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Use of SNP-arrays for ChIP assays: computational aspects

Item Type:Article
Title:Use of SNP-arrays for ChIP assays: computational aspects
Creators Name:Muro, E.M. and McCann, J.A. and Rudnicki, M.A. and Andrade-Navarro, M.A.
Abstract:The simultaneous genotyping of thousands of single nucleotide polymorphisms (SNPs) in a genome using SNP-Arrays is a very important tool that is revolutionizing genetics and molecular biology. We expanded the utility of this technique by using it following chromatin immunoprecipitation (ChIP) to assess the multiple genomic locations protected by a protein complex recognized by an antibody. The power of this technique is illustrated through an analysis of the changes in histone H4 acetylation, a marker of open chromatin and transcriptionally active genomic regions, which occur during differentiation of human myoblasts into myotubes. The findings have been validated by the observation of a significant correlation between the detected histone modifications and the expression of the nearby genes, as measured by DNA expression microarrays. This chapter focuses on the computational analysis of the data.
Keywords:Chromatin, Histone, Acetylation, Microarray, Chromatin Immunoprecipitation, Single Nucleotide Polymorphism, Database Analysis, Genome Analysis
Source:Methods in Molecular Biology
ISSN:1064-3745
Publisher:Springer / Humana Press (U.S.A.)
Volume:567
Page Range:145-154
Date:2009
Official Publication:https://doi.org/10.1007/978-1-60327-414-2_10
PubMed:View item in PubMed

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