iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
Open accessAbstract
In the nucleus of eukaryotic cells, nascent transcripts are associated with heterogeneous nuclear ribonucleoprotein (hnRNP) particles that are nucleated by hnRNP C. Despite their abundance, however, it remained unclear whether these particles control pre-mRNA processing. Here, we developed individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) to study the role of hnRNP C in splicing regulation. iCLIP data show that hnRNP C recognizes uridine tracts with a defined long-range spacing consistent with hnRNP particle organization. hnRNP particles assemble on both introns and exons but remain generally excluded from splice sites. Integration of transcriptome-wide iCLIP data and alternative splicing profiles into an 'RNA map' indicates how the positioning of hnRNP particles determines their effect on the inclusion of alternative exons. The ability of high-resolution iCLIP data to provide insights into the mechanism of this regulation holds promise for studies of other higher-order ribonucleoprotein complexes.
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Recovery of chimeric fragments requires that reverse transcription read through the protein:RNA crosslink site.
“Next, as recovery of chimeric fragments requires that the reverse transcription read through the protein:RNA crosslink site (rather than terminate at this adduct, as often occurs in CLIP (Konig et al., 2010))”
From Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP (2022) · cites this paper as Konig et al., 2010
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- Authors
- König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J.
- Affiliations
- MRC Laboratory of Molecular Biology (GB)
- European Bioinformatics Institute (GB)
- University of Ljubljana (SI)
- Wellcome Sanger Institute (GB)
- Corresponding author
- Ule, Jernej
- ORCID
- Venue
- Nature Structural & Molecular Biology
- Published
- 2010-07
- Volume
- 17
- Issue
- 7
- Pages
- 909-915
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC3000544
- OpenAlex
- W2114532236
- Cited by
- 1,126
- References
- 5
- Citations by year
- 2026: 43 · 2025: 48 · 2024: 67 · 2023: 66 · 2022: 65 · 2021: 84 · 2020: 78 · 2019: 78 · 2018: 88 · 2017: 104 · 2016: 87 · 2015: 93 · 2014: 84 · 2013: 45 · 2012: 49
- FWCI
- 16.99
- Type
- journal article
- Language
- en
- Open access
- Licence
- other-oa
- www.springer.com/tdm (tdm)
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Repository of the University of Ljubljana (University of Ljubljana) (publishedVersion, other-oa)
- PubMed Central (acceptedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- Wellcome Trust (089701)
- Biotechnology and Biological Sciences Research Council (BB/E01075X/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- HNRNPC, pre-mRNA splicing, alternative splicing, iCLIP, nascent RNA, exon inclusion
- MeSH terms
- Base Sequence, HeLa Cells, Humans, Molecular Sequence Data, Nucleotides, Protein Binding, RNA Precursors, Ultraviolet Rays, Uridine, Alternative Splicing, Heterogeneous-Nuclear Ribonucleoproteins, Immunoprecipitation
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