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

• DOI: 10.1016/j.isci.2020.101318
• Publication Date: 2020-06-28T05:32:55Z
• Authors: Jeetayu Biswas; Reazur Rahman; Varun Gupta; Michael Rosbash; Robert H. Singer
• Keywords: Transcription

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