Using RNase sequence specificity to refine the identification of RNA-protein binding regions

dc.contributor.authorWang, Xin
dc.contributor.authorWang, Guohua
dc.contributor.authorShen, Changyu
dc.contributor.authorLi, Lang
dc.contributor.authorWang, Xinguo
dc.contributor.authorMooney, Sean D.
dc.contributor.authorEdenberg, Howard J.
dc.contributor.authorSanford, Jeremy R.
dc.contributor.authorLiu, Yunlong
dc.contributor.departmentMedicine, School of Medicineen_US
dc.date.accessioned2021-02-24T17:23:51Z
dc.date.available2021-02-24T17:23:51Z
dc.date.issued2008-03-20
dc.description.abstractMassively parallel pyrosequencing is a high-throughput technology that can sequence hundreds of thousands of DNA/RNA fragments in a single experiment. Combining it with immunoprecipitation-based biochemical assays, such as cross-linking immunoprecipitation (CLIP), provides a genome-wide method to detect the sites at which proteins bind DNA or RNA. In a CLIP-pyrosequencing experiment, the resolutions of the detected protein binding regions are partially determined by the length of the detected RNA fragments (CLIP amplicons) after trimming by RNase digestion. The lengths of these fragments usually range from 50-70 nucleotides. Many genomic regions are marked by multiple RNA fragments. In this paper, we report an empirical approach to refine the localization of protein binding regions by using the distribution pattern of the detected RNA fragments and the sequence specificity of RNase digestion. We present two regions to which multiple amplicons map as examples to demonstrate this approach.en_US
dc.eprint.versionFinal published versionen_US
dc.identifier.citationWang, X., Wang, G., Shen, C. et al. Using RNase sequence specificity to refine the identification of RNA-protein binding regions. BMC Genomics 9, S17 (2008). https://doi.org/10.1186/1471-2164-9-S1-S17en_US
dc.identifier.urihttps://hdl.handle.net/1805/25278
dc.language.isoen_USen_US
dc.publisherBioMed Centralen_US
dc.relation.isversionof10.1186/1471-2164-9-S1-S17en_US
dc.relation.journalBMC Genomicsen_US
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.sourcePublisheren_US
dc.subjectGenomic Regionen_US
dc.subjectSequence Specificityen_US
dc.subjectProtein Binding Siteen_US
dc.titleUsing RNase sequence specificity to refine the identification of RNA-protein binding regionsen_US
dc.typeArticleen_US
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