Zebrafish promoter microarrays identify actively transcribed embryonic genes

Abstract

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Zebrafish promoter microarray <p>The development and verification of a genomic microarray for ChIP-chip analysis of zebrafish genes is described.</p> AbstractWe have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation with an antibody directed against tri-methylated lysine 4 of Histone H3, we demonstrate the feasibility of this method in zebrafish. This approach will allow investigators to determine the genomic binding locations of DNA interacting proteins during development and expedite the assembly of the genetic networks that regulate embryogenesis.

Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites

“…More recently, ChIP-on-chip has been applied to early zebrafish embryos to investigate the binding of modified hi-stones within the genome. Initial studies confirmed that H3K4me3 binding was enriched at transcriptional start sites similar to findings in mammalian cells (Wardle et al, 2006). More recently, a similar approach was used to demonstrate that both H3K4me3 and H3K27me3 marks are deposited at developmentally regulated genes independently of transcriptional activation immediately prior to the onset of zygotic transcription in zebrafish (Vastenhouw et al, 2010).…”

Tiling Histone H3 Lysine 4 and 27 Methylation in Zebrafish Using High-Density Microarrays

“…Nevertheless, a noticeable difference in the distribution of H3K4me3 among species or cell types examined to date lies in the detection of a “dip” immediately upstream of the TSS in mouse and human cells [7], [10], [22], [29]. This dip is not apparent in the Xenopus ChIP-chip or ChIP-seq data [15], [16], nor in the zebrafish ChIP-chip data [17], [18] (this study). This difference is unlikely to be due to array design, in particular probe spacing, because that is very similar (80–92 bp) in the mouse [7], human [10] or zebrafish [18] (this study) arrays used.…”

Reproductive and developmental toxicity of dioxin in fish

“…Fortunately, transcriptome analysis and interactome mapping (Alexeyenko et al, 2010) along with new methodologies in zebrafish such as ChIP-chip (Wardle et al, 2006), more rapid transgenic construction techniques (Kwan et al, 2007), RNA-Seq (Wang et al, 2009), genome-wide quantitative trait loci (QTL) analysis (Waits and Nebert, 2011) and advances in morpholino technology (Shestopalov et al, 2007) can be expected to further accelerate knowledge of AHR biology, including the identification of new transcriptional targets and mechanisms underlying the diverse endpoints of TCDD toxicity (Alexeyenko et al, 2010; Waits and Nebert, 2011; Yoshioka et al, 2011). …”