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. Overall design: 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.