Transcriptomics

Dataset Information

4

Gene expression at four stages of the developing zebrafish embryo


ABSTRACT: Nucleosome arrangement in promoter regions has been shown to play an important role in gene regulation. Genome wide studies in yeast, flies, worms, mammalian ES and transformed cell lines have found well positioned nucleosomes with an area of nucleosome depletion flanking transcription start sites. This Nucleosome arrangement has been shown to be dependent on sequence (cis-regulatory factors), DNA binding factors (trans-regulatory factors) and ATP-dependant chromatin modifiers. However, little is understood about how the nascent embryonic genome positions nucleosomes during development. This is particularly intriguing since the embryonic genome undergoes a whole scale rechromatinization event upon fusion of sperm and oocyte. Using four stages of early embryonic zebrafish development we map nucleosome positions at the promoter region of 34 zebrafish hox genes. We find that nucleosome arrangement at the hox promoters is a dynamic process which happens over several stages. We also find evidence that trans-regulatory factors play a greater role in nucleosome positioning over cis-regulatory elements. Finally we provide evidence that transcriptional activation is the driving force behind the arrangement of nucleosomes at the promoters of hox gene during early development. Four tissue types: 2, 4, 6, and 9 hours post fertilzation embryos. Two treatments: Untreated (WT), and Retinoic Acid treated embryos(RA).

ORGANISM(S): Danio rerio  

SUBMITTER: Steven Weicksel   Charles G Sagerstrom  Steven E Weicksel 

PROVIDER: E-GEOD-43756 | ArrayExpress | 2013-12-09

SECONDARY ACCESSION(S): GSE43756PRJNA187332

REPOSITORIES: GEO, ArrayExpress

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Publications

Dynamic nucleosome organization at hox promoters during zebrafish embryogenesis.

Weicksel Steven E SE   Xu Jia J   Sagerström Charles G CG  

PloS one 20130509 5


Nucleosome organization at promoter regions plays an important role in regulating gene activity. Genome-wide studies in yeast, flies, worms, mammalian embryonic stem cells and transformed cell lines have found well-positioned nucleosomes flanking a nucleosome depleted region (NDR) at transcription start sites. This nucleosome arrangement depends on DNA sequence (cis-elements) as well as DNA binding factors and ATP-dependent chromatin modifiers (trans-factors). However, little is understood about  ...[more]

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