Spatiotemporally resolved transcriptomics reveals subcellular RNA kinetic landscape
Authors/Creators
- 1. Department of Chemistry, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard
- 2. Broad Institute of MIT and Harvard
- 3. Whitehead Institute for Biomedical Research Cambridge; Howard Hughes Medical Institute, Massachusetts Institute of Technology
- 4. John A. Paulson School of Engineering and Applied Sciences, Harvard University
- 5. Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School
- 6. Broad Institute of MIT and Harvard; John A. Paulson School of Engineering and Applied Sciences, Harvard University
- 7. Broad Institute of MIT and Harvard; Computational and Systems Biology Program, Massachusetts Institute of Technology,
- 8. Department of Chemistry, Massachusetts Institute of Technology
Description
Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression
and cellular function. However, the intricate subcellular dynamics of RNA synthesis, decay,
export, and translocation remain obscured due to the limitations of existing transcriptomics
methods Here, we report a spatiotemporally resolved RNA mapping method (TEMPOmap) to
uncover subcellular RNA profiles across time and space at the single-cell level in heterogeneous
cell populations. TEMPOmap integrates pulse-chase metabolic labeling of the transcriptome with
highly multiplexed three-dimensional (3D) in situ sequencing to simultaneously profile the age
and location of individual RNA molecules. Using TEMPOmap, we constructed the subcellular
RNA kinetic landscape of 991 genes in human HeLa cells from upstream transcription to
downstream subcellular translocation. Clustering analysis of critical 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 to serve molecular and
cellular functions in a cell-cycle-dependent manner. We further demonstrated that functionallysegregated
RNA kinetics could be seen in heterogeneous human primary cell cultures, revealing
cell-type-dependent RNA dynamic regulation. Together, these single-cell spatiotemporally
resolved transcriptomics measurements provide us the gateway to uncovering new gene regulation
principles and understanding how kinetic strategies enable precise RNA expression in time and
space.
Files
2022-03-28-TEMPOmap-images.zip
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