Cell-Type-Specific Survey of Epigenetic Modification by Tandem Chromatin Immunoprecipitation Sequencing

[Background]: Nervous system of higher eukaryotes is composed of numerous types of neurons and glia, which together orchestrate complex neuronal responses. However, the complex pool of cells usually poses analytic challenges to investigate gene expression profile and its epigenetic basis in specific cell type. Here we developed a novel method that enables cell-type-specific analyses of epigenetic modification using tandem chromatin immunoprecipitation sequencing (tChIP-Seq). [Results]: FLAG-tagged histone H2B, a constitutive chromatin component, was firstly expressed in Camk2a-positive pyramidal cortical neurons and was used to purify the chromatin in a cell-type-specific manner. The subsequent chromatin immunoprecipitation using antibodies against H3K4me3—an active promoter mark—allowed us to survey neuron specific coding and noncoding transcripts. Indeed, tChIP-Seq identified hundreds of genes associated with neuronal functions as well as genes with unknown function expressed in cortical neurons. [Conclusions]: tChIP-Seq thus provides a versatile approach to investigate epigenetic modifications of particular cell types in vivo. Overall design: ChIP-Seq