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Dev Biol. 2013 Aug 15;380(2):351-62. doi: 10.1016/j.ydbio.2013.05.006. Epub 2013 May 14.

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

Author information

1
Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Postfach 3640, 76021 Karlsruhe, Germany.

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 24h 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.

KEYWORDS:

Atlas of gene expression; Basal transcription; Chromatin; Genome; Phylotypic stage; RNAseq; Transcription; Transcription factor; Zebrafish

PMID:
23684812
PMCID:
PMC4351915
DOI:
10.1016/j.ydbio.2013.05.006
[Indexed for MEDLINE]
Free PMC Article
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