Genome-wide mapping of allele-specific protein-DNA interactions in human cells.
We describe a high-throughput method, named ChIP-SNP, for the identification of allele-specific protein-DNA interactions throughout the human genome. ChIP-SNP combines chromatin immunoprecipitation (ChIP) with whole-genome single nucleotide polymorphism (SNP) genotyping microarray analysis. We demonstrated that it can be used to accurately identify allele-specific binding of RNA polymerase II (RNAP) in the human fibroblast genome, uncovering imprinted genes and other allele-specific binding events. ChIP-SNP will facilitate the study of mechanisms of allele-specific gene expression.
Maynard
Nathaniel D
ND
Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Ave., La Jolla, California 92037, USA.
Chen
Jing
J
Stuart
Rhona K
RK
Fan
Jian-Bing
JB
Ren
Bing
B
D000483:Alleles; D002460:Cell Line; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002874:Chromosome Mapping; D004247:DNA / Q000235:genetics*; D005347:Fibroblasts / Q000201:enzymology / Q000378:metabolism; D015870:Gene Expression; D015894:Genome, Human; D018392:Genomic Imprinting; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D012319:RNA Polymerase II / Q000235:genetics* / Q000378:metabolism
D004247:DNA; D012319:RNA Polymerase II