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Title: Quantifying Stochastic Noise in Cultured Circadian Reporter Cells

Abstract

Stochastic noise at the cellular level has been shown to play a fundamental role in circadian oscillations, influencing how groups of cells entrain to external cues and likely serving as the mechanism by which cell-autonomous rhythms are generated. Despite this importance, few studies have investigated how clock perturbations affect stochastic noise—even as increasing numbers of high-throughput screens categorize how gene knockdowns or small molecules can change clock period and amplitude. This absence is likely due to the difficulty associated with measuring cell-autonomous stochastic noise directly, which currently requires the careful collection and processing of single-cell data. In this study, we show that the damping rate of population-level bioluminescence recordings can serve as an accurate measure of overall stochastic noise, and one that can be applied to future and existing high-throughput circadian screens. Using cell-autonomous fibroblast data, we first show directly that higher noise at the single-cell results in faster damping at the population level. Next, we show that the damping rate of cultured cells can be changed in a dose-dependent fashion by small molecule modulators, and confirm that such a change can be explained by single-cell noise using a mathematical model. We further demonstrate the insights that can be gainedmore » by applying our method to a genome-wide siRNA screen, revealing that stochastic noise is altered independently from period, amplitude, and phase. Finally, we hypothesize that the unperturbed clock is highly optimized for robust rhythms, as very few gene perturbations are capable of simultaneously increasing amplitude and lowering stochastic noise. As a result, this study demonstrates the importance of considering the effect of circadian perturbations on stochastic noise, particularly with regard to the development of small-molecule circadian therapeutics.« less

Authors:
 [1];  [2]
  1. Univ. of California, Santa Barbara, CA (United States). Dept. of Chemical Engineering; National Renewable Energy Lab. (NREL), Golden, CO (United States). Biosciences Center
  2. Univ. of California, Santa Barbara, CA (United States). Dept. of Chemical Engineering; Harvard Univ., Cambridge, MA (United States). Paulson School of Engineering and Applied Sciences
Publication Date:
Research Org.:
National Renewable Energy Laboratory (NREL), Golden, CO (United States)
Sponsoring Org.:
National Institutes of Health/National Institute of General Medical Sciences; US Army Research Office (ARO); USDOE
OSTI Identifier:
1235423
Alternate Identifier(s):
OSTI ID: 1235424
Report Number(s):
NREL/JA-2700-65654
Journal ID: ISSN 1553-734X
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS Computational Biology
Additional Journal Information:
Journal Volume: 11; Journal Issue: 11; Journal ID: ISSN 1553-734X
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; circadian oscillators; genetic oscillators; circadian rhythms; bioluminescence; small molecules; small interfering RNAs; chronobiology; sine waves

Citation Formats

John, Peter C., and Doyle, III, Francis J. Quantifying Stochastic Noise in Cultured Circadian Reporter Cells. United States: N. p., 2015. Web. doi:10.1371/journal.pcbi.1004451.
John, Peter C., & Doyle, III, Francis J. Quantifying Stochastic Noise in Cultured Circadian Reporter Cells. United States. https://doi.org/10.1371/journal.pcbi.1004451
John, Peter C., and Doyle, III, Francis J. 2015. "Quantifying Stochastic Noise in Cultured Circadian Reporter Cells". United States. https://doi.org/10.1371/journal.pcbi.1004451. https://www.osti.gov/servlets/purl/1235423.
@article{osti_1235423,
title = {Quantifying Stochastic Noise in Cultured Circadian Reporter Cells},
author = {John, Peter C. and Doyle, III, Francis J.},
abstractNote = {Stochastic noise at the cellular level has been shown to play a fundamental role in circadian oscillations, influencing how groups of cells entrain to external cues and likely serving as the mechanism by which cell-autonomous rhythms are generated. Despite this importance, few studies have investigated how clock perturbations affect stochastic noise—even as increasing numbers of high-throughput screens categorize how gene knockdowns or small molecules can change clock period and amplitude. This absence is likely due to the difficulty associated with measuring cell-autonomous stochastic noise directly, which currently requires the careful collection and processing of single-cell data. In this study, we show that the damping rate of population-level bioluminescence recordings can serve as an accurate measure of overall stochastic noise, and one that can be applied to future and existing high-throughput circadian screens. Using cell-autonomous fibroblast data, we first show directly that higher noise at the single-cell results in faster damping at the population level. Next, we show that the damping rate of cultured cells can be changed in a dose-dependent fashion by small molecule modulators, and confirm that such a change can be explained by single-cell noise using a mathematical model. We further demonstrate the insights that can be gained by applying our method to a genome-wide siRNA screen, revealing that stochastic noise is altered independently from period, amplitude, and phase. Finally, we hypothesize that the unperturbed clock is highly optimized for robust rhythms, as very few gene perturbations are capable of simultaneously increasing amplitude and lowering stochastic noise. As a result, this study demonstrates the importance of considering the effect of circadian perturbations on stochastic noise, particularly with regard to the development of small-molecule circadian therapeutics.},
doi = {10.1371/journal.pcbi.1004451},
url = {https://www.osti.gov/biblio/1235423}, journal = {PLoS Computational Biology},
issn = {1553-734X},
number = 11,
volume = 11,
place = {United States},
year = {Fri Nov 20 00:00:00 EST 2015},
month = {Fri Nov 20 00:00:00 EST 2015}
}

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Free Publicly Available Full Text
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Cited by: 12 works
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Works referenced in this record:

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journal, January 2011


Small molecule modifiers of circadian clocks
journal, November 2012


Amplitude Metrics for Cellular Circadian Bioluminescence Reporters
journal, December 2014


Time-Restricted Feeding without Reducing Caloric Intake Prevents Metabolic Diseases in Mice Fed a High-Fat Diet
journal, June 2012


Bayesian statistical analysis of circadian oscillations in fibroblasts
journal, December 2012


Disruption of the clock components CLOCK and BMAL1 leads to hypoinsulinaemia and diabetes
journal, June 2010


Circadian topology of metabolism
journal, November 2012


Design principles of biochemical oscillators
journal, October 2008


Structural basis of BAK activation in mitochondrial apoptosis initiation
journal, January 2022


Spatiotemporal separation of PER and CRY posttranslational regulation in the mammalian circadian clock
journal, January 2014


Circadian gene expression in mammalian fibroblasts revealed by real-time luminescence reporting: Temperature compensation and damping
journal, December 2003


RNAi Microarray Analysis in Cultured Mammalian Cells
journal, October 2003


Stochastic Phase Oscillators and Circadian Bioluminescence Recordings
journal, January 2007


Stochastic Gene Expression in a Single Cell
journal, August 2002


Identification of Small Molecule Activators of Cryptochrome
journal, July 2012


Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior
journal, April 1994


Temporal Precision in the Mammalian Circadian System: A Reliable Clock from Less Reliable Neurons
journal, February 2004


Wavelet-Based Time Series Analysis of Circadian Rhythms
journal, September 2011


Fibroblast PER2 Circadian Rhythmicity Depends on Cell Density
journal, June 2013


Quantification of Circadian Rhythms in Single Cells
journal, November 2009


Circadian Rhythms of PER2::LUC in Individual Primary Mouse Hepatocytes and Cultures
journal, February 2014


Works referencing / citing this record:

The choroid plexus is an important circadian clock component
journal, March 2018


Moran’s I quantifies spatio-temporal pattern formation in neural imaging data
journal, May 2017


The choroid plexus is an important circadian clock component
journal, March 2018


Moran’s I quantifies spatio-temporal pattern formation in neural imaging data
journal, May 2017