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Published February 11, 2021 | Accepted Version + Supplemental Material + Submitted
Journal Article Open

Integrated spatial genomics reveals global architecture of single nuclei


Identifying the relationships between chromosome structures, nuclear bodies, chromatin states and gene expression is an overarching goal of nuclear-organization studies. Because individual cells appear to be highly variable at all these levels, it is essential to map different modalities in the same cells. Here we report the imaging of 3,660 chromosomal loci in single mouse embryonic stem (ES) cells using DNA seqFISH+, along with 17 chromatin marks and subnuclear structures by sequential immunofluorescence and the expression profile of 70 RNAs. Many loci were invariably associated with immunofluorescence marks in single mouse ES cells. These loci form 'fixed points' in the nuclear organizations of single cells and often appear on the surfaces of nuclear bodies and zones defined by combinatorial chromatin marks. Furthermore, highly expressed genes appear to be pre-positioned to active nuclear zones, independent of bursting dynamics in single cells. Our analysis also uncovered several distinct mouse ES cell subpopulations with characteristic combinatorial chromatin states. Using clonal analysis, we show that the global levels of some chromatin marks, such as H3 trimethylation at lysine 27 (H3K27me3) and macroH2A1 (mH2A1), are heritable over at least 3–4 generations, whereas other marks fluctuate on a faster time scale. This seqFISH+-based spatial multimodal approach can be used to explore nuclear organization and cell states in diverse biological systems.

Additional Information

© 2021 Nature Publishing Group. Received 01 April 2020; Accepted 16 December 2020; Published 27 January 2021. We thank I. Strazhnik for help with figures; A. Anderson for help with the manuscript; C. Karp for custom-made flow cells; H. -J. Ahn for the early phase of the antibody conjugation; and B. Bonev for the Hi-C data. This project is funded by NIH 4DN DA047732 and supplement, and the Paul G. Allen Frontiers Foundation Discovery Center. Data availability: The source data and processed data from this study are available at Zenodo (https://zenodo.org/record/3735329). Additional raw microscopy data obtained during this study are available from the corresponding author upon reasonable request. Publicly available datasets used in the study (GSE96107, 4DNESOJRTZZR, GSE17051, GSE102076, GSE48895, ENCSR000CFN, ENCSR000CGP, ENCSR000CGQ) are detailed in the Methods. Code availability: The custom written scripts used in this study are available at https://github.com/CaiGroup/dna-seqfish-plus. Author Contributions: Y.T. and L.C. conceived the idea and designed experiments. Y.T. designed probes with help from J.T. and C.-H.L.E. Y.T. and J.Y. prepared and validated all the experimental materials. Y.T. performed all the experiments with help from J.Y. Y.T. and N.P. performed image analysis with help from J.W. and S. Shah. Y.T., S.Z. and L.C. analysed data with N.O. and S. Suo. L.C., M.G. and G.-C.Y. supervised the analysis process. Y.T. and L.C. wrote the manuscript with input from C.-H.L.E. and G.-C.Y. L.C. supervised all aspects of the projects. Competing interests: L.C. is a co-founder of Spatial Genomics Inc. Peer review information: Nature thanks Peter Fraser and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

Attached Files

Accepted Version - nihms-1655948.pdf

Submitted - 2020.11.29.403055v1.full.pdf

Supplemental Material - 41586_2020_3126_Fig10_ESM.webp

Supplemental Material - 41586_2020_3126_Fig11_ESM.webp

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Supplemental Material - 41586_2020_3126_MOESM1_ESM.pdf

Supplemental Material - 41586_2020_3126_MOESM2_ESM.xlsx

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Supplemental Material - 41586_2020_3126_MOESM8_ESM.pdf


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Additional details

August 22, 2023
December 22, 2023