title: 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.
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Le A
authors.initials: LA
authors.lastname: Trinh
authors.affiliation: Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Chong-Morrison
authors.affiliation: Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
authors.forename: Daria
authors.initials: D
authors.lastname: Gavriouchkina
authors.affiliation: Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Hochgreb-Hägele
authors.affiliation: Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
authors.forename: Upeka
authors.initials: U
authors.lastname: Senanayake
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Scott E
authors.initials: SE
authors.lastname: Fraser
authors.affiliation: Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK. Electronic address: tatjana.sauka-spengler@imm.ox.ac.uk.
authors.forename: Tatjana
authors.initials: T
authors.lastname: Sauka-Spengler
mesh_terms: D000818:Animals; D002451:Cell Compartmentation / Q000235:genetics; D019070:Cell Lineage / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks / Q000235:genetics; D009432:Neural Crest / Q000254:growth & development*; D009928:Organ Specificity / Q000235:genetics; D014157:Transcription Factors / Q000096:biosynthesis* / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics* / Q000254:growth & development
chemical_list: D014157:Transcription Factors
keywords: bi-directional transcription; cis-regulation; enhancers; in vivo biotinylation; myocardium; neural crest; nuclear transcriptome