William J. Greenleaf
Assistant Professor of Genetics and by courtesy, of Applied Physics
Genetics Department
Stanford University School of Medicine
Single-cell chromatin accessibility reveals principles of regulatory variation
Cell-to-cell variation affects a wide range of biological phenomena, from developmental plasticity to tumour heterogeneity. The fundamental mechanisms that generate regulatory variability from identical DNA genomes remain elusive. We explore the principles of mammalian DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells using an assay for transposase-accessible chromatin (ATAC-seq) integrated into a programmable microfluidics platform. Single-cell ATAC-seq (scATAC-seq) maps aggregated from hundreds of single cells closely recapitulate accessibility profiles from tens of millions of cells and provide insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either increased or decreased cell-to-cell variability. We identify sets of trans-factors, such as lineage-sepcific transcription factors, associated with cell-type-specific accessibility variance across eight cell types. Targeted perturbations of cell cycle or transcription factor signaling networks lead to specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates the organization of chromosome compartments, potentially linking single-cell accessibility variation to three-dimensional genome organization. Overall, this ability to analyze DNA accessibility at the single cell level provides new insight into population-level variation of the ‘regulome.’
