chip-chip designs to interrogate the genome of xenopus embryos for transcription factor binding and epigenetic regulationchip-chip设计询问非洲爪蟾蜍胚胎基因组的转录因子绑定和表观遗传调控.pdfVIP

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chip-chip designs to interrogate the genome of xenopus embryos for transcription factor binding and epigenetic regulationchip-chip设计询问非洲爪蟾蜍胚胎基因组的转录因子绑定和表观遗传调控.pdf

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chip-chip designs to interrogate the genome of xenopus embryos for transcription factor binding and epigenetic regulationchip-chip设计询问非洲爪蟾蜍胚胎基因组的转录因子绑定和表观遗传调控

ChIP-Chip Designs to Interrogate the Genome of Xenopus Embryos for Transcription Factor Binding and Epigenetic Regulation 1. 1. 2,3 2 Robert C. Akkers , Simon J. van Heeringen , J. Robert Manak , Roland D. Green , Hendrik G. 1 1 Stunnenberg , Gert Jan C. Veenstra * 1 Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Nijmegen, The Netherlands, 2 Roche Nimblegen, Inc., Madison Wisconsin, United States of America, 3 Department of Biology, University of Iowa, Iowa City, Iowa, United States of America 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. Principal Findings: 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 59 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. Citation: Akkers RC, van Heeringen SJ, Manak JR, Gre