Tiling histone h3 lysine 4 and 27 methylation in zebrafish using high-density microarrays
- Lindeman, L.C., Reiner, A.H., Mathavan, S., Aleström, P., and Collas, P.
- PLoS One 5(12): e15651 (Journal)
- Registered Authors
- Aleström, Peter, Collas, Philippe, Mathavan, S.
- GEO:GSE23872, GEO:GSE23691, GEO:GSE23679
- MeSH Terms
- DNA Methylation
- Epigenesis, Genetic
- Gene Expression Regulation
- Oligonucleotide Array Sequence Analysis/methods*
- Promoter Regions, Genetic
- 21187971 Full text @ PLoS One
Lindeman, L.C., Reiner, A.H., Mathavan, S., Aleström, P., and Collas, P. (2010) Tiling histone h3 lysine 4 and 27 methylation in zebrafish using high-density microarrays. PLoS One. 5(12):e15651.
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
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Engineered Foreign Genes
Errata and Notes