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Updated: Jun 28, 2026
10:45
iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
Published on: April 30, 2011
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
Donny D Licatalosi1, Aldo Mele, John J Fak
1Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.
Nature
|November 4, 2008
Summary
High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) maps protein-RNA interactions in vivo. This method reveals how the Nova splicing factor regulates gene expression, including alternative splicing and polyadenylation in the brain.
Area of Science:
- Molecular Biology
- Genetics
- Neuroscience
Background:
- Protein-RNA interactions are crucial for gene expression.
- Studying these interactions in living tissues using biochemical methods is challenging.
Purpose of the Study:
- To develop a genome-wide method for mapping protein-RNA binding sites in vivo.
- To investigate the in vivo RNA-binding landscape of the neuron-specific splicing factor Nova.
Main Methods:
- High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP).
- Analysis of Nova-RNA interactions in mouse brains.
Main Results:
- HITS-CLIP generated reproducible genome-wide RNA-binding maps for Nova in vivo.
- These maps confirmed Nova's role in determining alternative splicing outcomes and predicted its action de novo.
- Numerous Nova-RNA interactions were identified in 3' untranslated regions, revealing Nova's regulation of alternative polyadenylation in the brain.
Conclusions:
- HITS-CLIP is a robust and unbiased method for identifying functional protein-RNA interactions in vivo.
- This technique provides novel insights into the regulation of gene expression by splicing factors like Nova.
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