PUBLICATION

Tiling histone h3 lysine 4 and 27 methylation in zebrafish using high-density microarrays

Authors
Lindeman, L.C., Reiner, A.H., Mathavan, S., Aleström, P., and Collas, P.
ID
ZDB-PUB-110103-28
Date
2010
Source
PLoS One   5(12): e15651 (Journal)
Registered Authors
Aleström, Peter, Collas, Philippe, Mathavan, S.
Keywords
none
Datasets
GEO:GSE23872, GEO:GSE23691, GEO:GSE23679
MeSH Terms
  • Animals
  • Chromatin/chemistry
  • DNA Methylation
  • Epigenesis, Genetic
  • Fibroblasts/cytology
  • Gene Expression Regulation
  • Histones/chemistry*
  • Histones/genetics
  • Humans
  • Immunoprecipitation
  • Lysine/chemistry*
  • Methylation
  • Mice
  • Oligonucleotide Array Sequence Analysis/methods*
  • Promoter Regions, Genetic
  • Zebrafish
PubMed
21187971 Full text @ PLoS One
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. PRINCIPAL FINDINGS: 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.
Genes / Markers
Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Errata and Notes