UC San Diego

Mammalian brain cells show a remarkable diversity, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. Cytosine DNA methylation, a covalent modification in the genome, is a critical player in brain cell gene regulation. Recent advances in single-cell technologies allow studying this epigenomic modification at an unprecedented resolution. During my Ph.D., I have developed and used single-cell methylome and multi-omic technologies to profile mouse and human brains to establish the brain cell atlas. In chapter 1, I access the epigenomes of mouse brain cell types by applying single-nucleus DNA methylation sequencing to profile 103,982 nuclei from the mouse cerebrum. I constructed cell taxonomies containing 161 epigenetic clusters and annotated each cluster with signature genes, regulatory elements, and transcription factors. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. By combining multi-omic datasets from single nuclei and annotating the regulatory genome of these cell types, the DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse cerebrum. In chapter 2, colleagues and I devised single-nucleus methylcytosine, chromatin accessibility, and transcriptome sequencing (snmCAT-seq) and applied it to postmortem human frontal cortex tissue. We developed a cross-validation approach using multi-modal information to validate fine-grained cell types. We reconstructed regulatory lineages for cortical cell populations and found specific enrichment of genetic risk for neuropsychiatric traits, enabling the prediction of cell types associated with diseases. In chapter 3, I developed a comprehensive computational package called ALLCools to solve the computational challenges brought up by the single-cell methylome and multi-omic dataset. This package includes data formats specialized for the single-cell DNA methylation data and various functions covering cellular and genomic analysis. As a result, my Ph.D. study has produced high-resolution single-cell DNA methylome datasets in the mouse brain, developed new multi-omic technologies applicable to the human brain, and established comprehensive analysis frameworks to analyze the extensive data. Together, these works create concrete deliverables that extend the understanding of brain epigenome diversity and enable future studies to understand the molecular source of brain cellular diversity and link the psychological diseases to their molecular basis.