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

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 bio...

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Autores principales: Trinh, Le A., Chong-Morrison, Vanessa, Gavriouchkina, Daria, Hochgreb-Hägele, Tatiana, Senanayake, Upeka, Fraser, Scott E., Sauka-Spengler, Tatjana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cell Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400779/
https://www.ncbi.nlm.nih.gov/pubmed/28402863
http://dx.doi.org/10.1016/j.celrep.2017.03.045
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author Trinh, Le A.
Chong-Morrison, Vanessa
Gavriouchkina, Daria
Hochgreb-Hägele, Tatiana
Senanayake, Upeka
Fraser, Scott E.
Sauka-Spengler, Tatjana
author_facet Trinh, Le A.
Chong-Morrison, Vanessa
Gavriouchkina, Daria
Hochgreb-Hägele, Tatiana
Senanayake, Upeka
Fraser, Scott E.
Sauka-Spengler, Tatjana
author_sort Trinh, Le A.
collection PubMed
description 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.
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spelling pubmed-54007792017-05-01 Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome Trinh, Le A. Chong-Morrison, Vanessa Gavriouchkina, Daria Hochgreb-Hägele, Tatiana Senanayake, Upeka Fraser, Scott E. Sauka-Spengler, Tatjana Cell Rep Resource 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. Cell Press 2017-04-11 /pmc/articles/PMC5400779/ /pubmed/28402863 http://dx.doi.org/10.1016/j.celrep.2017.03.045 Text en © 2017 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Resource
Trinh, Le A.
Chong-Morrison, Vanessa
Gavriouchkina, Daria
Hochgreb-Hägele, Tatiana
Senanayake, Upeka
Fraser, Scott E.
Sauka-Spengler, Tatjana
Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome
title Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome
title_full Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome
title_fullStr Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome
title_full_unstemmed Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome
title_short Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome
title_sort biotagging of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400779/
https://www.ncbi.nlm.nih.gov/pubmed/28402863
http://dx.doi.org/10.1016/j.celrep.2017.03.045
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