PUBLICATION

Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos

Authors
Armant, O., März, M., Schmidt, R., Ferg, M., Diotel, N., Ertzer, R., Bryne, J.C., Yang, L., Baader, I., Reischl, M., Legradi, J., Mikut, R., Stemple, D., Ijcken, W.V., van der Sloot, A., Lenhard, B., Strähle, U., and Rastegar, S.
ID
ZDB-PUB-130611-31
Date
2013
Source
Developmental Biology   380(2): 351-62 (Journal)
Registered Authors
Armant, Olivier, Baader, Isabelle, Diotel, Nicolas, Ertzer, Raymond, Ferg, Marco, Legradi, Jessica, Mikut, Ralf, Rastegar, Sepand, Rodriguez Viales, Rebecca, Stemple, Derek L., Strähle, Uwe, Yang, Lixin
Keywords
transcription, chromatin, basal transcription, RNAseq, transcription factor, zebrafish, atlas of gene expression, genome, phylotypic stage
Datasets
GEO:GSE39703, GEO:GSE39728
MeSH Terms
  • Animals
  • Body Patterning
  • Gene Expression Regulation, Developmental*
  • Gene Library
  • Genes, Regulator*
  • Transcription, Genetic
  • Zebrafish/embryology*
  • Zebrafish/genetics
PubMed
23684812 Full text @ Dev. Biol.
Abstract

Transcription is the primary step in the retrieval of genetic information. A substantial proportion of the protein repertoire of each organism consists of transcriptional regulators (TRs). It is believed that the differential expression and combinatorial action of these TRs is essential for vertebrate development and body homeostasis. We mined the zebrafish genome exhaustively for genes encoding TRs and determined their expression in the zebrafish embryo by sequencing to saturation and in situ hybridisation. At the evolutionary conserved phylotypic stage, 75% of the 3302 TR genes encoded in the genome are already expressed. The number of expressed TR genes increases only marginally in subsequent stages and is maintained during adulthood suggesting important roles of the TR genes in body homeostasis. Fewer than half of the TR genes (45%, n=1711 genes) are expressed in a tissue-restricted manner in the embryo. Transcripts of 207 genes were detected in a single tissue in the 24 h embryo, potentially acting as regulators of specific processes. Other TR genes were expressed in multiple tissues. However, with the exception of certain territories in the nervous system, we did not find significant synexpression suggesting that most tissue-restricted TRs act in a freely combinatorial fashion. Our data indicate that elaboration of body pattern and function from the phylotypic stage onward relies mostly on redeployment of TRs and post-transcriptional processes.

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