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

Robert C Akkers; Simon J van Heeringen; J Robert Manak; Roland D Green; Hendrik G Stunnenberg; Gert Jan C Veenstra

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

Journal article

Open access

Peer reviewed

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

Robert C Akkers, Simon J van Heeringen, J Robert Manak, Roland D Green, Hendrik G Stunnenberg and Gert Jan C Veenstra

PloS one, Vol.5(1), pp.e8820-e8820

01/21/2010

DOI: 10.1371/journal.pone.0008820

PMCID: PMC2809088

PMID: 20098671

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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.

Animals

Chromatin Immunoprecipitation

Epigenesis, Genetic

Genome

Oligonucleotide Array Sequence Analysis

Promoter Regions, Genetic

Protein Binding

Transcription Factors - metabolism

Xenopus - embryology

Xenopus - genetics

Details

Title: Subtitle: ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation
Creators: Robert C Akkers - Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Nijmegen, The Netherlands
Simon J van Heeringen
J Robert Manak
Roland D Green
Hendrik G Stunnenberg
Gert Jan C Veenstra
Resource Type: Journal article
Publication Details: PloS one, Vol.5(1), pp.e8820-e8820
DOI: 10.1371/journal.pone.0008820
PMID: 20098671
PMCID: PMC2809088
NLM abbreviation: PLoS One
ISSN: 1932-6203
eISSN: 1932-6203
Grant note: R01 HD054356-03 / NICHD NIH HHS 5 R01 HD054356 / NICHD NIH HHS R01 HD054356 / NICHD NIH HHS
Language: English
Date published: 01/21/2010
Academic Unit: Stead Family Department of Pediatrics; Biology; Craniofacial Anomalies Research Center
Record Identifier: 9984217528602771

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