TITLE: “Multimodal Single-Cell Epigenomic Sequencing of the Developing Human Cerebral Cortex.”
ABSTRACT: Single cell epigenomic technologies allow the measurement of unique molecular signatures within cells, however cell type complexity remains highly enigmatic. Emerging methods have enabled multiple modalities of epigenomic sequencing to be gathered from the same cell. Single-nucleus methyl-3C sequencing (sn-m3C-seq) delivers the capacity to capture chromatin conformation and DNA methylation information of 5’-methylcytosines with single cell fidelity. Developing neurons accumulate significant DNA methylation at non-CG sites (mCH), adjust patterns of CG methylation (mCG), and endure rearrangements of chromatin domains. These patterns of mCH, mCG, and chromatin interactions are specific to neuronal subtypes. We collected prefrontal cortex samples from 13 individuals at several developmental time stamps divided into four major age groups, second trimester (2T), third trimester (3T), infant, and adult. Applying sn-m3C-seq to our data of >29,000 cells we identify 27 adult cell types and their developmental trajectories from five 2T cell types. The methylation features allow for intricate, deeply specific cell type annotations and while the 3C modality highlights less specific cell types, it can pick up forward trajectory signals that methylation either does not or that resolve as a single heterogeneous cell type in methylation; We observe developing glial progenitor cells identified in 3C that cluster as radial glia in the methylation feature space alone. The temporal forward stepping of the 3C feature set further allows us to validate cell types in different sample age groups. The integration of single cell modalities in sn-m3C-seq allows for the highly robust cell type classification as well as strong downstream analysis of epigenetic divergences of developing cell lineages.
