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Published January 2022 | public
Journal Article Open

Single-cell measurement of higher-order 3D genome organization with scSPRITE


Although three-dimensional (3D) genome organization is central to many aspects of nuclear function, it has been difficult to measure at the single-cell level. To address this, we developed 'single-cell split-pool recognition of interactions by tag extension' (scSPRITE). scSPRITE uses split-and-pool barcoding to tag DNA fragments in the same nucleus and their 3D spatial arrangement. Because scSPRITE measures multiway DNA contacts, it generates higher-resolution maps within an individual cell than can be achieved by proximity ligation. We applied scSPRITE to thousands of mouse embryonic stem cells and detected known genome structures, including chromosome territories, active and inactive compartments, and topologically associating domains (TADs) as well as long-range inter-chromosomal structures organized around various nuclear bodies. We observe that these structures exhibit different levels of heterogeneity across the population, with TADs representing dynamic units of genome organization across cells. We expect that scSPRITE will be a critical tool for studying genome structure within heterogeneous populations.

Additional Information

© 2021 Nature Publishing Group. Received 20 July 2020; Accepted 25 June 2021; Published 23 August 2021. We would like to thank F. Gao from Caltech's Bioinformatics Resource Center and I. Antoshechkin from Caltech's Millard and Muriel Jacobs Genetics and Genomics Laboratory for assistance. We would also like to thank C. Chen, V. Trinh, E. Detmar, E. Soehalim, A. Narayanan and I. Goronzy for their contributions in helping develop scSPRITE and analysis. We would like to thank M. Thompson's laboratory for allowing us to use their MiSeq instrument and the ENCODE Consortium and the ENCODE production laboratory of B. Ren (University of California, San Diego) for making their data publicly available. We also thank N. Shelby and S. Hiley for contributions to the writing and editing this manuscript and I.-M. Strazhnik for helping with illustrations. Funding: This work was funded by the National Institutes of Health 4DN Program (U01 DA040612 and U01 HL130007), the National Human Genome Research Institute Genomics of Gene Regulation Program (U01 HG007910), the New York Stem Cell Foundation (NYSCF-R-I13), the Sontag Foundation and funds from Caltech. M.V.A. and S.A.Q. were funded by a National Science Foundation Graduate Research Fellowship Program fellowship. M.V.A. was additionally funded by the Earle C. Anthony Fellowship (Caltech). M. Guttman is an NYSCF-Robertson Investigator. Data availability: The datasets (Figs. 1–5 and Extended Data Figs. 1−5) generated and analyzed in the current study are available in the Gene Expression Omnibus repository under accession number GSE154353 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154353). Code availability: scSPRITE software is available at https://github.com/caltech-bioinformatics-resource-center/Guttman_Ismagilov_Labs. These authors contributed equally: Mary V. Arrastia, Joanna W. Jachowicz. Author Contributions: M.V.A. conducted the experiments to develop and validate the method, conceptualized and performed the analyses and wrote the manuscript. J.W.J. contributed to and supervised the experiments to develop and validate the method, conceptualized and performed the analyses and wrote the manuscript. N.O. conceptualized and performed analysis to validate the method, developed the pipeline for the workup of scSPRITE sequencing data and contributed to writing the manuscript. M.S.C. contributed to the experiments to develop the method. C.A.L. developed a pipeline to sort cells by cell-specific barcodes. S.A.Q. contributed to the experiments to develop and validate the method. D.A.S. contributed to conceptualize scSPRITE and to the experiments to develop the method. R.F.I. conceptualized scSPRITE and supervised the experiments and the analysis to develop the method. M.G. conceptualized scSPRITE, supervised the experiments and the analysis to validate the method and wrote the manuscript. For detailed author contributions, please see Supplementary Note 5. Competing interests: This paper is the subject of a patent application filed by Caltech. R.F.I. has a financial interest in Talis Biomedical Corp. S.A.Q. and M.G. are inventors on a patent owned by Caltech on SPRITE. The remaining authors declare no competing financial interests. Peer review information: Nature Biotechnology thanks Andrew Adey and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Attached Files

Submitted - 2020.08.11.242081v1.full.pdf

Supplemental Material - 41587_2021_998_Fig10_ESM.webp

Supplemental Material - 41587_2021_998_Fig6_ESM.webp

Supplemental Material - 41587_2021_998_Fig7_ESM.webp

Supplemental Material - 41587_2021_998_Fig8_ESM.webp

Supplemental Material - 41587_2021_998_Fig9_ESM.webp

Supplemental Material - 41587_2021_998_MOESM1_ESM.pdf

Supplemental Material - 41587_2021_998_MOESM2_ESM.pdf

Supplemental Material - 41587_2021_998_MOESM3_ESM.xlsx


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Additional details

August 22, 2023
September 11, 2023