Chromatin immunoprecipitation technique for study of transcriptional dysregulation in intact mouse brain

Transcriptional dysregulation has emerged as an important pathologic mechanism underlying the pathogenesis of Huntington's disease (HD). The control of transcription depends on appropriate binding of transcription factor proteins to specific promoter regions of genes. Chromatin immunoprecipitation (ChIP) is a technique that has been used to study the association of transcription factors with DNA. To address the hypothesis that there is altered transcription factor-DNA association in HD, we have recently adapted the ChIP technique to the study of transgenic mouse brain. Here, we describe our method of performing ChIP in intact mouse brain. We have optimized conditions for formaldehyde crosslinking, antibody immunoprecipitation, and quantitative real-time polymerase chain reaction detection. Using ChIP, one can measure the association of transcription factors with specific genes and determine if this association is altered in transgenic HD mouse models. ChIP applied to whole-mouse brain can thus offer a window into mechanisms of transcriptional dysregulation.