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Spatially Resolved Single-cell Translatomics at Molecular Resolution

Hu Zeng, Jiahao Huang, Jingyi Ren, Connie Kangni Wang, Zefang Tang, Yiming Zhou, Abhishek Aditham, View ORCID ProfileHailing Shi, View ORCID ProfileXin Sui, View ORCID ProfileXiao Wang
doi: https://doi.org/10.1101/2022.09.27.509605
Hu Zeng
1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Jiahao Huang
1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Jingyi Ren
1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Connie Kangni Wang
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Zefang Tang
1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Yiming Zhou
1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
3Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Abhishek Aditham
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Hailing Shi
1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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  • ORCID record for Hailing Shi
Xin Sui
1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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  • ORCID record for Xin Sui
Xiao Wang
1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
3Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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  • ORCID record for Xiao Wang
  • For correspondence: xwangx@mit.edu
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Abstract

The precise control of mRNA translation is a crucial step in post-transcriptional gene regulation of cellular physiology. However, it remains a major challenge to systematically study mRNA translation at the transcriptomic scale with spatial and single-cell resolutions. Here, we report the development of RIBOmap, a three-dimensional (3D) in situ profiling method to detect mRNA translation for thousands of genes simultaneously in intact cells and tissues. By applying RIBOmap to 981 genes in HeLa cells, we revealed remarkable dependency of translation on cell-cycle stages and subcellular localization. Furthermore, we profiled single-cell translatomes of 5,413 genes in the adult mouse brain tissue with a spatial cell atlas of 62,753 cells. This spatial translatome profiling detected widespread patterns of localized translation in neuronal and glial cells in intact brain tissue networks. Together, RIBOmap presents the first spatially resolved single-cell translatomics technology, accelerating our understanding of protein synthesis in the context of subcellular architecture, cell types, and tissue anatomy.

Competing Interest Statement

X.W., H.Z., and J.R. are inventors on pending patent applications related to RIBOmap. All methods, protocols, and sequences are freely available to nonprofit institutions and investigators.

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 September 28, 2022.
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Spatially Resolved Single-cell Translatomics at Molecular Resolution
Hu Zeng, Jiahao Huang, Jingyi Ren, Connie Kangni Wang, Zefang Tang, Yiming Zhou, Abhishek Aditham, Hailing Shi, Xin Sui, Xiao Wang
bioRxiv 2022.09.27.509605; doi: https://doi.org/10.1101/2022.09.27.509605
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Spatially Resolved Single-cell Translatomics at Molecular Resolution
Hu Zeng, Jiahao Huang, Jingyi Ren, Connie Kangni Wang, Zefang Tang, Yiming Zhou, Abhishek Aditham, Hailing Shi, Xin Sui, Xiao Wang
bioRxiv 2022.09.27.509605; doi: https://doi.org/10.1101/2022.09.27.509605

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