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Capturing the Interactome of Newly Transcribed RNA

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE100756 | GEO | 2017/12/12

SECONDARY ACCESSION(S): PRJNA392921

REPOSITORIES: GEO

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Capturing the interactome of newly transcribed RNA.

Project description:We combine the labeling of newly transcribed RNAs with 5-ethynyluridine with the characterization of bound proteins. This approach, named capture of the newly transcribed RNA interactome using click chemistry (RICK), systematically captures proteins bound to a wide range of RNAs, including nascent RNAs and traditionally neglected nonpolyadenylated RNAs. RICK has identified mitotic regulators amongst other novel RNA-binding proteins with preferential affinity for nonpolyadenylated RNAs, revealed a link between metabolic enzymes/factors and nascent RNAs, and expanded the known RNA-bound proteome of mouse embryonic stem cells. RICK will facilitate an in-depth interrogation of the total RNA-bound proteome in different cells and systems.

| S-EPMC5967874 | biostudies-literature

Capturing the Interactome of Newly Transcribed RNA (RICK)

Project description:Key features of gene transcription, such as transcriptional pausing, divergent transcription, and enhancer RNA production can be explored using techniques based on the incorporation of synthetic nucleoside analogs into RNA, followed by pull-down and high-throughput sequencing. Whether these approaches can be adapted to expand our knowledge of the RNA-bound proteome is, however, unexplored. Here, we have designed a methodology (isolation of the newly transcribed RNA Interactome using ClicK reaction; RICK) based on the incorporation of 5-ethynyluridine (EU) into newly transcribed RNAs to systematically capture proteins bound to RNAs of wide scope including traditionally neglected non-polyadenylated RNAs. Amongst the novel RNA-binding proteins identified by RICK, we found mitotic regulators, components of the DNA damage response pathway, and epigenetic regulators. Because the protocol can be easily modified to include variations such as labeling time or transcriptional interference, RICK will enable an in depth and global interrogation of the RNA-bound proteome.

2017-12-12 | GSE100755 | GEO