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

Abstract

Summary: 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. : A genetically encoded in vivo biotinylation system in zebrafish developed by Trinh et al. reveals cell-type- and subcellular-compartment-specific coding and non-coding RNAs in developing cardiomyocytes and neural crest cells. Characterization of non-coding RNAs in neural crest reveals bidirectionally transcribed cis-regulatory elements that define a specific gene regulatory signature. Keywords: in vivo biotinylation, nuclear transcriptome, neural crest, myocardium, enhancers, cis-regulation, bi-directional transcription