Trinh, LA;
Chong-Morrison, V;
Gavriouchkina, D;
Hochgreb-Hagele, T;
Senanayake, U;
Fraser, SE;
Sauka-Spengler, T;
(2017)
Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome.
Cell Reports
, 19
(2)
pp. 425-440.
10.1016/j.celrep.2017.03.045.
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Abstract
Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types and robust methods for biochemical profiling of target proteins. We have developed a versatile, tissue-specific binary in vivo biotinylation system in zebrafish termed biotagging that uses genetically encoded components to biotinylate target proteins, enabling in-depth genome-wide analyses of their molecular interactions. Using tissue-specific drivers and cell-compartment-specific effector lines, we demonstrate the specificity of the biotagging toolkit at the biochemical, cellular, and transcriptional levels. We use biotagging to characterize the in vivo transcriptional landscape of migratory neural crest and myocardial cells in different cellular compartments (ribosomes and nucleus). These analyses reveal a comprehensive network of coding and non-coding RNAs and cis-regulatory modules, demonstrating that tissue-specific identity is embedded in the nuclear transcriptomes. By eliminating background inherent to complex embryonic environments, biotagging allows analyses of molecular interactions at high resolution.
Type: | Article |
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Title: | Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome |
Open access status: | An open access version is available from UCL Discovery |
DOI: | 10.1016/j.celrep.2017.03.045 |
Publisher version: | https://doi.org/10.1016/j.celrep.2017.03.045 |
Language: | English |
Additional information: | © 2017 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
Keywords: | in vivo biotinylation, nuclear transcriptome, neural crest, myocardium, enhancers, cis-regulation, bi-directional transcription |
UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Cell and Developmental Biology |
URI: | https://discovery.ucl.ac.uk/id/eprint/10055159 |
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