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RNA interactome capture identifies key proteins for herpesviral gene expression

ABSTRACT: RNA interactome capture identifies key proteins for herpesviral gene expression

PROVIDER: PRJNA1065267 | ENA |

REPOSITORIES: ENA

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RNA interactome capture identifies key proteins for herpesviral gene expression

Project description:The primary mRNA sequence determines its secondary structure and the repertoire of interacting RNA-binding proteins (RBPs). The resulting mRNA ribonucleoprotein complex (mRNP) then influences all stages of the life of an mRNA. Here, we determined the mRNP composition of individual Kaposi Sarcoma Herpesviral (KSHV) mRNAs. In KSHV, the viral RNA regulator ORF57 ensures the translation of viral mRNAs by increasing mRNA stability and nuclear export. By optimizing an LNA/DNA mixmer RNA capture protocol to both transfection and virus replication settings, we identified the RBPome of specific ORF57-dependent viral transcripts. Both capture and eCLIP experiments robustly detected ORF57 as a direct RNA binder to an AU-rich motif, which may enable ORF57 to discriminate viral from cellular RNAs. Furthermore, we identified the RNA processing factor SRSF3 as a key regulator of viral replication. This work facilitates RNA-interactome studies of specific mRNAs and sheds light on how the mRNP composition orchestrates gene expression.

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RNA interactome capture identifies key proteins for herpesviral gene expression

Project description:The primary mRNA sequence determines its secondary structure and the repertoire of interacting RNA binding proteins (RBPs). The resulting mRNA ribonucleoprotein complex (mRNP) then influences all stages of the life of an mRNA. Here, we determined the mRNP composition of individual Kaposi Sarcoma Herpesviral (KSHV) mRNAs. In KSHV, the viral RNA regulator ORF57 ensures the translation of viral mRNAs by increasing mRNA stability and nuclear export. By optimizing an LNA/DNA mixmer RNA capture protocol to both transfection and virus replication settings, we identified the RBPome of specific ORF57-dependent viral transcripts. Both capture and eCLIP experiments robustly detected ORF57 as a direct RNA binder to an AU-rich motif, which may enable ORF57 to discriminate viral from cellular RNAs. Furthermore, we identified the RNA processing factor SRSF3 as a key regulator of viral replication. This work facilitates RNA-interactome studies of specific mRNAs and sheds light on how the mRNP composition orchestrates gene expression.

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Project description:RNA-binding proteins (RPBs) are deeply involved in fundamental cellular processes in bacteria and are vital for their survival. Despite this, few studies have so far been dedicated to globally identifying bacterial RBPs. We have adapted the RNA interactome capture (RIC) technique, originally developed for eukaryotic systems, to globally identify RBPs in bacteria. RIC takes advantage of the base pairing potential of poly(A) tails to pull-down mRNA-protein complexes. By overexpressing poly(A) polymerase I, we drastically increase the fraction of polyadenylated RNA in Escherichia coli, allowing us to pull-down RNA-protein complexes using immobilized oligo-d(T) as bait. With this approach, we identified 169 putative RBPs, roughly half of which are already annotated as RNA-binding

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