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The characterization of protein-deoxyribonucleic acid (DNA) interactions occurring at an allele-specific level is important to resolving the functional consequences of genetic variation in non-coding DNA for gene expression and regulation. The approach of haplotype-specific chromatin immunoprecipitation (i.e., haploChIP) resolves in living cells relative protein-DNA binding to a particular allele through immunoprecipitation of proteins crosslinked to DNA. Single-nucleotide polymorphisms present in a heterozygous form are used as markers to differentiate allelic origin. This in turn allows resolution of specific haplotypes showing differences in relative protein occupancy. The haploChIP approach allows testing of in vitro hypotheses that a transcription factor protein shows haplotype specific occupancy. In addition, the haploChIP approach allows screening of haplotypes for differences in relative gene expression by immunoprecipitation using antibodies to phosphorylated Pol II.

Original publication

DOI

10.1385/1-59259-957-5:049

Type

Journal article

Journal

Methods Mol Biol

Publication Date

2005

Volume

311

Pages

49 - 60

Keywords

Alleles, Cell Line, Chromatin, Chromatin Immunoprecipitation, Haplotypes, Lymphocytes, Nuclear Proteins, Phosphorylation, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Protein Binding, RNA Polymerase II