title: Tiling histone H3 lysine 4 and 27 methylation in zebrafish using high-density microarrays.
abstract: BACKGROUND
  Uncovering epigenetic states by chromatin immunoprecipitation and microarray hybridization (ChIP-chip) has significantly contributed to the understanding of gene regulation at the genome-scale level. Many studies have been carried out in mice and humans; however limited high-resolution information exists to date for non-mammalian vertebrate species.
  
  
  RESULTS
  We report a 2.1-million feature high-resolution Nimblegen tiling microarray for ChIP-chip interrogations of epigenetic states in zebrafish (Danio rerio). The array covers 251 megabases of the genome at 92 base-pair resolution. It includes ∼15 kb of upstream regulatory sequences encompassing all RefSeq promoters, and over 5 kb in the 5' end of coding regions. We identify with high reproducibility, in a fibroblast cell line, promoters enriched in H3K4me3, H3K27me3 or co-enriched in both modifications. ChIP-qPCR and sequential ChIP experiments validate the ChIP-chip data and support the co-enrichment of trimethylated H3K4 and H3K27 on a subset of genes. H3K4me3- and/or H3K27me3-enriched genes are associated with distinct transcriptional status and are linked to distinct functional categories.
  
  
  CONCLUSIONS
  We have designed and validated for the scientific community a comprehensive high-resolution tiling microarray for investigations of epigenetic states in zebrafish, a widely used developmental and disease model organism.
authors.affiliation: Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, and Norwegian Center for Stem Cell Research, Oslo, Norway.
authors.forename: Leif C
authors.initials: LC
authors.lastname: Lindeman
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Reiner
authors.forename: Sinnakaruppan
authors.initials: S
authors.lastname: Mathavan
authors.forename: Peter
authors.initials: P
authors.lastname: Aleström
authors.forename: Philippe
authors.initials: P
authors.lastname: Collas
mesh_terms: D000818:Animals; D002843:Chromatin / Q000737:chemistry; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005347:Fibroblasts / Q000166:cytology; D005786:Gene Expression Regulation; D006657:Histones / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D047468:Immunoprecipitation; D008239:Lysine / Q000737:chemistry*; D008745:Methylation; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011401:Promoter Regions, Genetic; D015027:Zebrafish
chemical_list: D002843:Chromatin; D006657:Histones; D008239:Lysine