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PLoS One 2010 Jan 21;51:e8820. doi: 10.1371/journal.pone.0008820.
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ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation.

Akkers RC , van Heeringen SJ , Manak JR , Green RD , Stunnenberg HG , Veenstra GJ .

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. Here we report on two genome tile path ChIP-chip designs for interrogating the Xenopus tropicalis genome. In particular, a whole-genome microarray design was used to identify active promoters by close proximity to histone H3 lysine 4 trimethylation. A second microarray design features these experimentally derived promoter regions in addition to currently annotated 5' ends of genes. These regions truly represent promoters as shown by binding of TBP, a key transcription initiation factor. A whole-genome and a promoter tile path microarray design was developed. Both designs can be used to study epigenetic phenomena and transcription factor binding in developing Xenopus embryos.

PubMed ID: 20098671
PMC ID: PMC2809088
Article link: PLoS One
Grant support: [+]

Species referenced: Xenopus tropicalis
Genes referenced: cdkn2c faf1 fas mapk1 ppil2 rnf11 rnf11.2 tbp tuba1c uxs1 ypel1

Article Images: [+] show captions
References [+] :
Akkers, A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. 2009, Pubmed, Xenbase