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

By Raffaella Santoro

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

Topics: Department of Molecular Mechanisms of Disease, 570 Life sciences; biology
Publisher: Humana Press (Springer)
Year: 2014
DOI identifier: 10.1007/978-1-62703-706-8_25
OAI identifier: oai:www.zora.uzh.ch:89059
Provided by: ZORA
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