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A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells

Arrastia, Mary V. and Jachowicz, Joanna W. and Ollikainen, Noah and Curtis, Matthew S. and Lai, Charlotte and Quinodoz, Sofia A. and Selck, David A. and Guttman, Mitchell and Ismagilov, Rustem F. (2020) A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200813-130113364

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Abstract

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.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.08.11.242081DOIDiscussion Paper
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154353Related ItemData/Code
https://github.com/caltech-bioinformatics-resource-center/Guttman_Ismagilov_LabsRelated ItemData/Code
ORCID:
AuthorORCID
Arrastia, Mary V.0000-0002-0723-3574
Jachowicz, Joanna W.0000-0002-1599-682X
Ollikainen, Noah0000-0002-1174-2400
Curtis, Matthew S.0000-0002-9662-3266
Quinodoz, Sofia A.0000-0003-1862-5204
Guttman, Mitchell0000-0003-4748-9352
Ismagilov, Rustem F.0000-0002-3680-4399
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Posted August 12, 2020. We would like to thank the assistance from Fan Gao from Caltech’s Bioinformatics Resource Center and Igor Antoshechkin from Caltech’s Millard and Muriel Jacobs Genetics and Genomics Laboratory. We would like to thank Chris Chen, Vicky Trinh, Elizabeth Detmar, Elizabeth Soehalim, and Aditi Narayanan for their contributions in helping develop scSPRITE. We would like to thank Matt Thompson’s lab for allowing us to use their MiSeq instrument. We also thank Natasha Shelby and Shawna Hiley for contributions to writing and editing this manuscript and Inna-Marie Strazhnik for helping with illustrations. This work was funded in part by the NIH 4DN Program (U01 DA040612 and U01 HL130007), NHGRI GGR Program (U01 HG007910), New York Stem Cell Foundation (NYSCF-R-I13), Sontag Foundation, and funds from Caltech. M.V.A. and S.A.Q. were funded by NSF GRFP fellowships (DGE‐1144469). M.V.A. was additionally funded by the Earle C. Anthony Fellowship (Caltech). M. Guttman is a NYSCF-Robertson Investigator. Author Contributions: M.V.A. conducted the experiments to develop and validate method, conceptualized and performed the analyses, wrote the manuscript; J.W.J contributed the experiments to develop and validate the method, conceptualized and performed analyses, wrote the manuscript; N.O conceptualized and performed analysis to validate the method, developed the pipeline for the workup of scSPRITE sequencing data, 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; M.G. conceptualized scSPRITE, supervised the experiments and the analysis to validate the method, wrote the manuscript; R.F.I conceptualized scSPRITE, supervised the experiments and analysis to develop the method, wrote the manuscript. Data Availability Statement: The datasets (Fig. 1-5; supplemental figures S1-S5) generated during and analyzed during the current study are available in the GEO repository under accession number GSE154353 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154353). scSPRITE software is available at https://github.com/caltech-bioinformatics-resource-center/Guttman_Ismagilov_Labs. Conflict of Interest: This paper is the subject of a patent application filed by Caltech. R.F.I. has a financial interest in Talis Biomedical Corp.
Group:Millard and Muriel Jacobs Genetics and Genomics Laboratory
Funders:
Funding AgencyGrant Number
NIHU01 DA040612
NIHU01 HL130007
NIHU01 HG007910
New York Stem Cell FoundationNYSCF-R-I13
Sontag FoundationUNSPECIFIED
NSF Graduate Research FellowshipDGE‐1144469
Caltech Earle C. Anthony FellowshipUNSPECIFIED
Record Number:CaltechAUTHORS:20200813-130113364
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200813-130113364
Official Citation:A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells. Mary V. Arrastia, Joanna W. Jachowicz, Noah Ollikainen, Matthew S. Curtis, Charlotte Lai, Sofia Quinodoz, David A. Selck, Mitchell Guttman, Rustem F. Ismagilov. bioRxiv 2020.08.11.242081; doi: https://doi.org/10.1101/2020.08.11.242081
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:104955
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:13 Aug 2020 20:20
Last Modified:13 Aug 2020 20:20

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