Epigenomic mapping approaches for cell-type classification in the brain

Salk Institute For Biological Studies, La Jolla CA

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Abstract

? DESCRIPTION (provided by applicant): Understanding the exact cell-type composition in brain regions is fundamental to integrating physiological, behavioral and neurochemical data to systematically understand the brain structure and function. At present, although the major categories of cell-types present in brain have been defined, the different subtypes within these categories, as well as their location and connectivity are far from understood. DNA methylation (mC) is a stable covalent modification that persists in post-mitotic cells throughout their lifetim, defining their cellular identity. It was recently demonstrated that mC patterns in brain are highly dynamic throughout development, and that there are clear differences between the major types of cells i.e., neurons and glia, in the rodent and human cortex. These analyses have been taken a step further and have produced data at the cell-type level that shows that each neuronal type carry specific mC signatures in their genomes that define the population they belong to. These results now open the possibility of producing a catalog of cell-types in brain defined by methylome signatures. This proposal will utilize this cell-type-specific base-resolution methylome data to produce complete maps of cell-types in the rodent brain in situ, and by this means develop a systematic inventory and census of cell types in the brain based on an integrated view of their molecular identity. Based on preliminary results showing clear-cut differences between the methylomes of specific neuronal types, we propose to use cutting edge technology to discover and test specific differentially methylated regions that define, at the molecular level, cell-populations in the frontal cortex of mice. The results obtained will be made publically available, and will serve as foundation to produce a complete genomic census of cell-types in a brain region that can be scaled to the whole brain. If successful, the approach could be ultimately tested in the primate brain. This proposal is thus responsive to RFA MH-14-215 BRAIN Initiative: Transformative Approaches for Cell-Type Classification in the Brain (U01).