Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver
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Abstract
In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of RNA accumulation and affecting the distribution of transcripts in different subcellular compartments. Our study analysed the nuclear and cytoplasmic, poly(A) and total transcriptomes of mouse livers collected over the course of a day. These data provide a genome-wide temporal inventory of enrichment in subcellular RNA, and revealed specific signatures of splicing, nuclear export and cytoplasmic mRNA stability related to transcript and gene lengths. Combined with a mathematical model describing rhythmic RNA profiles, we could test the rhythmicity of export rates and cytoplasmic degradation rates of approximately 1400 genes. With nuclear export times usually much shorter than cytoplasmic half-lives, we found that nuclear export contributes to the modulation and generation of rhythmic profiles of 10% of the cycling nuclear mRNAs. This study contributes to a better understanding of the dynamic regulation of the transcriptome during the day-night cycle.
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Cites
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- Authors
- Hurni, C., Weger, B. D., Gobet, C., & Naef, F.
- Affiliations
- École Polytechnique Fédérale de Lausanne (CH)
- Venue
- PLOS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2022-08-03
- Volume
- 18
- Issue
- 8
- Pages
- e1009903
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC9377612
- OpenAlex
- W4289637900
- Cited by
- 14
- References
- 6
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 4 · 2023: 5
- FWCI
- 1.45
- Type
- journal article
- Language
- en
- Update notices
- new_version (2022-08-15)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030_173079, 310030B_201267)
- EPFL
- Topics
- Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Circular RNAs in diseases
- Keywords
- circadian rhythm, circadian transcriptome, nuclear transcriptome, mouse liver, RNA export, mRNA stability, RNA splicing, polyadenylated RNA, rhythmic gene expression, diurnal cycle, transcript length
- MeSH terms
- Animals, Cell Nucleus, Cytoplasm, Liver, RNA, Mice, Transcriptome
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