Use of SNP-arrays for ChIP assays: computational aspects.
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.
Muro
Enrique M
EM
Max-Delbrück Center for Molecular Medicine, Berlin, Germany.
McCann
Jennifer A
JA
Rudnicki
Michael A
MA
Andrade-Navarro
Miguel A
MA
D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D006801:Humans; D020407:Internet; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011381:Programming Languages; D012984:Software