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High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites.

Author(s): Mihailovic, Mia K; Vazquez-Anderson, Jorge; Li, Yan; Fry, Victoria; Vimalathas, Praveen; et al

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dc.contributor.authorMihailovic, Mia K-
dc.contributor.authorVazquez-Anderson, Jorge-
dc.contributor.authorLi, Yan-
dc.contributor.authorFry, Victoria-
dc.contributor.authorVimalathas, Praveen-
dc.contributor.authorHerrera, Daniel-
dc.contributor.authorLease, Richard A-
dc.contributor.authorPowell, Warren B-
dc.contributor.authorContreras, Lydia M-
dc.date.accessioned2021-10-11T14:17:47Z-
dc.date.available2021-10-11T14:17:47Z-
dc.date.issued2018-10-04en_US
dc.identifier.citationMihailovic, Mia K, Vazquez-Anderson, Jorge, Li, Yan, Fry, Victoria, Vimalathas, Praveen, Herrera, Daniel, Lease, Richard A, Powell, Warren B, Contreras, Lydia M. (2018). High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites.. Nature communications, 9 (1), 4084 - ?. doi:10.1038/s41467-018-06207-zen_US
dc.identifier.issn2041-1723-
dc.identifier.urihttp://arks.princeton.edu/ark:/88435/pr1h87t-
dc.description.abstractHerein we introduce a high-throughput method, INTERFACE, to reveal the capacity of contiguous RNA nucleotides to establish in vivo intermolecular RNA interactions for the purpose of functional characterization of intracellular RNA. INTERFACE enables simultaneous accessibility interrogation of an unlimited number of regions by coupling regional hybridization detection to transcription elongation outputs measurable by RNA-seq. We profile over 900 RNA interfaces in 71 validated, but largely mechanistically under-characterized, Escherichia coli sRNAs in the presence and absence of a global regulator, Hfq, and find that two-thirds of tested sRNAs feature Hfq-dependent regions. Further, we identify in vivo hybridization patterns that hallmark functional regions to uncover mRNA targets. In this way, we biochemically validate 25 mRNA targets, many of which are not captured by typically tested, top-ranked computational predictions. We additionally discover direct mRNA binding activity within the GlmY terminator, highlighting the information value of high-throughput RNA accessibility data.en_US
dc.format.extent4084 - ?en_US
dc.languageengen_US
dc.language.isoen_USen_US
dc.relation.ispartofNature communicationsen_US
dc.rightsFinal published version. This is an open access article.en_US
dc.titleHigh-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites.en_US
dc.typeJournal Articleen_US
dc.identifier.doidoi:10.1038/s41467-018-06207-z-
dc.identifier.eissn2041-1723-
pu.type.symplectichttp://www.symplectic.co.uk/publications/atom-terms/1.0/journal-articleen_US

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