PUBLICATION

Identification of sensory hair-cell transcripts by thiouracil-tagging in zebrafish

Authors
Erickson, T., Nicolson, T.
ID
ZDB-PUB-151024-5
Date
2015
Source
BMC Genomics   16: 842 (Journal)
Registered Authors
Erickson, Timothy, Nicolson, Teresa
Keywords
none
MeSH Terms
  • Animals
  • Animals, Genetically Modified
  • Gene Expression Regulation
  • Hair Cells, Auditory, Inner/metabolism*
  • High-Throughput Nucleotide Sequencing
  • Larva/genetics*
  • Larva/growth & development
  • Organ Specificity/genetics
  • Pentosyltransferases/biosynthesis
  • Pentosyltransferases/genetics*
  • RNA, Messenger/biosynthesis*
  • RNA, Messenger/genetics
  • Thiouracil/administration & dosage
  • Thiouracil/analogs & derivatives
  • Zebrafish/genetics
PubMed
26494580 Full text @ BMC Genomics
Abstract
Sensory hair cells are exquisitely sensitive to mechanical stimuli and as such, are prone to damage and apoptosis during dissections or in vitro manipulations. Thiouracil (TU)-tagging is a noninvasive method to label cell type-specific transcripts in an intact organism, thereby meeting the challenge of how to analyze gene expression in hair cells without the need to sort cells. We adapted TU-tagging to zebrafish to identify novel transcripts expressed in the sensory hair cells of the developing acoustico-lateralis organs.
We created a transgenic line of zebrafish expressing the T.gondii uracil phospho-ribosyltransferase (UPRT) enzyme specifically in the hair cells of the inner ear and lateral line organ. RNA was labeled by exposing 3 days post-fertilization (dpf) UPRT transgenic larvae to 2.5 mM 4-thiouracil (4TU) for 15 hours. Following total RNA isolation, poly(A) mRNA enrichment, and purification of TU-tagged RNA, deep sequencing was performed on the input and TU-tagged RNA samples.  RESULTS: Analysis of the RNA sequencing data revealed the expression of 28 transcripts that were significantly enriched (adjusted p-value < 0.05) in the UPRT TU-tagged RNA relative to the input sample. Of the 25 TU-tagged transcripts with mammalian homologs, the expression of 18 had not been previously demonstrated in zebrafish hair cells. The hair cell-restricted expression for 17 of these transcripts was confirmed by whole mount mRNA in situ hybridization in 3 dpf larvae.
The hair cell-restricted pattern of expression of these genes offers insight into the biology of this receptor cell type and may serve as useful markers to study the development and function of sensory hair cells. In addition, our study demonstrates the utility of TU-tagging to study nascent transcripts in specific cell types that are relatively rare in the context of the whole zebrafish larvae.
Genes / Markers
Figures
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Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes