Hox Genes pp 231-239 | Cite as

Chromatin Immunoprecipitation and Chromatin Immunoprecipitation with Massively Parallel Sequencing on Mouse Embryonic Tissue

  • Shilu Amin
  • Nicoletta BobolaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1196)


Regulation of gene expression must be tightly controlled during embryonic development. A central mechanism to control gene expression is the binding of sequence-specific transcription factors to cis-regulatory elements in the genome. Chromatin immunoprecipitation (ChIP) is a widely used technique to analyze binding of transcription factors and histone modifications on chromatin; however, it is limited to looking at a small number of genes. ChIP with massively parallel sequencing (ChIP-seq) is a recently developed powerful tool to analyze genome-wide binding of transcription factors and histone modifications and provides a vast amount of information into the regulation of gene expression. This chapter describes how ChIP and ChIP-seq are performed on mouse embryonic tissue.

Key words

ChIP ChIP-seq Embryo Mouse Transcription factor DNA 



The authors thank Eva Kutejova for her invaluable input in setting up the ChIP protocol. S.A. is supported by the Biotechnology and Biological Sciences Research Council BB/H018123/2 to N.B.


  1. 1.
    Barski A, Zhao K (2009) Genomic location analysis by ChIP-Seq. J Cell Biochem 107:11–18PubMedCrossRefGoogle Scholar
  2. 2.
    Farnham PJ (2009) Insights from genomic profiling of transcription factors. Nat Rev Genet 10:605–616PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837PubMedCrossRefGoogle Scholar
  4. 4.
    Mikkelsen TS, Ku M, Jaffe DB et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Robertson G, Hirst M, Bainbridge M et al (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651–657PubMedCrossRefGoogle Scholar
  6. 6.
    Johnson DS, Mortazavi A, Myers RM et al (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497–1502PubMedCrossRefGoogle Scholar
  7. 7.
    Jiang C, Pugh BF (2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 10:161–172PubMedCrossRefGoogle Scholar
  8. 8.
    Schones DE, Zhao K (2008) Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 9:179–191PubMedCrossRefGoogle Scholar
  9. 9.
    Rhee HS, Pugh BF (2011) Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147:1408–1419PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Adli M, Bernstein BE (2011) Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc 6:1656–1668PubMedCrossRefGoogle Scholar
  11. 11.
    Kutejova E, Engist B, Self M et al (2008) Six2 functions redundantly immediately downstream of Hoxa2. Development 135:1463–1470PubMedCrossRefGoogle Scholar
  12. 12.
    Donaldson IJ, Amin S, Hensman JJ et al (2012) Genome-wide occupancy links Hoxa2 to Wnt-β-catenin signaling in mouse embryonic development. Nucleic Acids Res 40:3990–4001PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.School of Dentistry, Faculty of Medical & Human SciencesUniversity of ManchesterManchesterUK
  2. 2.Centre for Endocrinology & Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Science CentreUniversity of ManchesterManchesterUK
  3. 3.School of DentistryThe University of ManchesterManchesterUK

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