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

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

Abstract

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 

Notes

Acknowledgements

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

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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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