We are analyzing https://link.springer.com/article/10.1186/gb-2012-13-8-r67.

Title:
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions | Genome Biology
Description:
UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data sets to confirm that both methods identify protein-RNA cross-link sites, and to identify a slight uridine preference of UV-C-induced cross-linking. Comparing Nova CLIP and iCLIP data revealed that cDNA deletions have a preference for TTT motifs, whereas iCLIP cDNA truncations are more likely to identify clusters of YCAY motifs as the primary Nova binding sites. In conclusion, we demonstrate how each method impacts the analysis of protein-RNA binding specificity.
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Keywords {🔍}

iclip, sites, cdna, clip, cdnas, deletions, crosslink, nova, ycay, pubmed, rna, figure, motifs, article, deletion, position, crosslinking, binding, google, scholar, motif, enrichment, analysis, truncations, file, cas, additional, data, proportion, sequence, ttt, nucleotide, identify, central, score, methods, proteins, identified, nsun, genome, compared, site, darnell, truncated, readthrough, studies, protein, positions, proteinrna, splicing,

Topics {✒️}

false discovery rate uv-c-induced cross-linking uv-c-induced cross-linking [22] perform uv-independent cross-linking protein-rna cross-link sites article number r67 article download pdf par-clip requires pre-incubation nova-dependent splicing enhancer nova-dependent splicing regulation nova splicing-regulatory network genome-wide rna maps identify protein-rna interactions protein-rna cross-linking uv-induced cross-linking nop2/sun domain family cross-link sites induced photoactivatable ribonucleoside-enhanced clip cross-linking predominantly occurs hyper-variable ca microsatellite article sugimoto cross-link sites influence spontaneous covalent cross-linking nova k-homology domains covalent cross-linking protocols identify cross-link sites position-dependent splicing regulation cross-link sites identified cross-link induced mutations cross-link-induced mutations kh rna-binding domains protein-rna binding specificity sequence-specific rna binding study protein-rna interactions 1186/gb-2009-10-3-r25 mapping rna-protein interactions full-length nova proteins understand post-transcriptional regulation vivo protein-rna interactions identifying cross-link sites cross-linking bias accession number e-mtab-1008 individual-nucleotide resolution clip alternative splicing regulation author information authors cross-link site identification cross-link sites starting high-affinity binding sites isolate rnas cross-linked julian könig & jernej ule

Schema {🗺️}

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         headline:Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
         description:UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data sets to confirm that both methods identify protein-RNA cross-link sites, and to identify a slight uridine preference of UV-C-induced cross-linking. Comparing Nova CLIP and iCLIP data revealed that cDNA deletions have a preference for TTT motifs, whereas iCLIP cDNA truncations are more likely to identify clusters of YCAY motifs as the primary Nova binding sites. In conclusion, we demonstrate how each method impacts the analysis of protein-RNA binding specificity.
         datePublished:2012-08-03T00:00:00Z
         dateModified:2012-08-03T00:00:00Z
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            Sequence Bias
            False Discovery Rate Threshold
            Deletion Site
            cDNA Truncation
            Nova Protein
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
      description:UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data sets to confirm that both methods identify protein-RNA cross-link sites, and to identify a slight uridine preference of UV-C-induced cross-linking. Comparing Nova CLIP and iCLIP data revealed that cDNA deletions have a preference for TTT motifs, whereas iCLIP cDNA truncations are more likely to identify clusters of YCAY motifs as the primary Nova binding sites. In conclusion, we demonstrate how each method impacts the analysis of protein-RNA binding specificity.
      datePublished:2012-08-03T00:00:00Z
      dateModified:2012-08-03T00:00:00Z
      pageStart:1
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         Sequence Bias
         False Discovery Rate Threshold
         Deletion Site
         cDNA Truncation
         Nova Protein
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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      affiliation:
            name:MRC Laboratory of Molecular Biology
            address:
               name:MRC Laboratory of Molecular Biology, Cambridge, UK
               type:PostalAddress
            type:Organization
      name:Shobbir Hussain
      affiliation:
            name:The Wellcome Trust Centre for Stem Cell Research
            address:
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               type:PostalAddress
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               type:PostalAddress
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            address:
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      affiliation:
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            address:
               name:The Wellcome Trust Centre for Stem Cell Research, Cambridge, UK
               type:PostalAddress
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      name:The Wellcome Trust Centre for Stem Cell Research, Cambridge, UK
      name:Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
      name:Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
      name:The Wellcome Trust Centre for Stem Cell Research, Cambridge, UK
      name:MRC Laboratory of Molecular Biology, Cambridge, UK

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