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Functional network inference of the suprachiasmatic nucleus

John H. Abel, Kirsten Meeker, Daniel Granados-Fuentes, Peter C. St. John, Thomas J. Wang, Benjamin B. Bales, Francis J. Doyle III, Erik D. Herzog, and Linda R. Petzold
PNAS April 19, 2016 113 (16) 4512-4517; published ahead of print April 4, 2016 https://doi.org/10.1073/pnas.1521178113
John H. Abel
aDepartment of Chemical Engineering, University of California, Santa Barbara, CA 93106;bSystems Biology Program, Harvard University, Cambridge, MA 02138;
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Kirsten Meeker
cDepartment of Computer Science, University of California, Santa Barbara, CA 93106;
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Daniel Granados-Fuentes
dDepartment of Biology, Washington University in St. Louis, St. Louis, MO 63130;
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Peter C. St. John
aDepartment of Chemical Engineering, University of California, Santa Barbara, CA 93106;eBiosciences Center, National Renewable Energy Laboratory, Golden, CO 80401;
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Thomas J. Wang
dDepartment of Biology, Washington University in St. Louis, St. Louis, MO 63130;
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Benjamin B. Bales
cDepartment of Computer Science, University of California, Santa Barbara, CA 93106;
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Francis J. Doyle
aDepartment of Chemical Engineering, University of California, Santa Barbara, CA 93106;fHarvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
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Erik D. Herzog
dDepartment of Biology, Washington University in St. Louis, St. Louis, MO 63130;
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Linda R. Petzold
cDepartment of Computer Science, University of California, Santa Barbara, CA 93106;
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  • For correspondence: petzold@engineering.ucsb.edu
  1. Edited by Joseph S. Takahashi, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, and approved March 7, 2016 (received for review November 3, 2015)

This article has corrections. Please see:

  • Correction for Abel et al., Functional network inference of the suprachiasmatic nucleus
  • Correction to Supporting Information for Abel et al., Functional network inference of the suprachiasmatic nucleus
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Significance

In mammals, circadian rhythms are controlled by a network of neurons in the brain. The structure of this network dictates organism-wide behavior and adaptation to the environment. We used a neurotoxin to desynchronize this circadian network and then used tools from information theory to determine which cells communicate to establish synchronization. Our results show that this functional network consists of two densely-connected cores, surrounded by sparsely connected shell regions. These findings represent the first time, to our knowledge, that this network has been examined at single cell resolution and show that the importance of these core network regions is independent of light input.

Abstract

In the mammalian suprachiasmatic nucleus (SCN), noisy cellular oscillators communicate within a neuronal network to generate precise system-wide circadian rhythms. Although the intracellular genetic oscillator and intercellular biochemical coupling mechanisms have been examined previously, the network topology driving synchronization of the SCN has not been elucidated. This network has been particularly challenging to probe, due to its oscillatory components and slow coupling timescale. In this work, we investigated the SCN network at a single-cell resolution through a chemically induced desynchronization. We then inferred functional connections in the SCN by applying the maximal information coefficient statistic to bioluminescence reporter data from individual neurons while they resynchronized their circadian cycling. Our results demonstrate that the functional network of circadian cells associated with resynchronization has small-world characteristics, with a node degree distribution that is exponential. We show that hubs of this small-world network are preferentially located in the central SCN, with sparsely connected shells surrounding these cores. Finally, we used two computational models of circadian neurons to validate our predictions of network structure.

  • systems biology
  • synchronization
  • circadian oscillator
  • biological clock
  • mathematical model

Footnotes

  • ↵1J.H.A. and K.M. contributed equally to this work.

  • ↵2To whom correspondence should be addressed. Email: petzold{at}engineering.ucsb.edu.
  • Author contributions: J.H.A., K.M., D.G.-F., P.C.S.J., T.J.W., F.J.D., E.D.H., and L.R.P. designed research; J.H.A., K.M., D.G.-F., P.C.S.J., T.J.W., B.B.B., and E.D.H. performed research; J.H.A., K.M., D.G.-F., P.C.S.J., B.B.B., F.J.D., E.D.H., and L.R.P. analyzed data; and J.H.A., B.B.B., and E.D.H. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1521178113/-/DCSupplemental.

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Network inference of the suprachiasmatic nucleus
John H. Abel, Kirsten Meeker, Daniel Granados-Fuentes, Peter C. St. John, Thomas J. Wang, Benjamin B. Bales, Francis J. Doyle, Erik D. Herzog, Linda R. Petzold
Proceedings of the National Academy of Sciences Apr 2016, 113 (16) 4512-4517; DOI: 10.1073/pnas.1521178113

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Network inference of the suprachiasmatic nucleus
John H. Abel, Kirsten Meeker, Daniel Granados-Fuentes, Peter C. St. John, Thomas J. Wang, Benjamin B. Bales, Francis J. Doyle, Erik D. Herzog, Linda R. Petzold
Proceedings of the National Academy of Sciences Apr 2016, 113 (16) 4512-4517; DOI: 10.1073/pnas.1521178113
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