iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

By J. König, K. Zarnack, G. Rot, Tomaž Curk, M. Kayikci, Blaz Zupan, D. Turner, Nicholas M. Luscombe, Jernej Ule. Nature Structural &Molecular Biology, 2010

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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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f614e75e5463ef47973240b6972365c3e4824c7b

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Citations in the corpus

Complexity of the Alternative Splicing Landscape in Plants[C][W][OPEN] (2013, background): “These studies suggest the functional significance of AS as a result of tandem acceptor in plants.”
A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation (2015, background): “During this procedure, cross-linking-induced mutation sites (CIMSs; including single-base substitutions, deletions, and insertions) (Zhang and Darnell 2011) and cross-linking-induced truncation sites (CITSs) occur (Konig et al. 2010), which subsequently assist inmore precisemapping of m6A.”
UMI-tools: Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy (2016, methodology): “To test this we turned to a previously defined measure of iCLIP reproducibility (König et al. 2010) .”
RNA-Binding Proteins in Cancer: Old Players and New Actors. (2017, background): “A higher efficiency has also been achieved in cDNA library-preparation protocols, enabling precise mapping of RBP–RNA interactions at single-nucleotide resolution, termed individual-nucleotide resolution (i)CLIP [226].”
Integrative regulatory mapping indicates that the RNA-binding protein HuR (ELAVL1) couples pre-mRNA processing and mRNA stability (2011, methodology): “A number of subsequent methods utilizing crosslinking followed by immunoprecipitation have addressed this deficiency to varying degrees (Ule et al., 2003; König et al., 2010; Hafner et al., 2010).”