3K27me1, H3K27me2, and H3K27me3 had evidently higher signals in internal exons than in the following introns and were clearly related to exon expression. These observations are suggestive of roles in splicing. Thus, exons are not only characterized by their coding capacity, but also by their nucleosome organization, which seems evolutionarily conserved since it is present in both primates and nematodes.
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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 Andersson et al, 2009
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References 52 · Cited by 325
- Authors
- Andersson, R., Enroth, S., Rada-Iglesias, A., Wadelius, C., & Komorowski, J.
- Affiliations
- Uppsala University (SE)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2009-08-17
- Volume
- 19
- Issue
- 10
- Pages
- 1732-1741
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2765275
- OpenAlex
- W1964188377
- Cited by
- 325
- References
- 52
- Citations by year
- 2026: 6 · 2025: 10 · 2024: 5 · 2023: 9 · 2022: 9 · 2021: 20 · 2020: 8 · 2019: 13 · 2018: 8 · 2017: 17 · 2016: 14 · 2015: 23 · 2014: 26 · 2013: 35 · 2012: 32
- Type
- posted content
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- Locations
- Genome Research (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Stiftelsen för Strategisk Forskning
- Knut och Alice Wallenbergs Stiftelse
- Vetenskapsrådet
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- nucleosome positioning, histone modifications, exons, introns, H3K36me3, H3K27me1, H3K27me2, H3K27me3, RNA polymerase II, transcription start sites, splicing, exon expression, Caenorhabditis elegans, human genome, evolutionary conservation
- MeSH terms
- Histone Methyltransferases, Animals, Caenorhabditis, Cells, Cultured, Exons, Gene Expression Regulation, Histones, Humans, Nucleosomes, Primates, Histone-Lysine N-Methyltransferase, Protein Processing, Post-Translational, Transcription, Genetic, Alternative Splicing, Gene Order, Mice
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