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• Education
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🌠 Phenomenal Traffic: 5M - 10M visitors per month


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Keywords {🔍}

ppss, pipseq, figure, file, identified, rna, additional, sites, article, crosslinking, pps, google, scholar, interaction, rnase, rnaprotein, interactions, binding, protein, regions, sequencing, motifs, analysis, experiments, mrnas, proteins, cell, cells, sequences, snps, human, rnas, control, formaldehyde, average, footprint, rbps, approach, found, transcriptome, digestion, utr, rnabinding, number, site, specific, nucleotides, results, dsrnase, data,

Topics {✒️}

hgs_dootheruser=submit&hgs_otherusername=pipseq&hgs_otherusersessionname=pps formaldehyde-cross-linked ssrnase-treated libraries formaldehyde-cross-linked ssrnase-treated footprint porphyria cutanea tarda formaldehyde-cross-linked pip-seq experiments additional formaldehyde-cross-linked ssrnase-treated uv-cross-linked pip-seq samples cross-linked rna–protein complexes formaldehyde-cross-linked dsrnase-treated replicates cross-links protein–nucleic acid cross-linked rbp-binding densities rnase-protected rna–rbp complexes formaldehyde-cross-linked ssrnase-treated formaldehyde-cross-linked pip-seq nuclease-sensitivity sequencing assays cross-linked pip-seq experiments formaldehyde-treated pip-seq samples cross-linked pip-seq sample uv-cross-linked ssrnase-treated ptb-rna interactions reveals rna-protein interaction networks formaldehyde-cross-linked dsrnase-treated rna–protein-binding event identified average siphy-π scores rna–protein interaction sites cross-linking pip-seq experiments rna steady-state abundance rna-binding protein hur larger multi-protein complexes dgcr8 hits-clip reveals uv-cross-linked pps density map rna-binding sites dsrnase-treated pip-seq samples rbp–rna interaction sites multi-rna-binding domain rna–protein interactions underlies strand-specific library preparation direct rna–protein contact rna–protein interaction motifs photoactivatable ribonucleoside cross-linking quantify protein-bound rna pip-seq libraries made post-transcriptional operon hypothesis uv-cross-linked libraries putative rbp-binding motifs transacting rna-binding proteins enhance rbp–rna interactions protein-binding site density post-transcriptional regulatory processes differential cross-linking specificities

Questions {❓}

• Edu/cgi-bin/hgTracks?
• Edu/jbrowse/?

Schema {🗺️}

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         headline:RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
         description:Although numerous approaches have been developed to map RNA-binding sites of individual RNA-binding proteins (RBPs), few methods exist that allow assessment of global RBP–RNA interactions. Here, we describe PIP-seq, a universal, high-throughput, ribonuclease-mediated protein footprint sequencing approach that reveals RNA-protein interaction sites throughout a transcriptome of interest. We apply PIP-seq to the HeLa transcriptome and compare binding sites found using different cross-linkers and ribonucleases. From this analysis, we identify numerous putative RBP-binding motifs, reveal novel insights into co-binding by RBPs, and uncover a significant enrichment for disease-associated polymorphisms within RBP interaction sites.
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            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      description:Although numerous approaches have been developed to map RNA-binding sites of individual RNA-binding proteins (RBPs), few methods exist that allow assessment of global RBP–RNA interactions. Here, we describe PIP-seq, a universal, high-throughput, ribonuclease-mediated protein footprint sequencing approach that reveals RNA-protein interaction sites throughout a transcriptome of interest. We apply PIP-seq to the HeLa transcriptome and compare binding sites found using different cross-linkers and ribonucleases. From this analysis, we identify numerous putative RBP-binding motifs, reveal novel insights into co-binding by RBPs, and uncover a significant enrichment for disease-associated polymorphisms within RBP interaction sites.
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      name:Department of Biology, University of Pennsylvania, Philadelphia, USA
      name:PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, USA
      name:Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, USA
      name:Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, USA

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