title: Canonical nucleosome organization at promoters forms during genome activation.
abstract: 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.
authors.affiliation: School of Life Science and Technology, Tongji University, Shanghai 200092, China;
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Nadine L
authors.initials: NL
authors.lastname: Vastenhouw
authors.forename: Jianxing
authors.initials: J
authors.lastname: Feng
authors.forename: Kai
authors.initials: K
authors.lastname: Fu
authors.forename: Chenfei
authors.initials: C
authors.lastname: Wang
authors.forename: Ying
authors.initials: Y
authors.lastname: Ge
authors.forename: Andrea
authors.initials: A
authors.lastname: Pauli
authors.forename: Paul
authors.initials: P
authors.lastname: van Hummelen
authors.forename: Alexander F
authors.initials: AF
authors.lastname: Schier
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D000818:Animals; D004268:DNA-Binding Proteins / Q000235:genetics*; D047108:Embryonic Development / Q000235:genetics*; D016678:Genome; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics; D009707:Nucleosomes / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D015533:Transcriptional Activation / Q000235:genetics*; D015027:Zebrafish
chemical_list: D004268:DNA-Binding Proteins; D009707:Nucleosomes; D011495:Histone-Lysine N-Methyltransferase; D012319:RNA Polymerase II