Abstract
BackgroundUncovering 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 FindingsWe 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.ConclusionsWe 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.
Highlights
The advent of chromatin immunoprecipitation (ChIP) combined with ChIP DNA hybridization to microarrays (ChIP-chip) or high-throughput sequencing (ChIP-seq) has enabled genomewide mapping of post-translational histone modifications and binding sites for transcription factors and chromatin regulators in a variety of mammalian cell types [1,2,3,4,5,6,7]
H3K4 methylation has been detected by ChIP-chip on promoter regions of Drosophila embryos [11] along with, in cultured cells, regions marked by methylated H3K27 [12,13]
Using a peak detection algorithm with a false discovery rate (FDR) of #0.1 for each modification, we identified a total of 8435 H3K4me3-enriched promoters and 3199 H3K27me3-enriched promoters (Figure 4B)
Summary
The advent of chromatin immunoprecipitation (ChIP) combined with ChIP DNA hybridization to microarrays (ChIP-chip) or high-throughput sequencing (ChIP-seq) has enabled genomewide mapping of post-translational histone modifications and binding sites for transcription factors and chromatin regulators in a variety of mammalian cell types [1,2,3,4,5,6,7]. Embryonic stem cells harbor chromatin domains co-enriched in H3K4me and H3K27me, which contain transcriptionally ‘poised’ developmentally-regulated genes [1]. Genome-wide epigenetic state maps are being built in nonmammalian species such as Drosophila melanogaster and Xenopus laevis primarily because of their attractiveness in developmental studies. 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; limited high-resolution information exists to date for non-mammalian vertebrate species
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
