1. Computational and Systems Biology
  2. Chromosomes and Gene Expression
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Natural changes in light interact with circadian regulation at promoters to control gene expression in cyanobacteria

  1. Joseph Robert Piechura
  2. Kapil Amarnath
  3. Erin K O'Shea  Is a corresponding author
  1. Harvard University, United States
Research Article
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Cite as: eLife 2017;6:e32032 doi: 10.7554/eLife.32032


The circadian clock interacts with other regulatory pathways to tune physiology to predictable daily changes and unexpected environmental fluctuations. However, the complexity of circadian clocks in higher organisms has prevented a clear understanding of how natural environmental conditions affect circadian clocks and their physiological outputs. Here, we dissect the interaction between circadian regulation and responses to fluctuating light in the cyanobacterium Synechococcus elongatus. We demonstrate that natural changes in light intensity substantially affect the expression of hundreds of circadian-clock-controlled genes, many of which are involved in key steps of metabolism. These changes in expression arise from circadian and light-responsive control of RNA polymerase recruitment to promoters by a network of transcription factors including RpaA and RpaB. Using phenomenological modeling constrained by our data, we reveal simple principles that underlie the small number of stereotyped responses of dusk circadian genes to changes in light.

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Author details

  1. Joseph Robert Piechura

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
    Competing interests
    No competing interests declared.
    ORCID icon 0000-0001-5349-4567
  2. Kapil Amarnath

    FAS Center for Systems Biology, Harvard University, Cambridge, United States
    Competing interests
    No competing interests declared.
    ORCID icon 0000-0003-2589-9684
  3. Erin K O'Shea

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
    For correspondence
    Competing interests
    Erin K O'Shea, President of Howard Hughes Medical Institute, one of the three founding funders of eLife.
    ORCID icon 0000-0002-2649-1018


Howard Hughes Medical Institute

  • Erin K O'Shea

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Naama Barkai, Reviewing Editor, Weizmann Institute of Science, Israel

Publication history

  1. Received: September 15, 2017
  2. Accepted: December 13, 2017
  3. Accepted Manuscript published: December 14, 2017 (version 1)
  4. Accepted Manuscript updated: December 15, 2017 (version 2)
  5. Version of Record published: January 25, 2018 (version 3)


© 2017, Piechura et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.


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