ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation.

PloS One
Robert C AkkersGert Jan C Veenstra

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. 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.

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Citations

Aug 19, 2015·Developmental Biology·Shinichi HayashiHitoshi Yokoyama
Dec 6, 2011·Genesis : the Journal of Genetics and Development·Ozren BogdanovićGert Jan C Veenstra

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Datasets Mentioned

BETA
GSE19413
GSE14025
AL132957

Methods Mentioned

BETA
immunoprecipitation
acetylation
ChIP
ChIP-chip
ChIP-seq
PCR

Software Mentioned

UCSC Genome Browser
TileMap
xenTro2
JGI
Xtev

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