UC San Diego

Chromatin accessibility captures in vivo protein-chromosome binding status, and is considered an informative proxy for protein-DNA interactions. DNase I and Tn5 transposase assays require thousands to millions of fresh cells for comprehensive chromatin mapping. Applying Tn5 tagmentation to hundreds of cells and to single cells results in sparse chromatin maps at high throughput or dense chromatin maps at low throughput. We present a high throughput transposome hypersensitive sites sequencing assay for highly sensitive characterization of chromatin accessibility. Linear amplification of accessible DNA ends with in vitro transcription, coupled with an engineered Tn5 super-mutant, demonstrates improved sensitivity on limited input materials, and accessibility of small regions near distal enhancers, compared with ATAC-seq. Application to single cells was achieved by adapting THS-seq to combinatorial indexing to generate high sensitivity DNA accessibility maps for tens of thousands of single cells from the human adult visual and frontal cortex. Integrative analysis of snDrop-seq and scTHS-seq has allowed us to identify transcription factors and regulatory elements shaping the state of different brain cell types, and to map genetic risk factors of common human brain diseases to specific pathogenic cell types and subtypes. Overall we demonstrate the viability of scTHS-seq to quantitate DNA accessibility in single cells, and application to biological samples to shed insight on human brain diseases.