CaltechAUTHORS
  A Caltech Library Service

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

Trinh, Le A. and Chong-Morrison, Vanessa and Gavriouchkina, Daria and Hochgreb-Hägele, Tatiana and Senanayake, Upeka and Fraser, Scott E. and Sauka-Spengler, Tatjana (2017) Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome. Cell Reports, 19 (2). pp. 425-440. ISSN 2211-1247. PMCID PMC5400779. https://resolver.caltech.edu/CaltechAUTHORS:20170418-103825470

[img] PDF - Published Version
Creative Commons Attribution Non-commercial No Derivatives.

6Mb
[img] PDF (Supplemental Experimental Procedures, Figures S1–S7, and Tables S1 and S2) - Supplemental Material
Creative Commons Attribution Non-commercial No Derivatives.

27Mb
[img] MS Excel (List of Highly Regulated Genes Associated with Active CRMs, Related to Figure 6. ) - Supplemental Material
Creative Commons Attribution Non-commercial No Derivatives.

240Kb

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20170418-103825470

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://doi.org/10.1016/j.celrep.2017.03.045DOIArticle
http://www.sciencedirect.com/science/article/pii/S2211124717303911PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400779/PubMed CentralArticle
ORCID:
AuthorORCID
Fraser, Scott E.0000-0002-5377-0223
Sauka-Spengler, Tatjana0000-0001-9289-0263
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.
Funders:
Funding AgencyGrant Number
March of Dimes5-FY12-564
Lister InstituteUNSPECIFIED
Oxford UniversityRE/08/004
Clarendon Fund FellowshipUNSPECIFIED
Swiss National Fund (SNF)PBSKP3_145791
Subject Keywords:in vivo biotinylation; nuclear transcriptome; neural crest; myocardium; enhancers; cis-regulation; bi-directional transcription
Issue or Number:2
PubMed Central ID:PMC5400779
Record Number:CaltechAUTHORS:20170418-103825470
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170418-103825470
Official Citation:Le A. Trinh, Vanessa Chong-Morrison, Daria Gavriouchkina, Tatiana Hochgreb-Hägele, Upeka Senanayake, Scott E. Fraser, Tatjana Sauka-Spengler, Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome, Cell Reports, Volume 19, Issue 2, 11 April 2017, Pages 425-440, ISSN 2211-1247, http://doi.org/10.1016/j.celrep.2017.03.045. (http://www.sciencedirect.com/science/article/pii/S2211124717303911)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:76632
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:18 Apr 2017 18:14
Last Modified:03 Oct 2019 17:03

Repository Staff Only: item control page