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Updated: Jun 16, 2026
Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq
Published on: February 26, 2015
ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic
Robert C Akkers1, Simon J van Heeringen, J Robert Manak
1Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Nijmegen, The Netherlands.
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 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.
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02:36Chromatin Immunoprecipitation- ChIP
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
01:24Methods of Nuclear Reprogramming