PT  - JOURNAL ARTICLE
AU  - Mary V. Arrastia
AU  - Joanna W. Jachowicz
AU  - Noah Ollikainen
AU  - Matthew S. Curtis
AU  - Charlotte Lai
AU  - Sofia A. Quinodoz
AU  - David A. Selck
AU  - Mitchell Guttman
AU  - Rustem F. Ismagilov
TI  - A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells
AID  - 10.1101/2020.08.11.242081
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.08.11.242081
4099  - http://biorxiv.org/content/early/2020/08/12/2020.08.11.242081.short
4100  - http://biorxiv.org/content/early/2020/08/12/2020.08.11.242081.full
AB  - In eukaryotes, the nucleus is organized into a three dimensional structure consisting of both local interactions such as those between enhancers and promoters, and long-range higher-order structures such as nuclear bodies. This organization is central to many aspects of nuclear function, including DNA replication, transcription, and cell cycle progression. Nuclear structure intrinsically occurs within single cells; however, measuring such a broad spectrum of 3D DNA interactions on a genome-wide scale and at the single cell level has been a great challenge. To address this, we developed single-cell split-pool recognition of interactions by tag extension (scSPRITE), a new method that enables measurements of genome-wide maps of 3D DNA structure in thousands of individual nuclei. scSPRITE maximizes the number of DNA contacts detected per cell enabling high-resolution genome structure maps within each cells and is easy-to-use and cost-effective. scSPRITE accurately detects chromosome territories, active and inactive compartments, topologically associating domains (TADs), and higher-order structures within single cells. In addition, scSPRITE measures cell-to-cell heterogeneity in genome structure at different levels of resolution and shows that TADs are dynamic units of genome organization that can vary between different cells within a population. scSPRITE will improve our understanding of nuclear architecture and its relationship to nuclear function within an individual nucleus from complex cell types and tissues containing a diverse population of cells.Competing Interest StatementThis paper is the subject of a patent application filed by Caltech. R.F.I. has a financial interest in Talis Biomedical Corp.