Abstract
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.
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Notes
NOTE: In the version of this article initially published online, the graphs in Fig. 6 were unclear. It has been replaced with a revised Fig. 6 in the HTML and print versions of the article.
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Acknowledgements
We thank T. Maniatis for support and critical comments on this work and J. Rayman, B. Dynlacht and B. Ren for helpful technical advice regarding chromatin immunoprecipitation. This work was funded by Medical Research Council, UK.
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Knight, J., Keating, B., Rockett, K. et al. In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading. Nat Genet 33, 469–475 (2003). https://doi.org/10.1038/ng1124
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DOI: https://doi.org/10.1038/ng1124
