Evidence map›Paper›PMID 37038000›Full record

ArticleNature methods2023

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 and 10 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.

0numbers the graph read from it
0cells of the map it votes in
49citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

49 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Bridging maternal effects and epitranscriptomics: A novel perspective in developmental biology.Developmental dynamics : an official publication of the American Association of Anatomists · 2026
    Review
  6. A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Review
  7. Review
  8. Article
  9. Review
  10. Review
  11. Article
  12. Spatial architecture of development and disease.Nature reviews. Genetics · 2026
    Review
  13. Article
  14. Review
  15. Article
  16. Article
  17. Article
  18. Review
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors.

Jingyi Ren *Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
Haowen Zhou *Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Hu Zeng *Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
Connie Kangni WangBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-9616-5154
Jiahao HuangDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6349-9799
Xiaojie QiuWhitehead Institute for Biomedical Research Cambridge, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-7881-5395
Xin SuiDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-7286-9448
Qiang LiJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA.
Xunwei WuCutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.ORCID http://orcid.org/0000-0002-0822-1700
Zuwan LinBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Jennifer A LoBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-9520-6874
Kamal MaherBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Yichun HeBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Xin TangBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Judson LamDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
Hongyu ChenDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
Brian LiBroad Institute of MIT and Harvard, Cambridge, MA, USA.
David E FisherCutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.
Jia LiuJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA.ORCID http://orcid.org/0000-0003-2217-6982
Xiao WangDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. xwangx@mit.edu.ORCID http://orcid.org/0000-0002-3090-9894

Funding

DERMATOLOGY TRAINING GRANTT32AR007098 · NIAMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI THOMAS S. KUPPER · 1986 to 2026
$8.1M
Graduate Training in Computational and Systems BiologyT32GM087237 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BURGE, CHRISTOPHER B · 2009 to 2023
$4.6M
Single-cell in situ analysis of RNA modifications in intact tissuesDP2GM146245 · NIGMS · BROAD INSTITUTE, INC. · PI WANG, XIAO · 2021 to 2024
$2.4M
NIAMS NIH HHS T32 AR007098NIGMS NIH HHS DP2 GM146245NIGMS NIH HHS T32 GM087237
6 · The paper itself

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.

Indexed as

RNATranscriptomeGene Expression ProfilingGene Expression RegulationHumansKineticsSingle-Cell AnalysisRNA

Identifiers

PMID37038000
PMCPMC10172111

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.