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.
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Acknowledgements
This work was supported by the by the Swiss National Science Foundation (SNF, 310003A-135801) and the Mäxi Stiftung.
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Santoro, R. (2014). Analysis of Chromatin Composition of Repetitive Sequences: The ChIP-Chop Assay. In: Stockert, J., Espada, J., Blázquez-Castro, A. (eds) Functional Analysis of DNA and Chromatin. Methods in Molecular Biology, vol 1094. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-706-8_25
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DOI: https://doi.org/10.1007/978-1-62703-706-8_25
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