ArticleNucleic acids research2015
Leveraging cross-link modification events in CLIP-seq for motif discovery.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Review
- Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP.Genome biology · 2022Article
- RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites.PLoS computational biology · 2022Article
- Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes.Nature communications · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding.Cell reports methods · 2021Article
- Beyond CLIP: advances and opportunities to measure RBP-RNA and RNA-RNA interactions.Nucleic acids research · 2019Review
- Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.Molecular cell · 2019Article
- Discovery of Allele-Specific Protein-RNA Interactions in Human Transcriptomes.American journal of human genetics · 2019Article
- Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions.Methods (San Diego, Calif.) · 2019Review
- SSMART: sequence-structure motif identification for RNA-binding proteins.Bioinformatics (Oxford, England) · 2018Article
- Recent computational developments on CLIP-seq data analysis and microRNA targeting implications.Briefings in bioinformatics · 2018Review
- Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs.Quantitative biology (Beijing, China) · 2018Article
- Data Science Issues in Studying Protein-RNA Interactions with CLIP Technologies.Annual review of biomedical data science · 2018Article
- SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data.PLoS computational biology · 2018Article
- Global role of the bacterial post-transcriptional regulator CsrA revealed by integrated transcriptomics.Nature communications · 2017Article
- ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.Nucleic acids research · 2017Article
- CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome.Nucleic acids research · 2017Article
- A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications.Nucleic acids research · 2016Article
- αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome.Nucleic acids research · 2016Article
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4 authors.
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Abstract
High-throughput protein-RNA interaction data generated by CLIP-seq has provided an unprecedented depth of access to the activities of RNA-binding proteins (RBPs), the key players in co- and post-transcriptional regulation of gene expression. Motif discovery forms part of the necessary follow-up data analysis for CLIP-seq, both to refine the exact locations of RBP binding sites, and to characterize them. The specific properties of RBP binding sites, and the CLIP-seq methods, provide additional information not usually present in the classic motif discovery problem: the binding site structure, and cross-linking induced events in reads. We show that CLIP-seq data contains clear secondary structure signals, as well as technology- and RBP-specific cross-link signals. We introduce Zagros, a motif discovery algorithm specifically designed to leverage this information and explore its impact on the quality of recovered motifs. Our results indicate that using both secondary structure and cross-link modifications can greatly improve motif discovery on CLIP-seq data. Further, the motifs we recover provide insight into the balance between sequence- and structure-specificity struck by RBP binding.
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