In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading.
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.
Knight
Julian C
JC
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK. julian@well.ox.ac.uk
Keating
Brendan J
BJ
Rockett
Kirk A
KA
Kwiatkowski
Dominic P
DP
D000483:Alleles; D001324:Autoantigens; D002460:Cell Line; D002843:Chromatin / Q000378:metabolism; D005821:Genetic Techniques; D018392:Genomic Imprinting; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D008403:Mass Screening; D013058:Mass Spectrometry; D008957:Models, Genetic; D010766:Phosphorylation; D011110:Polymorphism, Genetic; D011233:Precipitin Tests; D011485:Protein Binding; D012319:RNA Polymerase II / Q000378:metabolism*; D017411:Ribonucleoproteins, Small Nuclear / Q000235:genetics*; D013997:Time Factors; D014158:Transcription, Genetic; D055517:snRNP Core Proteins
D001324:Autoantigens; D002843:Chromatin; D017411:Ribonucleoproteins, Small Nuclear; C526417:SNRPN protein, human; D055517:snRNP Core Proteins; D012319:RNA Polymerase II