RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.
Identifieur interne : 001A90 ( Ncbi/Checkpoint ); précédent : 001A89; suivant : 001A91RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.
Auteurs : Kate B. Cook [Canada] ; Shankar Vembu [Canada] ; Kevin C H. Ha [Canada] ; Hong Zheng [Canada] ; Kaitlin U. Laverty [Canada] ; Timothy R. Hughes [Canada] ; Debashish Ray [Canada] ; Quaid D. Morris [Canada]Source :
- Methods (San Diego, Calif.) [ 1095-9130 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : RNA-Binding Proteins.
- genetics : Base Sequence, RNA-Binding Proteins.
- methods : High-Throughput Nucleotide Sequencing, Sequence Analysis, RNA.
- Humans.
Abstract
RNA-binding proteins recognize RNA sequences and structures, but there is currently no systematic and accurate method to derive large (>12base) motifs de novo that reflect a combination of intrinsic preference to both sequence and structure. To address this absence, we introduce RNAcompete-S, which couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models). RNAcompete-S confirms that HuR, QKI, and SRSF1 prefer binding sites that are single stranded, and recapitulates known 8-10bp sequence and structure preferences for Vts1p and RBMY. We also derive an 18-base long SSM for Drosophila SLBP, which to our knowledge has not been previously determined by selections from pure random sequence, and accurately discriminates human replication-dependent histone mRNAs. Thus, RNAcompete-S enables accurate identification of large, intrinsic sequence-structure specificities with a uniform assay.
DOI: 10.1016/j.ymeth.2017.06.024
PubMed: 28651966
Affiliations:
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<front><div type="abstract" xml:lang="en">RNA-binding proteins recognize RNA sequences and structures, but there is currently no systematic and accurate method to derive large (>12base) motifs de novo that reflect a combination of intrinsic preference to both sequence and structure. To address this absence, we introduce RNAcompete-S, which couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models). RNAcompete-S confirms that HuR, QKI, and SRSF1 prefer binding sites that are single stranded, and recapitulates known 8-10bp sequence and structure preferences for Vts1p and RBMY. We also derive an 18-base long SSM for Drosophila SLBP, which to our knowledge has not been previously determined by selections from pure random sequence, and accurately discriminates human replication-dependent histone mRNAs. Thus, RNAcompete-S enables accurate identification of large, intrinsic sequence-structure specificities with a uniform assay.</div>
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