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PreprintCited by 14Circadian rhythm and melatoninRNA Research and SplicingCircular RNAs in diseases

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

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Hurni, Clémence, Weger, Benjamin, Gobet, Cédric, Naef, Felix·2021·PLoS Genetics
DOI 10.1101/2021.10.25.465667PMC PMC9377612

Preprint — published as 10.1371/journal.pgen.1009903 · Paper page

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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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Research works printed but not linked: 70

  1. 10.1186/s13059-020-1935-5 · DOI · Paper page
  2. 2011, Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain, Nature Structural & Molecular Biology, 18, 1435, 10.1038/nsmb.2143 · DOI · Paper page
  3. 10.1073/pnas.1515308112 · DOI
  4. 10.1016/S0960-9822(03)00014-9 · DOI
  5. 2015, Nuclear Retention of mRNA in Mammalian Tissues, Cell Reports, 13, 2653, 10.1016/j.celrep.2015.11.036 · DOI · Paper page
  6. 10.1016/j.cell.2015.11.018 · DOI · Paper page
  7. 2018, The RNA-Binding Protein NONO Coordinates Hepatic Adaptation to Feeding, Cell Metabolism, 27, 404, 10.1016/j.cmet.2017.12.010 · DOI
  8. 10.1016/j.cell.2012.05.043 · DOI
  9. 10.1101/gr.177790.114 · DOI · Paper page
  10. 10.1038/nbt.3519 · DOI · Paper page
  11. 2017, Comprehensive analysis of nucleocytoplasmic dynamics of mRNA in Drosophila cells, PLoS Genetics, 13, e1006929, 10.1371/journal.pgen.1006929 · DOI
  12. Chin, A. , & Lécuyer, E . (2017). RNA localization: Making its way to the center stage. Biochimica et Biophysica Acta (BBA) - General Subjects, 1861(11, Part B), 2956–2970. https://doi.org/10.1016/j.bbagen.2017.06.011 · DOI
  13. 10.1016/j.molcel.2009.01.026 · DOI · Paper page
  14. 10.1101/gad.183500 · DOI · Paper page
  15. 10.1038/nature11233 · DOI · Paper page
  16. 10.1016/j.molcel.2019.11.017 · DOI
  17. 10.7554/eLife.02510 · DOI
  18. 10.1016/j.molcel.2019.12.005 · DOI · Paper page
  19. 10.1016/J.CELL.2019.05.027 · DOI
  20. Furlan, M. , Galeota, E. , Gaudio, N. D. , Dassi, E. , Caselle, M. , Pretis, S. de , & Pelizzola, M. (2020). Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling. Genome Research. https://doi.org/10.1101/gr.260984.120 · DOI
  21. 10.1016/j.cell.2013.10.026 · DOI
  22. 10.1038/nbt.3269 · DOI · Paper page
  23. 10.1038/nrm2104 · DOI · Paper page
  24. 2021, Nuclear mechanisms of gene expression control: Pre-mRNA splicing as a life or death decision, Current Opinion in Genetics & Development, 67, 67, 10.1016/j.gde.2020.11.002 · DOI
  25. 10.1101/gad.287094.116 · DOI
  26. 10.1101/gr.232025.117 · DOI
  27. 2017, Thiol-linked alkylation of RNA to assess expression dynamics, Nature Methods, 14, 1198, 10.1038/nmeth.4435 · DOI · Paper page
  28. 10.1101/cshperspect.a000752 · DOI
  29. 2009, Harmonics of Circadian Gene Transcription in Mammals, PLOS Genetics, 5, e1000442, 10.1371/journal.pgen.1000442 · DOI
  30. 10.1186/1471-2164-8-39 · DOI
  31. 2000, The balance sheet for transcription: An analysis of nuclear RNA metabolism in mammalian cells, The FASEB Journal, 14, 242, 10.1096/fasebj.14.2.242 · DOI
  32. 10.1261/rna.034090.112 · DOI
  33. 10.1101/gad.178962.111 · DOI · Paper page
  34. 2012, Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals, Science (New York, N.Y.), 338, 349, 10.1126/science.1226339 · DOI · Paper page
  35. 10.1101/gad.208306.112 · DOI
  36. 10.1093/nar/gkw377 · DOI · Paper page
  37. 10.1186/gb-2001-2-10-research0041 · DOI
  38. 10.1371/journal.pone.0037936 · DOI
  39. 10.1186/s13059-014-0550-8 · DOI · Paper page
  40. 10.1146/annurev.genet.34.1.533 · DOI
  41. 2014, Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data, Cell Reports, 9, 741, 10.1016/j.celrep.2014.09.021 · DOI
  42. 10.1261/rna.062877.117 · DOI
  43. 10.1371/journal.pbio.1001442 · DOI
  44. 10.7554/eLife.00011 · DOI
  45. 10.1101/gad.312397.118 · DOI
  46. 10.1101/cshperspect.a028720 · DOI
  47. 10.1038/ncb2056 · DOI
  48. 10.1126/science.1217726 · DOI
  49. 10.1038/nrg3434 · DOI
  50. 10.1101/cshperspect.a032227 · DOI
  51. Palazzo, A. F. , & Lee, E. S . (2018). Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs. Frontiers in Genetics, 0. https://doi.org/10.3389/fgene.2018.00440 · DOI
  52. 10.1038/nbt.1861 · DOI · Paper page
  53. 10.1016/j.molcel.2017.11.014 · DOI
  54. 10.1016/j.jmb.2016.04.017 · DOI
  55. 10.1126/science.288.5468.1013 · DOI · Paper page
  56. 10.1093/emboj/16.23.7146 · DOI
  57. 10.1371/journal.pbio.2001069 · DOI
  58. 10.1016/j.cell.2016.02.005 · DOI
  59. 10.1101/gr.130559.111 · DOI
  60. 10.1101/gr.134445.111 · DOI
  61. 10.7554/eLife.14837 · DOI
  62. 10.1073/pnas.0909591106 · DOI · Paper page
  63. 2017, Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver, Cell Metabolism, 25, 102, 10.1016/j.cmet.2016.10.003 · DOI
  64. 10.1073/pnas.1715225115 · DOI
  65. 10.1073/pnas.2020698118 · DOI
  66. 2019, Multiplexed detection of RNA using MERFISH and branched DNA amplification, Scientific Reports, 9, 7721, 10.1038/s41598-019-43943-8 · DOI
  67. 2009, Attenuation of transcriptional bursting in mRNA transport, Physical Biology, 7, 016005, 10.1088/1478-3975/7/1/016005 · DOI
  68. 10.1038/msb.2011.62 · DOI
  69. 10.1073/pnas.1408886111 · DOI · Paper page
  70. 10.1261/rna.068288.118 · DOI

Metadata

Authors
Hurni, C., Weger, B., Gobet, C., & Naef, F.
Affiliations
École Polytechnique Fédérale de Lausanne (CH)
ORCID
Venue
PLoS Genetics
Publisher
openRxiv
Published
2021-10-26
Volume
18
Issue
8
Pages
e1009903-e1009903
ISSN
1553-7390 (ISSN-L)
DOI
10.1101/2021.10.25.465667
PMC
PMC9377612
OpenAlex
W4289637900
Cited by
14
References
1
Citations by year
2026: 3 · 2025: 2 · 2024: 4 · 2023: 5
FWCI
1.45
Type
journal article
Language
en
Open access
Licence
cc-by
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
  • National Science Foundation
  • École Polytechnique Fédérale de Lausanne
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (201267, 173079)
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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