PUBLICATION
Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish
- Authors
- Trinh, L.A., Chong-Morrison, V., Sauka-Spengler, T.
- ID
- ZDB-PUB-180805-4
- Date
- 2018
- Source
- Methods (San Diego, Calif.) 150: 24-31 (Journal)
- Registered Authors
- Sauka-Spengler, Tatjana, Trinh, Le
- Keywords
- Cell-type specific in vivo biotinylation, Enhancer RNA, Nuclear transcriptome
- MeSH Terms
-
- Animals
- Biotinylation/methods*
- Cell Fractionation
- Gene Expression Profiling/methods*
- Gene Regulatory Networks/genetics
- Polyribosomes/genetics
- Polyribosomes/metabolism
- RNA/isolation & purification
- RNA/metabolism
- Staining and Labeling/methods*
- Transcriptome/genetics
- Zebrafish/genetics*
- Zebrafish/metabolism
- PubMed
- 30076893 Full text @ Methods
Citation
Trinh, L.A., Chong-Morrison, V., Sauka-Spengler, T. (2018) Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish. Methods (San Diego, Calif.). 150:24-31.
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping