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Published April 11, 2017 | Supplemental Material + Published
Journal Article Open

Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome

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.

Additional Information

© 2017 The Authors. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Received: August 1, 2014. Revised: December 21, 2016. Accepted: March 13, 2017. Published: April 11, 2017. This work was supported by a March of Dimes Basil O'Connor Award (#5-FY12-564), a Lister Institute Research Prize, and an Oxford BHF CRE award (#RE/08/004, to T.S.-S.), a Clarendon Fund Fellowship (to V.C.-M.), and an SNF Fellowship (PBSKP3_145791, to D.G.). We thank Tudor Fulga, Ferdinand Marlétaz, and Simon Restrepo for comments on the manuscript.

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Published - PIIS2211124717303911.pdf

Supplemental Material - mmc1.pdf

Supplemental Material - mmc2.xlsx

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