Single molecule imaging of transcription dynamics, RNA localization and fate in T cells DOI Creative Commons

Maria Valeria Lattanzio,

Nikolina Šoštarić,

Nandhini Kanagasabesan

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 11, 2024

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

Language: Английский

Attenuating ribosome load improves protein output from mRNA by limiting translation-dependent mRNA decay DOI Creative Commons
Alicia A. Bicknell, David W. Reid,

Marissa C. Licata

et al.

Cell Reports, Journal Year: 2024, Volume and Issue: 43(4), P. 114098 - 114098

Published: April 1, 2024

Developing an effective mRNA therapeutic often requires maximizing protein output per delivered molecule. We previously found that coding sequence (CDS) design can substantially affect output, with variants containing more optimal codons and higher secondary structure yielding the highest outputs due to their slow rates of decay. Here, we demonstrate CDS-dependent differences in translation initiation elongation lead translation- deadenylation-dependent decay rates, thus explaining effect CDS on half-life. Surprisingly, most stable highest-expressing mRNAs our test set have modest initiation/elongation ribosome loads, leading minimal translation-dependent These findings are potential interest for optimization from mRNAs, which may be achieved by attenuating rather than load.

Language: Английский

Citations

23
The regulatory landscape of 5′ UTRs in translational control during zebrafish embryogenesis DOI Creative Commons
Madalena M. Reimão-Pinto, Sebastian M. Castillo-Hair, Georg Seelig

et al.

Developmental Cell, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The 5' UTRs of mRNAs are critical for translation regulation during development, but their in vivo regulatory features poorly characterized. Here, we report the landscape early zebrafish embryogenesis using a massively parallel reporter assay 18,154 sequences coupled to polysome profiling. We found that UTR suffices confer temporal dynamics initiation and identified 86 motifs enriched with distinct ribosome recruitment capabilities. A quantitative deep learning model, Danio Optimus 5-Prime (DaniO5P), combined role length, site context, upstream AUGs, sequence on recruitment. DaniO5P predicts activities maternal zygotic isoforms indicates modulating length motif grammar contributes dynamics. This study provides first model UTR-based development lays foundation identifying underlying molecular effectors.

Language: Английский

Citations

1
Repressing cytokine storm-like response in macrophages by targeting the eIF2α-integrated stress response pathway DOI
Xiaoyun Wang,

Chaochao Dai,

Wen Cheng

et al.

International Immunopharmacology, Journal Year: 2025, Volume and Issue: 147, P. 113965 - 113965

Published: Jan. 2, 2025

Language: Английский

Citations

0
Sequence determinants as key regulators in gene expression of T cells DOI Creative Commons
Benoît P. Nicolet, Nordin D. Zandhuis, Veronica M. T. Lattanzio

et al.

Immunological Reviews, Journal Year: 2021, Volume and Issue: 304(1), P. 10 - 29

Published: Sept. 5, 2021

T cell homeostasis, differentiation, and effector function rely on the constant fine-tuning of gene expression. To alter state, substantial remodeling proteome is required. This depends intricate interplay regulatory mechanisms, including post-transcriptional regulation. In this review, we discuss how sequence a transcript influences these events. particular, review determinants such as conservation, GC content, chemical modifications define levels mRNA protein in cell. We describe effect different forms alternative splicing expression production, their subcellular localization. addition, role sequences structures binding hubs for miRNAs RNA-binding proteins cells. The thus highlights intimate mechanisms dictate cellular fate decisions

Language: Английский

Citations

21
Predicting the translation efficiency of messenger RNA in mammalian cells DOI Creative Commons
Dinghai Zheng, Jun Wang,

Logan Persyn

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 11, 2024

The degree to which translational control is specified by mRNA sequence poorly understood in mammalian cells. Here, we constructed and leveraged a compendium of 3,819 ribosomal profiling datasets, distilling them into transcriptome-wide atlas translation efficiency (TE) measurements encompassing >140 human mouse cell types. We subsequently developed RiboNN, multitask deep convolutional neural network, classic machine learning models predict TEs hundreds types from sequence-encoded features, achieving state-of-the-art performance (r=0.79 r=0.78 for mean TE across types). While the majority earlier solely considered 5′ UTR sequence, RiboNN integrates contributions full-length that UTR, CDS, 3′ respectively possess ~67%, 31%, 2% per-nucleotide information density specification TEs. Interpretation revealed spatial positioning low-level di- tri-nucleotide features (i.e., including codons) largely explain model performance, capturing mechanistic principles such as how processivity tRNA abundance output. predictive behavior base-modified therapeutic RNA, can evolutionary selection pressures UTRs. Finally, it detects common language governing regulatory highlights interconnectedness translation, stability, localization organisms.

Language: Английский

Citations

2
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution DOI Creative Commons

Jonathan Chacko,

Hakan Özadam, Can Cenik

et al.

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(6)

Published: June 1, 2024

Abstract Motivation Ribosome profiling is a widely-used technique for measuring ribosome occupancy at nucleotide resolution. However, the need to analyze this data resolution introduces unique challenges in visualization and analyses. Results In study, we introduce RiboGraph, dedicated tool designed work with .ribo files, specialized efficient format data. Unlike existing solutions that rely on large alignment files time-consuming preprocessing steps, RiboGraph operates purpose compact file type. This efficiency allows interactive, real-time ribosome-protected fragment length By providing an integrated toolset, empowers researchers conduct comprehensive visual analysis of Availability implementation Source code, step-by-step installation instructions links documentation are available GitHub: https://github.com/ribosomeprofiling/ribograph. On same page, provide test tutorial highlighting key features RiboGraph.

Language: Английский

Citations

1
Nanodynamo quantifies subcellular RNA dynamics revealing extensive coupling between steps of the RNA life cycle DOI Creative Commons
Lucia Coscujuela Tarrero, Valeria Famà, Giacomo d’Andrea

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 4, 2024

Language: Английский

Citations

1
Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair DOI Creative Commons
Fabien Aubé,

Nicolas Fontrodona,

Laura Guiguettaz

et al.

NAR Cancer, Journal Year: 2024, Volume and Issue: 6(2)

Published: April 8, 2024

Amino acid bioavailability impacts mRNA translation in a codon-dependent manner. Here, we report that the anti-cancer MAPK inhibitors (MAPKi) decrease intracellular concentration of aspartate and glutamate melanoma cells. This coincides with accumulation ribosomes on codons corresponding to these amino acids triggers translation-dependent degradation mRNAs encoding aspartate- glutamate-rich proteins, involved DNA metabolism such as replication repair. Consequently, cells survive MAPKi degrade likely generate energy, which simultaneously decreases their requirement for due downregulation proteins cell proliferation. Concomitantly, repair increases damage loads. Thus, defects, therefore mutations, are at least part secondary effect metabolic adaptation exposed MAPKi.

Language: Английский

Citations

0
Single molecule imaging of transcription dynamics, RNA localization and fate in T cells DOI Creative Commons

Maria Valeria Lattanzio,

Nikolina Šoštarić,

Nandhini Kanagasabesan

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 11, 2024

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

Language: Английский

Citations

0