title: ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Nijmegen, The Netherlands.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Akkers
authors.forename: Simon J
authors.initials: SJ
authors.lastname: van Heeringen
authors.forename: J Robert
authors.initials: JR
authors.lastname: Manak
authors.forename: Roland D
authors.initials: RD
authors.lastname: Green
authors.forename: Hendrik G
authors.initials: HG
authors.lastname: Stunnenberg
authors.forename: Gert Jan C
authors.initials: GJ
authors.lastname: Veenstra
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D044127:Epigenesis, Genetic; D016678:Genome; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*; D014981:Xenopus / Q000196:embryology* / Q000235:genetics
chemical_list: D014157:Transcription Factors