Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape

Jingyi Ren; Haowen Zhou; Hu Zeng; Connie Kangni Wang; Jiahao Huang; Xiaojie Qiu; Xin Sui; Qiang Li; Xunwei Wu; Zuwan Lin; Jennifer A Lo; Kamal Maher; Yichun He; Xin Tang; Judson Lam; Hongyu Chen; Brian Li; David E Fisher; Jia Liu; Xiao Wang

doi:10.1038/s41592-023-01829-8

Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape

Nat Methods. 2023 May;20(5):695-705. doi: 10.1038/s41592-023-01829-8. Epub 2023 Apr 10.

Authors

Jingyi Ren^#^{1

2}, Haowen Zhou^#², Hu Zeng^#^{1

2}, Connie Kangni Wang², Jiahao Huang^{1

2}, Xiaojie Qiu³, Xin Sui^{1

2}, Qiang Li⁴, Xunwei Wu⁵, Zuwan Lin^{2

6}, Jennifer A Lo², Kamal Maher^{2

7}, Yichun He^{2

4}, Xin Tang^{2

4}, Judson Lam¹, Hongyu Chen^{1

2}, Brian Li², David E Fisher⁵, Jia Liu⁴, Xiao Wang^{8

9}

Affiliations

¹ Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
² Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³ Whitehead Institute for Biomedical Research Cambridge, Cambridge, MA, USA.
⁴ John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA.
⁵ Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.
⁶ Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
⁷ Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁸ Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. xwangx@mit.edu.
⁹ Broad Institute of MIT and Harvard, Cambridge, MA, USA. xwangx@mit.edu.

^# Contributed equally.

Abstract

Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function. However, the intricate subcellular dynamics of RNA remain obscured due to the limitations of existing transcriptomics methods. Here, we report TEMPOmap-a method that uncovers subcellular RNA profiles across time and space at the single-cell level. TEMPOmap integrates pulse-chase metabolic labeling with highly multiplexed three-dimensional in situ sequencing to simultaneously profile the age and location of individual RNA molecules. Using TEMPOmap, we constructed the subcellular RNA kinetic landscape in various human cells from transcription and translocation to degradation. Clustering analysis of RNA kinetic parameters across single cells revealed 'kinetic gene clusters' whose expression patterns were shaped by multistep kinetic sculpting. Importantly, these kinetic gene clusters are functionally segregated, suggesting that subcellular RNA kinetics are differentially regulated in a cell-state- and cell-type-dependent manner. Spatiotemporally resolved transcriptomics provides a gateway to uncovering new spatiotemporal gene regulation principles.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling / methods
Gene Expression Regulation
Humans
Kinetics
RNA* / genetics
Single-Cell Analysis / methods
Transcriptome*

Substances

RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding