HITS-CLIP yields genome-wide insights into brain alternative RNA processing

By Donny D. Licatalosi, Aldo Mele, J. Fak, Jernej Ule, M. Kayikci, S. Chi, Tyson A. Clark, A. Schweitzer, J. Blume, Xuning Wang and 2 more. Nature, 2008

1,404 citations recorded by the source corpus.

Protein–RNA interactions have critical roles in all aspects of gene expression. However, applying biochemical methods to understand such interactions in living tissues has been challenging. Here we develop a genome-wide means of mapping protein–RNA binding sites in vivo, by high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova revealed extremely reproducible RNA-binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova–RNA interactions in 3′ untranslated regions, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein–RNA interactions in vivo.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1a7b24ca72ae99a34fe31f110836880d4292b0e0

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Citations in the corpus

Resolving RNA complexity to decipher regulatory rules governing biological networks (2010, neutral): “CLIP (and emerging methodological improvements to this metho”
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3' UTRs and Near Stop Codons (2012, neutral): “Thus, unlike CLIP-Seq tag clusters from RNA-binding proteins that influence splicing (Licatalosi et al., 2008), mA peaks did not significantly coincide with exon-exon junctions, suggesting that mA is unlikely to primarily function to directly influence the binding of splicing factors.”
TDP-43 and FUS/TLS: emerging roles in RNA processing and neurodegeneration. (2010, background): “Recent technologies coupled with high-throughput sequencing have yielded a global insight into RNA regulation (178,179), and such approaches are eagerly anticipated to understand the role of TDP-43 and FUS/TLS in neurodegeneration.”
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP (2010, methodology): “For comparison to conventional and high-throughput sequencing CLIP (Licatalosi et al., 2008; Ule et al., 2003), we also sequenced cDNA libraries prepared from UV 254 nm crosslinking.”
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution (2010, methodology): “UV cross-linking and immunoprecipitation (CLIP) combined with high-throughput sequencing was previously used to generate transcriptome-wide binding maps of several RNA-binding protein”
Genome regulation by long noncoding RNAs (2012, methodology): “These studies employ protein immunoprecipitation followed by microarray or deep-sequencing to enumerate all RNAs associated with a protein complex of interest (RIPseq) (108) (49, 109); often times crosslinking is performed to trap the relevant interactions in living cells (CLIP-seq) (110).”
A ceRNA hypothesis: the Rosetta stone of a hidden RNA language? (2011, background): “Importantly, microRNAs also regulate lncRNAs, as shown in recent global analysis of Argonaute (Ago)-bound transcripts through the HITS-CLIP technique (Chi et al., 2009; Licatalosi et al., 2008).”