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PreprintCited by 9RNA Research and SplicingGene Regulatory Network AnalysisSingle-cell and spatial transcriptomics

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A model explaining mRNA level fluctuations based on activity demands and RNA age

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Xu, Zhongneng, Asakawa, Shuichi·2020·PLoS Computational Biology
DOI 10.1101/2020.04.30.069674PMC PMC8336849

Preprint — published as 10.1371/journal.pcbi.1009188 · Paper page

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Abstract

Cellular RNA levels are usually fluctuated and are affected by many factors. However, knowledge on the fundamental relationships between RNA abundance, environmental stimuli, and RNA activities is lacking, and the effects of RNA age on RNA levels remain unknown. A model based on activity demands and RNA age was developed to explore the mechanisms of RNA level fluctuations. With single cell time-series gene expression experimental data, we could assess transcription rates, RNA degradation rates, RNA life spans, RNA demands, accumulated transcription amounts, and accumulated RNA degradation amounts by this model. The model could also predict RNA levels under simulation backgrounds, such as stimuli leading to regular oscillations in RNA abundance, stable RNA levels over time being resulted from the long shortage of total RNA activity or uncontrollable transcription, and relationship between RNA levels and protein levels. Given explaining partly mechanisms of some RNA level fluctuations by the present model, further proves and suitable applications are expected.

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Metadata

Authors
Xu, Z., & Asakawa, S.
Affiliations
  • Jinan University (CN)
  • The University of Tokyo (JP)
Corresponding author
Xu, Zhongneng
ORCID
Venue
PLoS Computational Biology
Publisher
openRxiv
Published
2020-04-30
Volume
17
Issue
7
Pages
e1009188-e1009188
ISSN
1553-734X (ISSN-L)
DOI
10.1101/2020.04.30.069674
PMC
PMC8336849
OpenAlex
W3185738930
Cited by
9
References
1
Citations by year
2025: 1 · 2024: 4 · 2023: 3 · 2020: 1
FWCI
0.55
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS Computational Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Keywords
transcription rate, metabolic rate, mathematical model
MeSH terms
Computer Simulation, Models, Biological, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae, Transcription, Genetic, Computational Biology, RNA Stability, Saccharomyces cerevisiae Proteins, Single-Cell Analysis, Transcriptome

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