MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing

Jeetayu Biswas, Reazur Rahman, Varun Gupta, Michael Rosbash, Robert H. Singer

Research output: Contribution to journalArticlepeer-review

Abstract

Both UV-cross-linking and immunoprecipitation (CLIP) and RNA editing (TRIBE) can identify the targets of RNA-binding proteins. To evaluate false-positives of CLIP and TRIBE, endogenous β-actin mRNA was tagged with MS2 stem loops, making it the only bona fide target mRNA for the MS2 capsid protein (MCP). CLIP and TRIBE detected β-actin, albeit with false-positives. False-positive CLIP signals were attributed to nonspecific antibody interactions. In contrast, putative false-positive TRIBE targets were genes spatially proximal to the β-actin gene. MCP-ADAR edited nearby nascent transcripts consistent with interchromosomal contacts observed in Hi-C. The identification of nascent contacts implies RNA regulatory proteins (e.g., splicing factors) associated with multiple nascent transcripts, forming domains of post-transcriptional activity. Repeating these results with an integrated inducible MS2 reporter indicated that MS2-TRIBE can be applied to a broad array of cells and transcripts to study spatial organization and nuclear RNA regulation.

Original languageEnglish (US)
Article number101318
JournaliScience
Volume23
Issue number7
DOIs
StatePublished - Jul 24 2020

Keywords

  • Molecular Biology Experimental Approach
  • Transcriptomics

ASJC Scopus subject areas

  • General

Fingerprint Dive into the research topics of 'MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing'. Together they form a unique fingerprint.

Cite this