In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading.

Journal article

In vivo characterization of regulatory polymorphisms is a key requirement for next-generation human genetic analysis. Here we describe haploChIP, a method that uses chromatin immunoprecipitation (ChIP) and mass spectrometry to identify differential protein-DNA binding in vivo associated with allelic variants of a gene. We demonstrate this approach with the imprinted gene SNRPN. HaploChIP showed close correlation between the level of bound phosphorylated RNA polymerase II at the SNRPN locus and allele-specific expression. Application of the approach to the TNF/LTA locus identified functionally important haplotypes that correlate with allele-specific transcription of LTA. The haploChIP method may be useful in high-throughput screening for common DNA polymorphisms that affect gene regulation in vivo.

Authors: Knight, J; Keating, B; Rockett, K; Kwiatkowski, D

• Publication status: Published
• Journal: Nature genetics
• Volume: 33
• Issue: 4
• Pages: 469-475
• Publication date: 2003-04-01
• DOI: 10.1038/ng1124
• EISSN: 1546-1718
• ISSN: 1061-4036
• Language: English
• Keywords: snRNP Core Proteins; Humans; Transcription, Genetic; Genomic Imprinting; Precipitin Tests; Phosphorylation; Polymorphism, Genetic; Alleles; Cell Line; Chromatin; Protein Binding; Haplotypes; Genetic Techniques; Mass Spectrometry; Mass Screening; RNA Polymerase II; Time Factors; Models, Genetic; Ribonucleoproteins, Small Nuclear; Autoantigens; Genotype