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Global architecture of the nucleus in single cells by DNA seqFISH+ and multiplexed immunofluorescence

Yodai Takei, Jina Yun, Noah Ollikainen, Shiwei Zheng, Nico Pierson, Jonathan White, Sheel Shah, Julian Thomassie, Chee-Huat Linus Eng, Mitchell Guttman, Guo-cheng Yuan, Long Cai
doi: https://doi.org/10.1101/2020.11.29.403055
Yodai Takei
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena USA 91125
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Jina Yun
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena USA 91125
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Noah Ollikainen
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena USA 91125
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Shiwei Zheng
2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA 02215, USA
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Nico Pierson
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena USA 91125
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Jonathan White
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena USA 91125
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Sheel Shah
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena USA 91125
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Julian Thomassie
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena USA 91125
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Chee-Huat Linus Eng
3Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena USA 91125
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Mitchell Guttman
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena USA 91125
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Guo-cheng Yuan
2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA 02215, USA
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Long Cai
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena USA 91125
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  • For correspondence: lcai@caltech.edu
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Abstract

Identifying the relationships between chromosome structures, chromatin states, and gene expression is an overarching goal of nuclear organization studies. Because individual cells are highly variable at all three levels, it is essential to map all three modalities in the same single cell, a task that has been difficult to accomplish with existing tools. Here, we report the direct super-resolution imaging of over 3,660 chromosomal loci in single mouse embryonic stem cells (mESCs) by DNA seqFISH+, along with 17 chromatin marks by sequential immunofluorescence (IF) and the expression profile of 70 RNAs, in the same cells. We discovered that the nucleus is separated into zones defined by distinct combinatorial chromatin marks. DNA loci and nascent transcripts are enriched at the interfaces between specific nuclear zones, and the level of gene expression correlates with an association between active or nuclear speckle zones. Our analysis also uncovered several distinct mESCs subpopulations with characteristic combinatorial chromatin states that extend beyond known transcriptional states, suggesting that the metastable states of mESCs are more complex than previously appreciated. Using clonal analysis, we show that the global levels of some chromatin marks, such as H3K27me3 and macroH2A1 (mH2A1), are heritable over at least 3-4 generations, whereas other marks fluctuate on a faster time scale. The long-lived chromatin states may represent “hidden variables” that explain the observed functional heterogeneity in differentiation decisions in single mESCs. Our integrated spatial genomics approach can be used to further explore the existence and biological relevance of molecular heterogeneity within cell populations in diverse biological systems.

Competing Interest Statement

L.C. is a co-founder of Spatial Genomics Inc.

Copyright 
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-NC-ND 4.0 International license.
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Posted November 30, 2020.
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Global architecture of the nucleus in single cells by DNA seqFISH+ and multiplexed immunofluorescence
Yodai Takei, Jina Yun, Noah Ollikainen, Shiwei Zheng, Nico Pierson, Jonathan White, Sheel Shah, Julian Thomassie, Chee-Huat Linus Eng, Mitchell Guttman, Guo-cheng Yuan, Long Cai
bioRxiv 2020.11.29.403055; doi: https://doi.org/10.1101/2020.11.29.403055
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Global architecture of the nucleus in single cells by DNA seqFISH+ and multiplexed immunofluorescence
Yodai Takei, Jina Yun, Noah Ollikainen, Shiwei Zheng, Nico Pierson, Jonathan White, Sheel Shah, Julian Thomassie, Chee-Huat Linus Eng, Mitchell Guttman, Guo-cheng Yuan, Long Cai
bioRxiv 2020.11.29.403055; doi: https://doi.org/10.1101/2020.11.29.403055

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