The Circadian Oscillator Analysed at the Single-transcript Level

Overview

Journal Mol Syst Biol

Specialty Molecular Biology

Date 2021 Mar 15

PMID 33719202

Citations 9

Authors

Nicholas E Phillips

Alice Hugues

Jake Yeung

Eric Durandau

Damien Nicolas

Felix Naef

Affiliations

Soon will be listed here.

Abstract

The circadian clock is an endogenous and self-sustained oscillator that anticipates daily environmental cycles. While rhythmic gene expression of circadian genes is well-described in populations of cells, the single-cell mRNA dynamics of multiple core clock genes remain largely unknown. Here we use single-molecule fluorescence in situ hybridisation (smFISH) at multiple time points to measure pairs of core clock transcripts, Rev-erbα (Nr1d1), Cry1 and Bmal1, in mouse fibroblasts. The mean mRNA level oscillates over 24 h for all three genes, but mRNA numbers show considerable spread between cells. We develop a probabilistic model for multivariate mRNA counts using mixtures of negative binomials, which accounts for transcriptional bursting, circadian time and cell-to-cell heterogeneity, notably in cell size. Decomposing the mRNA variability into distinct noise sources shows that clock time contributes a small fraction of the total variability in mRNA number between cells. Thus, our results highlight the intrinsic biological challenges in estimating circadian phase from single-cell mRNA counts and suggest that circadian phase in single cells is encoded post-transcriptionally.

Citing Articles

Timely Questions Emerging in Chronobiology: The Circadian Clock Keeps on Ticking.

Chawla S, ONeill J, Knight M, He Y, Wang L, Maronde E J Circadian Rhythms. 2024; 22:2.

PMID: 38617710 PMC: 11011957. DOI: 10.5334/jcr.237.

Coupling allows robust mammalian redox circadian rhythms despite heterogeneity and noise.

Del Olmo M, Kalashnikov A, Schmal C, Kramer A, Herzel H Heliyon. 2024; 10(2):e24773.

PMID: 38312577 PMC: 10835301. DOI: 10.1016/j.heliyon.2024.e24773.

An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells.

Sahay S, Adhikari S, Hormoz S, Chakrabarti S Bioinformatics. 2023; 39(10).

PMID: 37769241 PMC: 10576164. DOI: 10.1093/bioinformatics/btad602.

An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells.

Sahay S, Adhikari S, Hormoz S, Chakrabarti S bioRxiv. 2023; .

PMID: 36993318 PMC: 10055182. DOI: 10.1101/2023.03.21.533651.

Approximating solutions of the Chemical Master equation using neural networks.

Sukys A, Ocal K, Grima R iScience. 2022; 25(9):105010.

PMID: 36117994 PMC: 9474291. DOI: 10.1016/j.isci.2022.105010.

References

Campbell K, Yau C . A descriptive marker gene approach to single-cell pseudotime inference. Bioinformatics. 2018; 35(1):28-35. PMC: 6298060. DOI: 10.1093/bioinformatics/bty498. View

Zechner C, Unger M, Pelet S, Peter M, Koeppl H . Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings. Nat Methods. 2014; 11(2):197-202. DOI: 10.1038/nmeth.2794. View

Llamosi A, Gonzalez-Vargas A, Versari C, Cinquemani E, Ferrari-Trecate G, Hersen P . What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast. PLoS Comput Biol. 2016; 12(2):e1004706. PMC: 4747589. DOI: 10.1371/journal.pcbi.1004706. View

Mermet J, Yeung J, Hurni C, Mauvoisin D, Gustafson K, Jouffe C . Clock-dependent chromatin topology modulates circadian transcription and behavior. Genes Dev. 2018; 32(5-6):347-358. PMC: 5900709. DOI: 10.1101/gad.312397.118. View

Itzkovitz S, van Oudenaarden A . Validating transcripts with probes and imaging technology. Nat Methods. 2011; 8(4 Suppl):S12-9. PMC: 3158979. DOI: 10.1038/nmeth.1573. View

Luck S, Thurley K, Thaben P, Westermark P . Rhythmic degradation explains and unifies circadian transcriptome and proteome data. Cell Rep. 2014; 9(2):741-51. DOI: 10.1016/j.celrep.2014.09.021. View

Aguilar-Arnal L, Hakim O, Patel V, Baldi P, Hager G, Sassone-Corsi P . Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nat Struct Mol Biol. 2013; 20(10):1206-13. PMC: 3885543. DOI: 10.1038/nsmb.2667. View

Schmidt E, Schibler U . Cell size regulation, a mechanism that controls cellular RNA accumulation: consequences on regulation of the ubiquitous transcription factors Oct1 and NF-Y and the liver-enriched transcription factor DBP. J Cell Biol. 1995; 128(4):467-83. PMC: 2199888. DOI: 10.1083/jcb.128.4.467. View

Reinke H, Asher G . Crosstalk between metabolism and circadian clocks. Nat Rev Mol Cell Biol. 2019; 20(4):227-241. DOI: 10.1038/s41580-018-0096-9. View

10.

Cheong J, Virshup D . Casein kinase 1: Complexity in the family. Int J Biochem Cell Biol. 2010; 43(4):465-9. DOI: 10.1016/j.biocel.2010.12.004. View

11.

Droin C, Paquet E, Naef F . Low-dimensional Dynamics of Two Coupled Biological Oscillators. Nat Phys. 2020; 15(10):1086-1094. PMC: 7289635. DOI: 10.1038/s41567-019-0598-1. View

12.

Balsalobre A, Damiola F, Schibler U . A serum shock induces circadian gene expression in mammalian tissue culture cells. Cell. 1998; 93(6):929-37. DOI: 10.1016/s0092-8674(00)81199-x. View

13.

Reddy A, Karp N, Maywood E, Sage E, Deery M, ONeill J . Circadian orchestration of the hepatic proteome. Curr Biol. 2006; 16(11):1107-15. DOI: 10.1016/j.cub.2006.04.026. View

14.

Chan T, Stumpf M, Babtie A . Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures. Cell Syst. 2017; 5(3):251-267.e3. PMC: 5624513. DOI: 10.1016/j.cels.2017.08.014. View

15.

Wu G, Ruben M, Schmidt R, Francey L, Smith D, Anafi R . Population-level rhythms in human skin with implications for circadian medicine. Proc Natl Acad Sci U S A. 2018; 115(48):12313-12318. PMC: 6275491. DOI: 10.1073/pnas.1809442115. View

16.

Dattani J, Barahona M . Stochastic models of gene transcription with upstream drives: exact solution and sample path characterization. J R Soc Interface. 2017; 14(126). PMC: 5310734. DOI: 10.1098/rsif.2016.0833. View

17.

Hansen M, Desai R, Simpson M, Weinberger L . Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability. Cell Syst. 2018; 7(4):384-397.e6. PMC: 6202163. DOI: 10.1016/j.cels.2018.08.002. View

18.

Relogio A, Westermark P, Wallach T, Schellenberg K, Kramer A, Herzel H . Tuning the mammalian circadian clock: robust synergy of two loops. PLoS Comput Biol. 2011; 7(12):e1002309. PMC: 3240597. DOI: 10.1371/journal.pcbi.1002309. View

19.

Mauvoisin D, Wang J, Jouffe C, Martin E, Atger F, Waridel P . Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver. Proc Natl Acad Sci U S A. 2013; 111(1):167-72. PMC: 3890886. DOI: 10.1073/pnas.1314066111. View

20.

Ukai-Tadenuma M, Yamada R, Xu H, Ripperger J, Liu A, Ueda H . Delay in feedback repression by cryptochrome 1 is required for circadian clock function. Cell. 2011; 144(2):268-81. DOI: 10.1016/j.cell.2010.12.019. View