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PreprintCited by 3RNA Research and SplicingSingle-cell and spatial transcriptomicsAdvanced Fluorescence Microscopy Techniques

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Single molecule imaging of transcription dynamics, RNA localization and fate in human T cells

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Lattanzio, M. Valeria, Šoštarić, Nikolina, Kanagasabesan, Nandhini, Popović, Branka, Bradarić, Antonia, Wardak, Leyma, Guislain, Aurélie, Savakis, Philipp, Tutucci, Evelina, Wolkers, Monika C.·2024·The EMBO Journal
DOI 10.1101/2024.11.11.622939PMC PMC12624010

Preprint — published as 10.1038/s44318-025-00592-0 · Paper page

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Abstract

Summary: T cells are critical effector cells against infections and malignancies. To achieve this, they produce pro-inflammatory cytokines, including IFN-γ and TNF. Cytokine production is a tightly regulated process. The relative contribution of transcriptional and post-transcriptional regulation to mRNA expression is, however, unknown. We therefore optimized single-molecule FISH for primary human T cells (T-cell smFISH) to simultaneously quantify nascent RNA, mature mRNA levels and its localization with single-cell resolution. T-cell smFISH uncovered heterogeneous cytokine mRNA levels, with high cytokine producers displaying biallelic IFNG / TNF RNA transcription activity. Throughout activation, nuclear cytokine mRNAs accumulated, whereas cytoplasmic cytokine mRNA was degraded through translation-dependent decay. Lastly, T-cell smFISH uncovered cytokine-specific regulation by the RNA-binding protein HuR. Thus, T-cell smFISH provides novel insights in the intricate (post)-transcriptional processes in T cells.

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Metadata

Authors
Lattanzio, M. V., Šoštarić, N., Kanagasabesan, N., Popović, B., Bradarić, A., Wardak, L., Guislain, A., Savakis, P., Tutucci, E., & Wolkers, M. C.
Affiliations
  • Sanquin (NL)
  • Vrije Universiteit Amsterdam (NL)
Corresponding author
  • Tutucci, Evelina
  • Wolkers, Monika C.
ORCID
Venue
The EMBO Journal
Publisher
openRxiv
Published
2024-11-11
Volume
44
Issue
22
Pages
6732-6749
ISSN
0261-4189 (ISSN-L)
DOI
10.1101/2024.11.11.622939
PMC
PMC12624010
OpenAlex
W4415141514
Cited by
3
References
2
Citations by year
2026: 3
FWCI
0.90
Type
journal article
Language
en
Open access
Licence
Locations
  • The EMBO Journal (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Pure Amsterdam UMC (publishedVersion, other-oa)
  • VU Research Portal (publishedVersion, cc-by)
Funders
  • Oncode Institute
  • European Research Council (817533)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
Keywords
T cells, single-molecule FISH, nascent RNA, cytokine mRNA, interferon-gamma, TNF-α, transcriptional regulation, post-transcriptional regulation, mRNA localization, HuR, cytokine gene expression, T cell activation
MeSH terms
ELAV-Like Protein 1, Single Molecule Imaging, Gene Expression Regulation, Humans, Interferon-gamma, RNA, Messenger, T-Lymphocytes, Transcription, Genetic, Tumor Necrosis Factor-alpha, Cytokines, In Situ Hybridization, Fluorescence

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