Canonical nucleosome organization at promoters forms during genome activation

The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate f...

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Bibliographic Details
Published in:Genome research 2014-02, Vol.24 (2), p.260-266
Main Authors: Zhang, Yong, Vastenhouw, Nadine L, Feng, Jianxing, Fu, Kai, Wang, Chenfei, Ge, Ying, Pauli, Andrea, van Hummelen, Paul, Schier, Alexander F, Liu, X Shirley
Format: Article
Language:English
Subjects:
Animals
Danio rerio
DNA-Binding Proteins - genetics
Embryonic Development - genetics
Genome
Histone-Lysine N-Methyltransferase - genetics
Nucleosomes - genetics
Promoter Regions, Genetic
RNA Polymerase II - genetics
Sequence Analysis, DNA
Transcription, Genetic
Transcriptional Activation - genetics
Zebrafish
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Summary:The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of histone H3 lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.157750.113