Cited by 1,352RNA Research and SplicingRNA regulation and diseaseCancer-related molecular mechanisms research

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

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Licatalosi, Donny D., Mele, Aldo, Fak, John J., Ule, Jernej, Kayikci, Melis, Chi, Sung Wook, Clark, Tyson A., Schweitzer, Anthony C., Blume, John E., Wang, Xuning, Darnell, Jennifer C., Darnell, Robert B.·2008·Nature

DOI 10.1038/nature07488PMC PMC2597294

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Abstract

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.

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Method
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Background
Microarray Meta-Analysis of RNA-Binding Protein Functions in Alternative Polyadenylation
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Mapping of In Vivo RNA-Binding Sites by Ultraviolet (UV)-Cross-Linking Immunoprecipitation (CLIP)Preprint
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Transcriptome Informatics
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“RNA immunoprecipitation with sequencing (RIP-seq) and crosslinking immunoprecipitation coupled with high-throughput sequencing (CLIP-seq or HITS-CLIP) are two experimental approaches for identifying RBP target molecules (Licatalosi et al., 2008; Zhao et al., 2010).”
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BackgroundMethod
Identification of Transcription Factor–DNA Interactions In Vivo
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Shankarling, G. S., & MacDonald, C. C. (2013) · Gene · doi:10.1016/j.gene.2013.08.007 · Cited by 10
“Donald). nd Biophysics, University of -6059, USA. ights reserved. between splicing and polyadenylation contributes to brain mRNA isoform diversity (Licatalosi et al., 2008), suggesting interacting roles.”
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Method
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“10 and 11).”
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Method
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Method
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Background
Clip for studying protein-RNA interactions that regulate virus replication
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Background
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“This positional dependency, or splicing regulatory map (Witten and Ule, 2011), was ﬁ rst discovered for NOVA1/2, which binds to clusters of YCAY motifs (Ule et al, 2006; Licatalosi et al, 2008), and has since been shown for most CTS SFs (Fig.”
Background
The alternative life of RNA —sequencing meets single molecule approaches
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Protein-RNA Interactome Analysis Reveals Wide Association of Kaposi’s Sarcoma-Associated Herpesvirus ORF57 with Host Noncoding RNAs and Polysomes
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PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing
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Method
HITS-CLIP reveals sex-differential RNA binding and alterative splicing regulation of SRm160 in Drosophila
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BackgroundMethod
PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks
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“To this end, Darnell and his colleagues developed a powerful method termed HITS‐CLIP (High‐Throughput Sequencing of RNA isolated by CrossLinking ImmunoPrecipitation, also known as CLIP‐seq) to investigate direct targets of a certain RBP at a genome‐wide scale [107].”
Method
Monitoring Protein-RNA Interaction Dynamics in vivo at High Temporal Resolution using χCRAC
McKellar, S. W., Ivanova, I., van Nues, R. W., Cordiner, R. A., Chauhan, M., Christopoulou, N., Worboys, W., Langford, A., Jensen, T. H., & Granneman, S. (2020) · Journal of Visualized Experiments · doi:10.3791/61027 · Cited by 8
“Next, the captured cross-linked RNAs were partially digested with RNases, radiolabeled at the 5’ end and adapters were ligated onto them (3).”
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Identifying Protein Interactomes of Target RNAs Using HyPR-MS
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Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes
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BackgroundSelf-citation
TRENDseq—A highly multiplexed high throughput RNA 3′ end sequencing for mapping alternative polyadenylation
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Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics
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Background
LncPTPred: predicting lncRNA–protein interaction based on crosslinking and immunoprecipitation (CLIP-Seq) data
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Regulation of RNA-binding proteins by small biomolecules
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Background
NOVA1 prevents overactivation of the unfolded protein response and facilitates chromatin access during human white adipogenesis
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Self-citation

Authors: Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., Darnell, J. C., & Darnell, R. B.
Affiliations: Howard Hughes Medical Institute (US)
MRC Laboratory of Molecular Biology (GB)
Affymetrix (United States) (US)
Rockefeller University (US)
Corresponding author: Darnell, Robert B.
ORCID: Licatalosi, Donny D.
Fak, John J.
Ule, Jernej
Kayikci, Melis
Chi, Sung Wook
Clark, Tyson A.
Blume, John E.
Wang, Xuning
Darnell, Robert B.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2008-11
Volume: 456
Issue: 7221
Pages: 464-469
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature07488
PMC: PMC2597294
OpenAlex: W2044117548
Cited by: 1,352
References: 51
Citations by year: 2026: 37 · 2025: 53 · 2024: 46 · 2023: 44 · 2022: 72 · 2021: 81 · 2020: 59 · 2019: 77 · 2018: 85 · 2017: 89 · 2016: 95 · 2015: 97 · 2014: 103 · 2013: 89 · 2012: 111
FWCI: 29.24
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
UCL Discovery (University College London) (submittedVersion)
Funders: Howard Hughes Medical Institute
National Institute of Neurological Disorders and Stroke (R01NS040955, R01 NS34389, R01NS034389)
Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD040647)
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 › Cancer Research › Cancer-related molecular mechanisms research
Keywords: HITS-CLIP, RNA-protein interactions, alternative splicing, nova, alternative polyadenylation, 3' untranslated region, RNA binding sites, brain, neurons, splicing factors, genome-wide mapping
MeSH terms: Neuro-Oncological Ventral Antigen, Animals, Antigens, Neoplasm, Cell Line, Cross-Linking Reagents, Exons, Humans, Neurons, Organ Specificity, RNA, Messenger, RNA-Binding Proteins, Genome, Alternative Splicing, Neocortex, Genomics, Polyadenylation, Immunoprecipitation, Mice

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

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