Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver

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 distribut...

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Published inPLoS genetics Vol. 18; no. 8; p. e1009903
Main Authors Hurni, Clémence, Weger, Benjamin D., Gobet, Cédric, Naef, Felix
Format Journal Article
LanguageEnglish
Published San Francisco Public Library of Science 03.08.2022
Public Library of Science (PLoS)
Subjects
Analysis
Biology and life sciences
Cell cycle
Circadian rhythm
Circadian rhythms
Cytoplasm
Gene expression
Genetic aspects
Genomes
Genomics
Liver
Localization
Mathematical models
Mice
mRNA stability
Nuclear transport
Ordinary differential equations
Principal components analysis
Proteins
Research and analysis methods
RNA
RNA polymerase
Rodents
Transcriptomes
Switzerland
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Summary: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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The authors have declared that no competing interests exist.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1009903