@article{1c5d05758dd34341aed55a03313f4759,
title = "MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing",
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.",
keywords = "Molecular Biology Experimental Approach, Transcriptomics",
author = "Jeetayu Biswas and Reazur Rahman and Varun Gupta and Michael Rosbash and Singer, {Robert H.}",
note = "Funding Information: The authors would also like to thank Charles Query (CCQ), members of the Singer Lab, and the Rosbash Lab for their helpful discussions and comments on the manuscript. We would also like to thank the members of the Cai and Fishman labs for access to their chromosome interaction data in MEFs. J.B. was supported with funding from an MSTP Training Grant T32GM007288 and predoctoral fellowship F30CA214009 . V.G. was supported by RO1GM57829 to CCQ. M.R. was supported by the Howard Hughes Medical Institute and R01DA037721 . R.H.S. was supported by National Institutes of Health grant R01NS083085 and the NIH Common Fund 4D Nucleome Program U01DA047729 . FACS sorting was performed with core support from NIH P30CA013330 . Funding Information: The authors would also like to thank Charles Query (CCQ), members of the Singer Lab, and the Rosbash Lab for their helpful discussions and comments on the manuscript. We would also like to thank the members of the Cai and Fishman labs for access to their chromosome interaction data in MEFs. J.B. was supported with funding from an MSTP Training Grant T32GM007288 and predoctoral fellowship F30CA214009. V.G. was supported by RO1GM57829 to CCQ. M.R. was supported by the Howard Hughes Medical Institute and R01DA037721. R.H.S. was supported by National Institutes of Health grant R01NS083085 and the NIH Common Fund 4D Nucleome Program U01DA047729. FACS sorting was performed with core support from NIH P30CA013330. Conceptualization, J.B. and R.H.S.; Methodology, J.B. V.G. and R.R.; Investigation, J.B. V.G. and R.R.; Writing ? Original Draft, J.B. and R.H.S.; Writing ? Review & Editing, J.B. R.R. M.R. and R.H.S.; Funding Acquisition, J.B. R.H.S. and M.R.; Resources, M.R. and R.H.S.; Supervision, M.R. and R.H.S. The authors have no competing interests. Publisher Copyright: {\textcopyright} 2020 The Author(s)",
year = "2020",
month = jul,
day = "24",
doi = "10.1016/j.isci.2020.101318",
language = "English (US)",
volume = "23",
journal = "iScience",
issn = "2589-0042",
publisher = "Elsevier Inc.",
number = "7",
}