In-situ cell-type specific chromatin topologies in the brain revealed by genome architecture mapping

We report the application of genome architecture mapping in specific cell types in mouse brain. We generated cell-type specific chromatin contact maps in mouse dopaminergic neurons from the midbrain ventral tegmental area (VTA DN), pyramidal glutamatergic neurons from the cornus ammonis 1 region of the hippocampus (CA1 PGN), and non-neuronal post-mitotic oligodendrocytes from the somatosensory cortex (SSC_Olig). We explored cell-type specific chromatin topologies genome-wide at multiple genomic scales. Our data demonstrates that chromatin organization is cell type specific and reflects cell specialization at all genomic scales. Briefly, we isolated single thin tissue sections by ultrathin cryosectioning (approx. 220 nm) of the mouse brain region of interest, and selected specific cell-types using immunofluorescence with specific AB markers. Following cell identification, 3 nuclear sections (nuclear profiles; NPs) were captured by laser microdissection in individual PCR caps. We then extracted, amplified and sequenced the DNA from each PCR cap.