PUBLICATION

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

Authors
Trinh, L.A., Chong-Morrison, V., Gavriouchkina, D., Hochgreb-Hägele, T., Senanayake, U., Fraser, S.E., Sauka-Spengler, T.
ID
ZDB-PUB-170414-11
Date
2017
Source
Cell Reports   19: 425-440 (Journal)
Registered Authors
Fraser, Scott E., Sauka-Spengler, Tatjana, Trinh, Le
Keywords
bi-directional transcription, cis-regulation, enhancers, in vivo biotinylation, myocardium, neural crest, nuclear transcriptome
Datasets
GEO:GSE89670
MeSH Terms
  • Animals
  • Cell Compartmentation/genetics
  • Cell Lineage/genetics
  • Conserved Sequence/genetics
  • Gene Expression Regulation, Developmental
  • Gene Regulatory Networks/genetics
  • Neural Crest/growth & development*
  • Organ Specificity/genetics
  • Transcription Factors/biosynthesis*
  • Transcription Factors/genetics
  • Transcriptome/genetics*
  • Zebrafish/genetics*
  • Zebrafish/growth & development
PubMed
28402863 Full text @ Cell Rep.
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.
Genes / Markers
Figures
Show all Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes