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Analysis of chromatin composition of repetitive sequences: the ChIP-Chop assay


Santoro, Raffaella (2014). Analysis of chromatin composition of repetitive sequences: the ChIP-Chop assay. In: Santoro, Raffaella. Functional Analysis of DNA and Chromatin. University of Zurich, Switzerland: Humana Press (Springer), 319-28.

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.

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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Additional indexing

Item Type:Book Section, refereed, original work
Communities & Collections:05 Vetsuisse Faculty > Department of Molecular Mechanisms of Disease
07 Faculty of Science > Department of Molecular Mechanisms of Disease
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2014
Deposited On:17 Jan 2014 08:54
Last Modified:05 Apr 2016 17:25
Publisher:Humana Press (Springer)
ISSN:1064-3745
Publisher DOI:https://doi.org/10.1007/978-1-62703-706-8_25
PubMed ID:24162999

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