Analysis of Chromatin Composition of Repetitive Sequences: The ChIP-Chop Assay

  • Raffaella Santoro
Part of the Methods in Molecular Biology book series (MIMB, volume 1094)


Chromatin immunoprecipitation (ChIP) is a powerful method that allows to probe specific protein-DNA interactions in vivo and to estimate the occupancy of proteins at specific sites of the genome. However, the traditional ChIP assay is not able to distinguish whether repeats that share identical sequences display a different composition of associated factors and, consequently, different functions. The ChIP-chop method provides a useful application to analyze the interaction of proteins with repetitive sequences based on their CpG methylation content. The detailed ChIP-chop protocol that serves to determine the chromatin composition of active and silent ribosomal RNA (rRNA) genes, repeats that share identical sequences but display distinct functions and chromatin compositions, is reported here.

Key words

Chromatin immunoprecipitation ChIP ChIP-chop DNA methylation Chromatin Epigenetics Ribosomal RNA genes rRNA rDNA 



This work was supported by the by the Swiss National Science Foundation (SNF, 310003A-135801) and the Mäxi Stiftung.


  1. 1.
    Santoro R (2011) The nucleolus. In: Olson MOJ (ed) Protein reviews, vol 15. Springer, New York, NY, pp 57–82Google Scholar
  2. 2.
    Conconi A, Widmer RM, Koller M et al (1989) Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell 57:753–761PubMedCrossRefGoogle Scholar
  3. 3.
    Santoro R, Grummt I (2001) Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription. Mol Cell 8:719–725PubMedCrossRefGoogle Scholar
  4. 4.
    Santoro R, Li J, Grummt I (2002) The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription. Nat Genet 32: 393–396PubMedCrossRefGoogle Scholar
  5. 5.
    Guetg C et al (2010) The NoRC complex mediates the heterochromatin formation and stability of silent rRNA genes and centromeric repeats. EMBO J 29:2135–2146PubMedCrossRefGoogle Scholar
  6. 6.
    Strohner R et al (2001) NoRC–a novel member of mammalian ISWI-containing chromatin remodeling machines. EMBO J 20: 4892–4900PubMedCrossRefGoogle Scholar
  7. 7.
    Boisvert FM, van Koningsbruggen S, Navascues J et al (2007) The multifunctional nucleolus. Nat Rev Mol Cell Biol 8:574–585PubMedCrossRefGoogle Scholar
  8. 8.
    Guetg C, Santoro R (2012) Formation of nuclear heterochromatin: the nucleolar point of view. Epigenetics 7:811–814PubMedCrossRefGoogle Scholar
  9. 9.
    Guetg C, Scheifele F, Rosenthal F et al (2012) Inheritance of silent rDNA chromatin Is mediated by PARP1 via noncoding RNA. Mol Cell 45:790–800PubMedCrossRefGoogle Scholar
  10. 10.
    Santoro R, Lienemann P, Fussenegger M (2009) Epigenetic engineering of ribosomal RNA genes enhances protein production. PLoS One 4:e6653PubMedCrossRefGoogle Scholar
  11. 11.
    Santoro R, Grummt I (2005) Epigenetic mechanism of rRNA gene silencing: temporal order of NoRC-mediated histone modification, chromatin remodeling, and DNA methylation. Mol Cell Biol 25:2539–2546PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  • Raffaella Santoro
    • 1
  1. 1.Institute of Veterinary Biochemistry and Molecular BiologyUniversity of ZurichZurichSwitzerland

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