CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
Open accessAbstract
Alternative splicing of pre-messenger RNA is a key feature of transcriptome expansion in eukaryotic cells, yet its regulation is poorly understood. Spliceosome assembly occurs co-transcriptionally, raising the possibility that DNA structure may directly influence alternative splicing. Supporting such an association, recent reports have identified distinct histone methylation patterns, elevated nucleosome occupancy and enriched DNA methylation at exons relative to introns. Moreover, the rate of transcription elongation has been linked to alternative splicing. Here we provide the first evidence that a DNA-binding protein, CCCTC-binding factor (CTCF), can promote inclusion of weak upstream exons by mediating local RNA polymerase II pausing both in a mammalian model system for alternative splicing, CD45, and genome-wide. We further show that CTCF binding to CD45 exon 5 is inhibited by DNA methylation, leading to reciprocal effects on exon 5 inclusion. These findings provide a mechanistic basis for developmental regulation of splicing outcome through heritable epigenetic marks.
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The methylation status around spliced exons could affect their inclusion level.
“suggesting that the methylation status surrounding the spliced exons could affect the inclusion level of these exons.”
From Transcription factors as readers and effectors of DNA methylation (2016) · cites this paper as [112]
CTCF binding to the exon or intron depends on DNA methylation.
“Importantly, the binding of CTCF to the exon or intron was dependent on DNA methylation”
From Transcription factors as readers and effectors of DNA methylation (2016) · cites this paper as [112]
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- Authors
- Shukla, S., Kavak, E., Gregory, M., Imashimizu, M., Shutinoski, B., Kashlev, M., Oberdoerffer, P., Sandberg, R., & Oberdoerffer, S.
- Affiliations
- National Cancer Institute (US)
- Frederick National Laboratory for Cancer Research (US)
- Karolinska Institutet (SE)
- Corresponding author
- Oberdoerffer, Shalini
- ORCID
- Venue
- Nature
- Published
- 2011-11
- Volume
- 479
- Issue
- 7371
- Pages
- 74-79
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC7398428
- OpenAlex
- W2092992881
- Cited by
- 973
- References
- 54
- Citations by year
- 2026: 28 · 2025: 37 · 2024: 46 · 2023: 39 · 2022: 48 · 2021: 78 · 2020: 51 · 2019: 66 · 2018: 63 · 2017: 61 · 2016: 64 · 2015: 104 · 2014: 103 · 2013: 100 · 2012: 79
- FWCI
- 37.10
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Vetenskapsrådet
- National Institutes of Health (1ziabc011636-01)
- National Cancer Institute (ZIABC011293)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- 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
- Keywords
- CTCF, RNA polymerase II pausing, DNA methylation, alternative splicing, co-transcriptional splicing, CD45, exon inclusion, histone methylation, nucleosome occupancy, transcription elongation, spliceosome assembly
- MeSH terms
- CCCTC-Binding Factor, Animals, Cell Line, Cells, Cultured, Exons, Humans, Protein Binding, Repressor Proteins, RNA Polymerase II, RNA, Messenger, Saccharomyces cerevisiae, Transcription, Genetic, Genome, Human, Alternative Splicing, Leukocyte Common Antigens, DNA Methylation, RNA Splice Sites, Epigenesis, Genetic, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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