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Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish

Trinh, LA; Chong-Morrison, V; Sauka-Spengler, T; (2018) Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish. Methods , 150 pp. 24-31. 10.1016/j.ymeth.2018.07.011. Green open access

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Abstract

Interrogation of gene regulatory circuits in complex organisms requires precise and robust methods to label cell-types for profiling of target proteins in a tissue-specific fashion as well as data analysis to understand interconnections within the circuits. There are several strategies for obtaining cell-type and subcellular specific genome-wide data. We have developed a methodology, termed “biotagging” that uses tissue-specific, genetically encoded components to biotinylate target proteins, enabling in depth genome-wide profiling in zebrafish. We have refined protocols to use the biotagging approach that led to enhanced isolation of coding and non-coding RNAs from ribosomes and nuclei of genetically defined cell-types. The ability to study both the actively translated and transcribed transcriptome in the same cell population, coupled to genomic accessibility assays has enabled the study of cell-type specific gene regulatory circuits in zebrafish due to the high signal-to-noise achieved via its stringent purification protocol. Here, we provide detailed methods to isolate, profile and analyze cell-type specific polyribosome and nuclear transcriptome in zebrafish.

Type: Article
Title: Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.ymeth.2018.07.011
Publisher version: https://doi.org/10.1016/j.ymeth.2018.07.011
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: Cell-type specific in vivo biotinylation, Nuclear transcriptome, Enhancer RNA
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Cell and Developmental Biology
URI: https://discovery.ucl.ac.uk/id/eprint/10057527
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