|ZFIN ID: ZDB-PUB-180805-4|
Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish
Trinh, L.A., Chong-Morrison, V., Sauka-Spengler, T.
|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|
|PubMed:||30076893 Full text @ Methods|
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.
ABSTRACTInterrogation 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.
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