Expansion genomics for high-resolution single-cell and spatial epigenomics

Project Summary The diversity of cell states observed across development, aging, and disease is regulated by the epigenome, an intricate medley of chromatin states, chemical modifications, protein interactions, and three-dimensional structures in the nucleus. We and others have developed techniques such as ATAC-seq, CUT&Tag, and In situ

Genome Sequencing (IGS) that use Tn5 transposase to selectively measure different components of the epigenome, increasingly at single-cell resolution. However, these techniques all suffer from poor yield due to an inherent challenge: the amount of physical space available for enzymatic reactions in the nucleus is limited. To

address this challenge, we propose a new platform called Expansion Genomics, which will leverage physical expansion of biological samples to de-crowd the nucleus, vastly increasing the resolution of single-cell and spatial epigenomics methods. In Aim 1, we describe Single-cell Expansion Genomics, which will combine

expansion with modern single-cell techniques to enable high-throughput, multi-modal measurements without the need for specialized microfluidic devices. In Aim 2, we describe Spatial Expansion Genomics, which will integrate expansion with multiplexed spatial imaging approaches to reveal the organization of the epigenome at

nanoscale. These technologies will be designed with ease and accessibility as a guiding principle to facilitate widespread adoption and broaden our understanding of gene regulatory mechanisms.