Research Article: ChIP-Chip Designs to Interrogate the Genome of Xenopus Embryos for Transcription Factor Binding and Epigenetic Regulation

Date Published: January 21, 2010

Publisher: Public Library of Science

Author(s): Robert C. Akkers, Simon J. van Heeringen, J. Robert Manak, Roland D. Green, Hendrik G. Stunnenberg, Gert Jan C. Veenstra, Ferenc Mueller.

Abstract: Chromatin immunoprecipitation combined with genome tile path microarrays or deep sequencing can be used to study genome-wide epigenetic profiles and the transcription factor binding repertoire. Although well studied in a variety of cell lines, these genome-wide profiles have so far been little explored in vertebrate embryos.

Partial Text: Chromatin immunoprecipitation combined with either microarray hybridization (ChIP-chip) or sequencing (ChIP-seq) allows to determine genomic association of DNA binding proteins and to analyze epigenetic regulation [1], [2], [3]. Active transcription coincides with epigenetic features like the presence of the histone H3 lysine 4 trimethylation (H3K4me3) and acetylation of lysine 9 of histone H3 (H3K9ac) at the 5′ end of transcriptionally active genes [4], [5], [6]. In the context of development little is known about epigenetic marks in embryos using ChIP profiling. H3K4me3 ChIP-chip using zebrafish embryos identified actively transcribed embryonic genes [7]. The latter mark was also detected in Drosophila embryos at promoter regions [8]. ChIP sequencing of H3K4me3 and H3K27me3, an inactive histone mark, was used to enhance 5′ gene annotation in Xenopus and to analyze spatial regulation of gene expression during gastrulation [9]. The two marks only appear after the onset of transcription at the mid-blastula transition with a hierarchy in deposition of H3K4me3 and H3K27me3, respectively.

Our results present ChIP microarray designs for X. tropicalis. So far gene regulatory networks and epigenetic regulation during vertebrate embryogenesis have not extensively been studied using genome-wide binding analysis. By contrast, many epigenetic profiles have been established for human cells in culture [12], providing a solid conceptual framework to analyze epigenetic regulation in other systems. The presence of H3K4me3 at the 5′ end of transcribed genes is consistent in many experimental systems [5], [7], [8], [9], [13], [14], [15], [16], [17], [18].



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