E-GEOD-44269 - Canonical nucleosome organization at promoters forms during genome activation

Released on 18 October 2013, last updated on 4 May 2014
Danio rerio
Samples (11)
Protocols (4)
The position of nucleosomes influences DNA accessibility to DNA-binding proteins. Genome-wide nucleosome profiles often report the observation of a canonical nucleosome organization at gene promoters where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. It is unclear how this canonical promoter nucleosome organization forms and how it is related to transcription activation and the establishment of histone marks during development. Here we report the genome-wide organization of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear in thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization cannot be explained by DNA sequence preference, and is independent of transcription and the presence of RNA polymerase II, but strongly correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3). Our study further suggests that promoter nucleosome structure primes genes to future transcription activation. Together, this study reveals that genome activation but not transcription underlies the organization of nucleosome arrays during early embryogenesis. MNase-seq to generate nucleosome organization in two stages of zebrafish development; two biological replicates for each stage. 7 ChIP-seq experiments in three stages.
Experiment types
ChIP-seq, other 
Yong Zhang <geo@ncbi.nlm.nih.gov>, Alexander F Schier, Chenfei Wang, Jianxing Feng, Kai Fu, Nadine L Vastenhouw, X S Liu
Exp. designProtocolsVariablesProcessedSeq. reads