Cookies on this website
We use cookies to ensure that we give you the best experience on our website. If you click 'Continue' we'll assume that you are happy to receive all cookies and you won't see this message again. Click 'Find out more' for information on how to change your cookie settings.

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.

Original publication

DOI

10.1016/j.celrep.2017.03.045

Type

Journal article

Journal

Cell Rep

Publication Date

11/04/2017

Volume

19

Pages

425 - 440

Keywords

bi-directional transcription, cis-regulation, enhancers, in vivo biotinylation, myocardium, neural crest, nuclear transcriptome, Animals, Cell Compartmentation, Cell Lineage, Conserved Sequence, Gene Expression Regulation, Developmental, Gene Regulatory Networks, Neural Crest, Organ Specificity, Transcription Factors, Transcriptome, Zebrafish