1
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Hoekstra MMB, Ness N, Badia-Soteras A, Brancaccio M. Bmal1 integrates circadian function and temperature sensing in the suprachiasmatic nucleus. Proc Natl Acad Sci U S A 2024; 121:e2316646121. [PMID: 38625943 PMCID: PMC11047078 DOI: 10.1073/pnas.2316646121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/22/2024] [Indexed: 04/18/2024] Open
Abstract
Circadian regulation and temperature dependency are important orchestrators of molecular pathways. How the integration between these two drivers is achieved, is not understood. We monitored circadian- and temperature-dependent effects on transcription dynamics of cold-response protein RNA Binding Motif 3 (Rbm3). Temperature changes in the mammalian master circadian pacemaker, the suprachiasmatic nucleus (SCN), induced Rbm3 transcription and regulated its circadian periodicity, whereas the core clock gene Per2 was unaffected. Rbm3 induction depended on a full Brain And Muscle ARNT-Like Protein 1 (Bmal1) complement: reduced Bmal1 erased Rbm3 responses and weakened SCN circuit resilience to temperature changes. By focusing on circadian and temperature dependency, we highlight weakened transmission between core clock and downstream pathways as a potential route for reduced circadian resilience.
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Affiliation(s)
- Marieke M. B. Hoekstra
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
| | - Natalie Ness
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
| | - Aina Badia-Soteras
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
| | - Marco Brancaccio
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
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2
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Chawla S, O’Neill J, Knight MI, He Y, Wang L, Maronde E, Rodríguez SG, van Ooijen G, Garbarino-Pico E, Wolf E, Dkhissi-Benyahya O, Nikhat A, Chakrabarti S, Youngstedt SD, Zi-Ching Mak N, Provencio I, Oster H, Goel N, Caba M, Oosthuizen M, Duffield GE, Chabot C, Davis SJ. Timely Questions Emerging in Chronobiology: The Circadian Clock Keeps on Ticking. J Circadian Rhythms 2024; 22:2. [PMID: 38617710 PMCID: PMC11011957 DOI: 10.5334/jcr.237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 04/16/2024] Open
Abstract
Chronobiology investigations have revealed much about cellular and physiological clockworks but we are far from having a complete mechanistic understanding of the physiological and ecological implications. Here we present some unresolved questions in circadian biology research as posed by the editorial staff and guest contributors to the Journal of Circadian Rhythms. This collection of ideas is not meant to be comprehensive but does reveal the breadth of our observations on emerging trends in chronobiology and circadian biology. It is amazing what could be achieved with various expected innovations in technologies, techniques, and mathematical tools that are being developed. We fully expect strengthening mechanistic work will be linked to health care and environmental understandings of circadian function. Now that most clock genes are known, linking these to physiological, metabolic, and developmental traits requires investigations from the single molecule to the terrestrial ecological scales. Real answers are expected for these questions over the next decade. Where are the circadian clocks at a cellular level? How are clocks coupled cellularly to generate organism level outcomes? How do communities of circadian organisms rhythmically interact with each other? In what way does the natural genetic variation in populations sculpt community behaviors? How will methods development for circadian research be used in disparate academic and commercial endeavors? These and other questions make it a very exciting time to be working as a chronobiologist.
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Affiliation(s)
| | - John O’Neill
- MRC Laboratory of Molecular Biology Cambridge, UK
| | | | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, China National Botanical Garden, Beijing 100093, CN
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, China National Botanical Garden, Beijing 100093, CN
| | - Erik Maronde
- Institut für Anatomie II, Dr. Senckenbergische Anatomie, Goethe-Universität Frankfurt, Theodor-Stern-Kai-7, 60590 Frankfurt, DE
| | - Sergio Gil Rodríguez
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Eduardo Garbarino-Pico
- Universidad Nacional de Córdoba (UNC), Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, AR
- CONICET-UNC, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, AR
| | - Eva Wolf
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch- Weg 17, 55128 Mainz, DE
| | - Ouria Dkhissi-Benyahya
- Inserm, Stem Cell and Brain Research Institute U1208, Univ Lyon, UniversitéClaude Bernard Lyon 1, 18 Avenue du Doyen Lépine, 69500, Bron, FR
| | - Anjoom Nikhat
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, IN
| | - Shaon Chakrabarti
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, IN
| | - Shawn D. Youngstedt
- Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ, US
- Department of Medicine, University of Arizona, Tucson, AZ, US
| | | | - Ignacio Provencio
- Department of Biology and Department of Ophthalmology, University of Virginia, Charlottesville, VA, US
| | - Henrik Oster
- Institute of Neurobiology, Center for Brain, Behavior & Metabolism (CBBM), University of Luebeck, 23562 Luebeck, DE
| | - Namni Goel
- Biological Rhythms Research Laboratory, Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, US
| | - Mario Caba
- Centro de Investigaciones Biomédicas, Universidad Veracruzana, Xalapa, Ver., MX
| | - Maria Oosthuizen
- Department of Zoology and Entomology, University of Pretoria, Pretoria, ZA
- Mammal Research Institute, University of Pretoria, Hatfield, ZA
| | - Giles E. Duffield
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, US
| | - Christopher Chabot
- Department of Biological Sciences, Plymouth State University, Plymouth, NH 03264, US
| | - Seth J. Davis
- Department of Biology, University of York, York YO105DD, UK
- State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, CN
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3
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Prasetyaningrum P, Litthauer S, Vegliani F, Battle MW, Wood MW, Liu X, Dickson C, Jones MA. Inhibition of RNA degradation integrates the metabolic signals induced by osmotic stress into the Arabidopsis circadian system. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5805-5819. [PMID: 37453132 PMCID: PMC10540740 DOI: 10.1093/jxb/erad274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The circadian clock system acts as an endogenous timing reference that coordinates many metabolic and physiological processes in plants. Previous studies have shown that the application of osmotic stress delays circadian rhythms via 3'-phospho-adenosine 5'-phosphate (PAP), a retrograde signalling metabolite that is produced in response to redox stress within organelles. PAP accumulation leads to the inhibition of exoribonucleases (XRNs), which are responsible for RNA degradation. Interestingly, we are now able to demonstrate that post-transcriptional processing is crucial for the circadian response to osmotic stress. Our data show that osmotic stress increases the stability of specific circadian RNAs, suggesting that RNA metabolism plays a vital role in circadian clock coordination during drought. Inactivation of XRN4 is sufficient to extend circadian rhythms as part of this response, with PRR7 and LWD1 identified as transcripts that are post-transcriptionally regulated to delay circadian progression.
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Affiliation(s)
| | | | - Franco Vegliani
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | - Xinmeng Liu
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Cathryn Dickson
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Matthew Alan Jones
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
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4
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Haniffa S, Narain P, Hughes MA, Petković A, Šušić M, Mlambo V, Chaudhury D. Chronic social stress blunts core body temperature and molecular rhythms of Rbm3 and Cirbp in mouse lateral habenula. Open Biol 2023; 13:220380. [PMID: 37463657 PMCID: PMC10353891 DOI: 10.1098/rsob.220380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/29/2023] [Indexed: 07/19/2023] Open
Abstract
Chronic social stress in mice causes behavioural and physiological changes that result in perturbed rhythms of body temperature, activity and sleep-wake cycle. To further understand the link between mood disorders and temperature rhythmicity in mice that are resilient or susceptible to stress, we measured core body temperature (Tcore) before and after exposure to chronic social defeat stress (CSDS). We found that Tcore amplitudes of stress-resilient and susceptible mice are dampened during exposure to CSDS. However, following CSDS, resilient mice recovered temperature amplitude faster than susceptible mice. Furthermore, the interdaily stability (IS) of temperature rhythms was fragmented in stress-exposed mice during CSDS, which recovered to control levels following stress. There were minimal changes in locomotor activity after stress exposure which correlates with regular rhythmic expression of Prok2 - an output signal of the suprachiasmatic nucleus. We also determined that expression of thermosensitive genes Rbm3 and Cirbp in the lateral habenula (LHb) were blunted 1 day after CSDS. Rhythmic expression of these genes recovered 10 days later. Overall, we show that CSDS blunts Tcore and thermosensitive gene rhythms. Tcore rhythm recovery is faster in stress-resilient mice, but Rbm3 and Cirbp recovery is uniform across the phenotypes.
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Affiliation(s)
- Salma Haniffa
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Priyam Narain
- Centre for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Michelle Ann Hughes
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Aleksa Petković
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Marko Šušić
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Vongai Mlambo
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Dipesh Chaudhury
- Department of Biology, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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5
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Haniffa S, Narain P, Hughes MA, Petković A, Šušić M, Mlambo V, Chaudhury D. Chronic social stress blunts core body temperature and molecular rhythms of Rbm3and Cirbpin mouse lateral habenula.. [DOI: 10.1101/2023.01.02.522528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
AbstractChronic social stress in mice causes behavioral and physiological changes that result in perturbed rhythms of body temperature, activity and sleep-wake cycle. To further understand the link between mood disorders and temperature rhythmicity in mice that are resilient or susceptible to stress, we measured core body temperature (Tcore) before and after exposure to chronic social defeat stress (CSDS). We found that Tcore amplitudes of stress-resilient and susceptible mice are dampened during exposure to CSDS. However, following CSDS, resilient mice recovered temperature amplitude faster than susceptible mice. Furthermore, the interdaily stability (IS) of temperature rhythms was fragmented in stress-exposed mice during CSDS, which recovered to control levels following stress. There were minimal changes in locomotor activity after stress exposure which correlates with regular rhythmic expression ofProk2- an output signal of the suprachiasmatic nucleus. We also determined that expression of thermosensitive genesRbm3andCirbpin the lateral habenula (LHb) were blunted 1-day after CSDS. Rhythmic expression of these genes recovered 10 days later. Overall, we show that CSDS blunts Tcore and thermosensitive gene rhythms. Tcore rhythm recovery is faster in stress-resilient mice, butRbm3andCirbprecovery is uniform across the phenotypes.
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6
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Castillo KD, Wu C, Ding Z, Lopez-Garcia OK, Rowlinson E, Sachs MS, Bell-Pedersen D. A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules. Cell Rep 2022; 41:111879. [PMID: 36577368 PMCID: PMC10241597 DOI: 10.1016/j.celrep.2022.111879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 09/13/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022] Open
Abstract
Phosphorylation of Neurospora crassa eukaryotic initiation factor 2 α (eIF2α), a conserved translation initiation factor, is clock controlled. To determine the impact of rhythmic eIF2α phosphorylation on translation, we performed temporal ribosome profiling and RNA sequencing (RNA-seq) in wild-type (WT), clock mutant Δfrq, eIF2α kinase mutant Δcpc-3, and constitutively active cpc-3c cells. About 14% of mRNAs are rhythmically translated in WT cells, and translation rhythms for ∼30% of these mRNAs, which we named circadian translation-initiation-controlled genes (cTICs), are dependent on the clock and CPC-3. Most cTICs are expressed from arrhythmic mRNAs and contain a P-body (PB) localization motif in their 5' leader sequence. Deletion of SNR-1, a component of cytoplasmic messenger ribonucleoprotein granules (cmRNPgs) that include PBs and stress granules (SGs), and the PB motif on one of the cTIC mRNAs, zip-1, significantly alters zip-1 rhythmic translation. These results reveal that the clock regulates rhythmic translation of specific mRNAs through rhythmic eIF2α activity and cmRNPg metabolism.
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Affiliation(s)
- Kathrina D Castillo
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Zhaolan Ding
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Emma Rowlinson
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Deborah Bell-Pedersen
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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7
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Oyama Y, Shuff SR, Burns N, Vohwinkel CU, Eckle T. Intense light-elicited alveolar type 2-specific circadian PER2 protects from bacterial lung injury via BPIFB1. Am J Physiol Lung Cell Mol Physiol 2022; 322:L647-L661. [PMID: 35272486 PMCID: PMC9037706 DOI: 10.1152/ajplung.00301.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Circadian amplitude enhancement has the potential to be organ protective but has not been studied in acute lung injury (ALI). Consistent light and dark cycles are crucial for the amplitude regulation of the circadian rhythm protein Period2 (PER2). Housing mice under intense instead of ambient light for 1 wk (light: dark cycle:14h:10h), we demonstrated a robust increase of pulmonary PER2 trough and peak levels, which is consistent with circadian amplitude enhancement. A search for the affected lung cell type suggested alveolar type 2 (ATII) cells as strong candidates for light induction of PER2. A head-to-head comparison of mice with cell-type-specific deletion of Per2 in ATII, endothelial, or myeloid cells uncovered a dramatic phenotype in mice with an ATII-specific deletion of Per2. During Pseudomonas aeruginosa-induced ALI, mice with Per2 deletion in ATII cells showed 0% survival, whereas 85% of control mice survived. Subsequent studies demonstrated that intense light therapy dampened lung inflammation or improved the alveolar barrier function during P. aeruginosa-induced ALI, which was abolished in mice with an ATII-specific deletion of Per2. A genome-wide mRNA array uncovered bactericidal/permeability-increasing fold-containing family B member 1 (BPIFB1) as a downstream target of intense light-elicited ATII-PER2 mediated lung protection. Using the flavonoid and PER2 amplitude enhancer nobiletin, we recapitulated the lung-protective and anti-inflammatory effects of light and BPIFB1, respectively. Together, our studies demonstrate that light-elicited amplitude enhancement of ATII-specific PER2 is a critical control point of inflammatory pathways during bacterial ALI.
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Affiliation(s)
- Yoshimasa Oyama
- 1Department of Anesthesiology, University of Colorado Denver School of Medicine, Aurora, Colorado,2Department of Anesthesiology and Intensive Care Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Sydney R. Shuff
- 1Department of Anesthesiology, University of Colorado Denver School of Medicine, Aurora, Colorado
| | - Nana Burns
- 3Developmental Lung Biology, Cardiovascular Pulmonary Research Laboratories, Division of Pediatric Critical Care, Department of Medicine and Pediatrics, University of Colorado, Aurora, Colorado
| | - Christine U. Vohwinkel
- 3Developmental Lung Biology, Cardiovascular Pulmonary Research Laboratories, Division of Pediatric Critical Care, Department of Medicine and Pediatrics, University of Colorado, Aurora, Colorado
| | - Tobias Eckle
- 1Department of Anesthesiology, University of Colorado Denver School of Medicine, Aurora, Colorado,4Department of Cell and Developmental Biology, University of Colorado Denver School of Medicine, Aurora, Colorado
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8
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Hargreaves JK, Oakenfull RJ, Davis AM, Pullen F, Knight MI, Pitchford JW, Davis SJ. Multiple metals influence distinct properties of the Arabidopsis circadian clock. PLoS One 2022; 17:e0258374. [PMID: 35381003 PMCID: PMC8982871 DOI: 10.1371/journal.pone.0258374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/08/2022] [Indexed: 11/19/2022] Open
Abstract
Circadian rhythms coordinate endogenous events with external signals, and are essential to biological function. When environmental contaminants affect these rhythms, the organism may experience fitness consequences such as reduced growth or increased susceptibility to pathogens. In their natural environment plants may be exposed to a wide range of industrial and agricultural soil pollutants. Here, we investigate how the addition of various metal salts to the root-interaction environment can impact rhythms, measured via the promoter:luciferase system. The consequences of these environmental changes were found to be varied and complex. Therefore, in addition to traditional Fourier-based analyses, we additionally apply novel wavelet-based spectral hypothesis testing and clustering methodologies to organize and understand the data. We are able to classify broad sets of responses to these metal salts, including those that increase, and those that decrease, the period, or which induce a lack of precision or disrupt any meaningful periodicity. Our methods are general, and may be applied to discover common responses and hidden structures within a wide range of biological time series data.
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Affiliation(s)
- Jessica K. Hargreaves
- Department of Mathematics, University of York, York, United Kingdom
- * E-mail: (JKH); (SJD)
| | | | - Amanda M. Davis
- Department of Biology, University of York, York, United Kingdom
| | - Freya Pullen
- Department of Biology, University of York, York, United Kingdom
| | - Marina I. Knight
- Department of Mathematics, University of York, York, United Kingdom
| | - Jon W. Pitchford
- Department of Mathematics, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Seth J. Davis
- Department of Biology, University of York, York, United Kingdom
- State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- * E-mail: (JKH); (SJD)
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9
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Abstract
Experiments that compare rhythmic properties across different genetic alterations and entrainment conditions underlie some of the most important breakthroughs in circadian biology. A robust estimation of the rhythmic properties of the circadian signals goes hand in hand with these discoveries. Widely applied traditional signal analysis methods such as fitting cosine functions or Fourier transformations rely on the assumption that oscillation periods do not change over time. However, novel high-resolution recording techniques have shown that, most commonly, circadian signals exhibit time-dependent changes of periods and amplitudes which cannot be captured with the traditional approaches. In this chapter we introduce a method to determine time-dependent properties of oscillatory signals, using the novel open-source Python-based Biological Oscillations Analysis Toolkit (pyBOAT). We show with examples how to detect rhythms, compute and interpret high-resolution time-dependent spectral results, analyze the main oscillatory component, and to subsequently determine these main components' time-dependent instantaneous period, amplitude, and phase. We introduce step-by-step how such an analysis can be done by means of the easy-to-use point-and-click graphical user interface (GUI) provided by pyBOAT or executed within a Python programming environment. Concepts are explained using simulated signals as well as experimentally obtained time series.
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Affiliation(s)
- Christoph Schmal
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany.
| | - Gregor Mönke
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Adrián E Granada
- Charité Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Morris EL, Patton AP, Chesham JE, Crisp A, Adamson A, Hastings MH. Single-cell transcriptomics of suprachiasmatic nuclei reveal a Prokineticin-driven circadian network. EMBO J 2021; 40:e108614. [PMID: 34487375 PMCID: PMC8521297 DOI: 10.15252/embj.2021108614] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 11/22/2022] Open
Abstract
Circadian rhythms in mammals are governed by the hypothalamic suprachiasmatic nucleus (SCN), in which 20,000 clock cells are connected together into a powerful time‐keeping network. In the absence of network‐level cellular interactions, the SCN fails as a clock. The topology and specific roles of its distinct cell populations (nodes) that direct network functions are, however, not understood. To characterise its component cells and network structure, we conducted single‐cell sequencing of SCN organotypic slices and identified eleven distinct neuronal sub‐populations across circadian day and night. We defined neuropeptidergic signalling axes between these nodes, and built neuropeptide‐specific network topologies. This revealed their temporal plasticity, being up‐regulated in circadian day. Through intersectional genetics and real‐time imaging, we interrogated the contribution of the Prok2‐ProkR2 neuropeptidergic axis to network‐wide time‐keeping. We showed that Prok2‐ProkR2 signalling acts as a key regulator of SCN period and rhythmicity and contributes to defining the network‐level properties that underpin robust circadian co‐ordination. These results highlight the diverse and distinct contributions of neuropeptide‐modulated communication of temporal information across the SCN.
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Affiliation(s)
- Emma L Morris
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew P Patton
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Johanna E Chesham
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alastair Crisp
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Antony Adamson
- The Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Michael H Hastings
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK
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11
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Chavan AG, Swan JA, Heisler J, Sancar C, Ernst DC, Fang M, Palacios JG, Spangler RK, Bagshaw CR, Tripathi S, Crosby P, Golden SS, Partch CL, LiWang A. Reconstitution of an intact clock reveals mechanisms of circadian timekeeping. Science 2021; 374:eabd4453. [PMID: 34618577 DOI: 10.1126/science.abd4453] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Archana G Chavan
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Jeffrey A Swan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Joel Heisler
- Department of Chemistry and Biochemistry, University of California, Merced, CA 95343, USA
| | - Cigdem Sancar
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dustin C Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mingxu Fang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph G Palacios
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Rebecca K Spangler
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Clive R Bagshaw
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Priya Crosby
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.,Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, CA 95343, USA.,Department of Chemistry and Biochemistry, University of California, Merced, CA 95343, USA.,Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, CA 95343, USA.,Health Sciences Research Institute, University of California, Merced, CA 95343, USA
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12
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Muroya M, Oshima H, Kobayashi S, Miura A, Miyamura Y, Shiota H, Onai K, Ishiura M, Manabe K, Kutsuna S. Circadian Clock in Arabidopsis thaliana Determines Flower Opening Time Early in the Morning and Dominantly Closes Early in the Afternoon. PLANT & CELL PHYSIOLOGY 2021; 62:883-893. [PMID: 33822207 DOI: 10.1093/pcp/pcab048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 03/28/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Many plant species exhibit diurnal flower opening and closing, which is an adaptation influenced by the lifestyle of pollinators and herbivores. However, it remains unclear how these temporal floral movements are modulated. To clarify the role of the circadian clock in flower movement, we examined temporal floral movements in Arabidopsis thaliana. Wild-type (accessions; Col-0, Ler-0 and Ws-4) flowers opened between 0.7 and 1.4 h in a 16-h light period and closed between 7.5 and 8.3 h in a diurnal light period. In the arrhythmic mutants pcl1-1 and prr975, the former flowers closed slowly and imperfectly and the latter ones never closed. Under continuous light conditions, new flowers emerged and opened within a 23-26 h window in the wild-type, but the flowers in pcl1-1 and prr975 developed straight petals, whose curvatures were extremely small. Anti-phasic circadian gene expression of CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYLE (LHY) and TIMING OF CAB EXPRESSION 1 (TOC1) occurred in wild-type flowers, but non-rhythmic expression was observed in pcl1-1 and prr975 mutants. Focusing on excised petals, bioluminescence monitoring revealed rhythmic promoter activities of genes expressed (CCA1, LHY and PHYTOCLOCK 1/LUX ARRHYTHMO, PCL1/LUX) in the morning and evening. These results suggest that the clock induces flower opening redundantly with unknown light-sensing pathways. By contrast, flower closing is completely dependent on clock control. These findings will lead to further exploration of the molecular mechanisms and evolutionary diversity of timing in flower opening and closing.
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Affiliation(s)
- Mitsuhiko Muroya
- Department of Life and Environmental System Science, Yokohama City University, Seto 22, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Haruka Oshima
- Department of Life and Environmental System Science, Yokohama City University, Seto 22, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Shoko Kobayashi
- Department of Life and Environmental System Science, Yokohama City University, Seto 22, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Aya Miura
- Department of Life and Environmental System Science, Yokohama City University, Seto 22, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Yohei Miyamura
- Department of Life and Environmental System Science, Yokohama City University, Seto 22, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Hajime Shiota
- Department of Life and Environmental System Science, Yokohama City University, Seto 22, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Kiyoshi Onai
- Centre for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-kuKyoto 606-8502Japan
| | - Masahiro Ishiura
- Centre for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Katsushi Manabe
- Department of Life and Environmental System Science, Yokohama City University, Seto 22, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Shinsuke Kutsuna
- Department of Life and Environmental System Science, Yokohama City University, Seto 22, Kanazawa-ku, Yokohama, 236-0027 Japan
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13
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Wang X, Jiang B, Gu L, Chen Y, Mora M, Zhu M, Noory E, Wang Q, Lin C. A photoregulatory mechanism of the circadian clock in Arabidopsis. NATURE PLANTS 2021; 7:1397-1408. [PMID: 34650267 DOI: 10.1038/s41477-021-01002-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/03/2021] [Indexed: 05/04/2023]
Abstract
Cryptochromes (CRYs) are photoreceptors that mediate light regulation of the circadian clock in plants and animals. Here we show that CRYs mediate blue-light regulation of N6-methyladenosine (m6A) modification of more than 10% of messenger RNAs in the Arabidopsis transcriptome, especially those regulated by the circadian clock. CRY2 interacts with three subunits of the METTL3/14-type N6-methyladenosine RNA methyltransferase (m6A writer): MTA, MTB and FIP37. Photo-excited CRY2 undergoes liquid-liquid phase separation (LLPS) to co-condense m6A writer proteins in vivo, without obviously altering the affinity between CRY2 and the writer proteins. mta and cry1cry2 mutants share common defects of a lengthened circadian period, reduced m6A RNA methylation and accelerated degradation of mRNA encoding the core component of the molecular oscillator circadian clock associated 1 (CCA1). These results argue for a photoregulatory mechanism by which light-induced phase separation of CRYs modulates m6A writer activity, mRNA methylation and abundance, and the circadian rhythms in plants.
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Affiliation(s)
- Xu Wang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Bochen Jiang
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yadi Chen
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Manuel Mora
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Mulangma Zhu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Eliace Noory
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Qin Wang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Chentao Lin
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
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14
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Muñoz-Guzmán F, Caballero V, Larrondo LF. A global search for novel transcription factors impacting the Neurospora crassa circadian clock. G3 (BETHESDA, MD.) 2021; 11:jkab100. [PMID: 33792687 PMCID: PMC8495738 DOI: 10.1093/g3journal/jkab100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/16/2021] [Indexed: 01/15/2023]
Abstract
Eukaryotic circadian oscillators share a common circuit architecture, a negative feedback loop in which a positive element activates the transcription of a negative one that then represses the action of the former, inhibiting its own expression. While studies in mammals and insects have revealed additional transcriptional inputs modulating the expression of core clock components, this has been less characterized in the model Neurospora crassa, where the participation of other transcriptional components impacting circadian clock dynamics remains rather unexplored. Thus, we sought to identify additional transcriptional regulators modulating the N. crassa clock, following a reverse genetic screen based on luminescent circadian reporters and a collection of transcription factors (TFs) knockouts, successfully covering close to 60% of them. Besides the canonical core clock components WC-1 and -2, none of the tested transcriptional regulators proved to be essential for rhythmicity. Nevertheless, we identified a set of 23 TFs that when absent lead to discrete, but significant, changes in circadian period. While the current level of analysis does not provide mechanistic information about how these new players modulate circadian parameters, the results of this screen reveal that an important number of light and clock-regulated TFs, involved in a plethora of processes, are capable of modulating the clockworks. This partial reverse genetic clock screen also exemplifies how the N. crassa knockout collection continues to serve as an expedite platform to address broad biological questions.
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Affiliation(s)
- Felipe Muñoz-Guzmán
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Valeria Caballero
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Luis F Larrondo
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
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15
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Feke A, Vanderwall M, Liu W, Gendron JM. Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function. PLoS One 2021; 16:e0235938. [PMID: 33730063 PMCID: PMC7968664 DOI: 10.1371/journal.pone.0235938] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/23/2021] [Indexed: 02/01/2023] Open
Abstract
The small LOV/F-box/Kelch family of E3 ubiquitin ligases plays an essential role in the regulation of plant circadian clocks and flowering time by sensing dusk. The family consists of three members, ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX PROTEIN 1 (FKF1), which share a unique protein domain architecture allowing them to act as photoreceptors that transduce light signals via altering stability of target proteins. Despite intensive study of this protein family we still lack important knowledge about the biochemical and functional roles of the protein domains that comprise these unique photoreceptors. Here, we perform comparative analyses of transgenic lines constitutively expressing the photoreceptor LOV domain or the Kelch repeat protein-protein interaction domains of ZTL, FKF1, and LKP2. Expression of each domain alone is sufficient to disrupt circadian rhythms and flowering time, but each domain differs in the magnitude of effect. Immunoprecipitation followed by mass spectrometry with the ZTL Kelch repeat domain identified a suite of potential interacting partners. Furthermore, the ZTL Kelch repeat domain can interact with the ZTL homologs, LKP2 and FKF1, and the LOV domain of ZTL itself. This suggests a hypothesis that the Kelch repeat domain of ZTL may mediate inter- and intra-molecular interactions of the three LOV/F-box/Kelch proteins and provides added insight into the composition of the protein complexes and an additional role for the Kelch repeat domain.
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Affiliation(s)
- Ann Feke
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United States of America
| | - Morgan Vanderwall
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United States of America
| | - Wei Liu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United States of America
| | - Joshua M. Gendron
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United States of America
- * E-mail:
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16
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Eelderink-Chen Z, Bosman J, Sartor F, Dodd AN, Kovács ÁT, Merrow M. A circadian clock in a nonphotosynthetic prokaryote. SCIENCE ADVANCES 2021; 7:eabe2086. [PMID: 33523996 PMCID: PMC7793578 DOI: 10.1126/sciadv.abe2086] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/13/2020] [Indexed: 05/06/2023]
Abstract
Circadian clocks create a 24-hour temporal structure, which allows organisms to occupy a niche formed by time rather than space. They are pervasive throughout nature, yet they remain unexpectedly unexplored and uncharacterized in nonphotosynthetic bacteria. Here, we identify in Bacillus subtilis circadian rhythms sharing the canonical properties of circadian clocks: free-running period, entrainment, and temperature compensation. We show that gene expression in B. subtilis can be synchronized in 24-hour light or temperature cycles and exhibit phase-specific characteristics of entrainment. Upon release to constant dark and temperature conditions, bacterial biofilm populations have temperature-compensated free-running oscillations with a period close to 24 hours. Our work opens the field of circadian clocks in the free-living, nonphotosynthetic prokaryotes, bringing considerable potential for impact upon biomedicine, ecology, and industrial processes.
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Affiliation(s)
- Zheng Eelderink-Chen
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Jasper Bosman
- Department of Bioinformatics, Hanze University of Applied Sciences, Groningen, Zernikeplein 11, 9747 AS Groningen, Netherlands
| | - Francesca Sartor
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Antony N Dodd
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Martha Merrow
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany.
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17
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Oyama Y, Bartman CM, Bonney S, Lee JS, Walker LA, Han J, Borchers CH, Buttrick PM, Aherne CM, Clendenen N, Colgan SP, Eckle T. Intense Light-Mediated Circadian Cardioprotection via Transcriptional Reprogramming of the Endothelium. Cell Rep 2020; 28:1471-1484.e11. [PMID: 31390562 PMCID: PMC6708043 DOI: 10.1016/j.celrep.2019.07.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 05/15/2019] [Accepted: 07/08/2019] [Indexed: 01/10/2023] Open
Abstract
Consistent daylight oscillations and abundant oxygen availability are fundamental to human health. Here, we investigate the intersection between light-sensing (Period 2 [PER2]) and oxygen-sensing (hypoxia-inducible factor [HIF1A]) pathways in cellular adaptation to myocardial ischemia. We demonstrate that intense light is cardioprotective via circadian PER2 amplitude enhancement, mimicking hypoxia-elicited adenosine- and HIF1A-metabolic adaptation to myocardial ischemia under normoxic conditions. Whole-genome array from intense light-exposed wild-type or Per2-/- mice and myocardial ischemia in endothelial-specific PER2-deficient mice uncover a critical role for intense light in maintaining endothelial barrier function via light-enhanced HIF1A transcription. A proteomics screen in human endothelia reveals a dominant role for PER2 in metabolic reprogramming to hypoxia via mitochondrial translocation, tricarboxylic acid (TCA) cycle enzyme activity regulation, and HIF1A transcriptional adaption to hypoxia. Translational investigation of intense light in human subjects identifies similar PER2 mechanisms, implicating the use of intense light for the treatment of cardiovascular disease.
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Affiliation(s)
- Yoshimasa Oyama
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Colleen M Bartman
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Graduate Training Program in Cell Biology, Stem Cells, and Development, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stephanie Bonney
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Graduate Training Program in Cell Biology, Stem Cells, and Development, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Scott Lee
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lori A Walker
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jun Han
- Department of Biochemistry and Microbiology, Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Christoph H Borchers
- Department of Biochemistry and Microbiology, Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada; Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Peter M Buttrick
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Carol M Aherne
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nathan Clendenen
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sean P Colgan
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tobias Eckle
- Mucosal Inflammation Program, Departments of Medicine and Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Graduate Training Program in Cell Biology, Stem Cells, and Development, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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18
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Patton AP, Edwards MD, Smyllie NJ, Hamnett R, Chesham JE, Brancaccio M, Maywood ES, Hastings MH. The VIP-VPAC2 neuropeptidergic axis is a cellular pacemaking hub of the suprachiasmatic nucleus circadian circuit. Nat Commun 2020; 11:3394. [PMID: 32636383 PMCID: PMC7341843 DOI: 10.1038/s41467-020-17110-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 06/05/2020] [Indexed: 12/01/2022] Open
Abstract
The hypothalamic suprachiasmatic nuclei (SCN) are the principal mammalian circadian timekeeper, co-ordinating organism-wide daily and seasonal rhythms. To achieve this, cell-autonomous circadian timing by the ~20,000 SCN cells is welded into a tight circuit-wide ensemble oscillation. This creates essential, network-level emergent properties of precise, high-amplitude oscillation with tightly defined ensemble period and phase. Although synchronised, regional cell groups exhibit differentially phased activity, creating stereotypical spatiotemporal circadian waves of cellular activation across the circuit. The cellular circuit pacemaking components that generate these critical emergent properties are unknown. Using intersectional genetics and real-time imaging, we show that SCN cells expressing vasoactive intestinal polypeptide (VIP) or its cognate receptor, VPAC2, are neurochemically and electrophysiologically distinct, but together they control de novo rhythmicity, setting ensemble period and phase with circuit-level spatiotemporal complexity. The VIP/VPAC2 cellular axis is therefore a neurochemically and topologically specific pacemaker hub that determines the emergent properties of the SCN timekeeper. Circadian activity modulation in the suprachiasmatic nucleus (SCN) is a network-level emergent property that requires neuropeptide VIP signaling, yet the precise cellular mechanisms are unknown. Patton et al. show that cells expressing VIP or its receptor VPAC2 together determine these emergent properties of the SCN.
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Affiliation(s)
- Andrew P Patton
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Mathew D Edwards
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.,UCL Sainsbury Wellcome Centre for Neural Circuits and Behaviour, London, UK
| | - Nicola J Smyllie
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Ryan Hamnett
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.,Department of Neurosurgery, Stanford University, Stanford, USA
| | - Johanna E Chesham
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Marco Brancaccio
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.,Department of Brain Sciences, UK Dementia Research Institute, Imperial College London, London, UK
| | - Elizabeth S Maywood
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Michael H Hastings
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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19
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Hargreaves JK, Knight MI, Pitchford JW, Oakenfull RJ, Chawla S, Munns J, Davis SJ. Wavelet spectral testing: Application to nonstationary circadian rhythms. Ann Appl Stat 2019. [DOI: 10.1214/19-aoas1246] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Brancaccio M, Edwards MD, Patton AP, Smyllie NJ, Chesham JE, Maywood ES, Hastings MH. Cell-autonomous clock of astrocytes drives circadian behavior in mammals. Science 2019; 363:187-192. [PMID: 30630934 DOI: 10.1126/science.aat4104] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 11/02/2018] [Indexed: 12/16/2022]
Abstract
Circadian (~24-hour) rhythms depend on intracellular transcription-translation negative feedback loops (TTFLs). How these self-sustained cellular clocks achieve multicellular integration and thereby direct daily rhythms of behavior in animals is largely obscure. The suprachiasmatic nucleus (SCN) is the fulcrum of this pathway from gene to cell to circuit to behavior in mammals. We describe cell type-specific, functionally distinct TTFLs in neurons and astrocytes of the SCN and show that, in the absence of other cellular clocks, the cell-autonomous astrocytic TTFL alone can drive molecular oscillations in the SCN and circadian behavior in mice. Astrocytic clocks achieve this by reinstating clock gene expression and circadian function of SCN neurons via glutamatergic signals. Our results demonstrate that astrocytes can autonomously initiate and sustain complex mammalian behavior.
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Affiliation(s)
- Marco Brancaccio
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
| | - Mathew D Edwards
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Andrew P Patton
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Nicola J Smyllie
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Johanna E Chesham
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Elizabeth S Maywood
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Michael H Hastings
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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21
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Xie Y, Tang Q, Chen G, Xie M, Yu S, Zhao J, Chen L. New Insights Into the Circadian Rhythm and Its Related Diseases. Front Physiol 2019; 10:682. [PMID: 31293431 PMCID: PMC6603140 DOI: 10.3389/fphys.2019.00682] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/13/2019] [Indexed: 12/18/2022] Open
Abstract
Circadian rhythms (CR) are a series of endogenous autonomous oscillators generated by the molecular circadian clock which acting on coordinating internal time with the external environment in a 24-h daily cycle. The circadian clock system is a major regulatory factor for nearly all physiological activities and its disorder has severe consequences on human health. CR disruption is a common issue in modern society, and researches about people with jet lag or shift works have revealed that CR disruption can cause cognitive impairment, psychiatric illness, metabolic syndrome, dysplasia, and cancer. In this review, we summarized the synchronizers and the synchronization methods used in experimental research, and introduced CR monitoring and detection methods. Moreover, we evaluated conventional CR databases, and analyzed experiments that characterized the underlying causes of CR disorder. Finally, we further discussed the latest developments in understanding of CR disruption, and how it may be relevant to health and disease. Briefly, this review aimed to synthesize previous studies to aid in future studies of CR and CR-related diseases.
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Affiliation(s)
- Yanling Xie
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingming Tang
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guangjin Chen
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengru Xie
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaoling Yu
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiajia Zhao
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lili Chen
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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22
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Nohales MA, Liu W, Duffy T, Nozue K, Sawa M, Pruneda-Paz JL, Maloof JN, Jacobsen SE, Kay SA. Multi-level Modulation of Light Signaling by GIGANTEA Regulates Both the Output and Pace of the Circadian Clock. Dev Cell 2019; 49:840-851.e8. [PMID: 31105011 PMCID: PMC6597437 DOI: 10.1016/j.devcel.2019.04.030] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 02/16/2019] [Accepted: 04/17/2019] [Indexed: 01/29/2023]
Abstract
Integration of environmental signals with endogenous biological processes is essential for organisms to thrive in their natural environment. Being entrained by periodic environmental changes, the circadian clock incorporates external information to coordinate physiological processes, phasing them to the optimal time of the day and year. Here, we present a pivotal role for the clock component GIGANTEA (GI) as a genome-wide regulator of transcriptional networks mediating growth and adaptive processes in plants. We provide mechanistic details on how GI integrates endogenous timing with light signaling pathways through the global modulation of PHYTOCHROME-INTERACTING FACTORs (PIFs). Gating of the activity of these transcriptional regulators by GI directly affects a wide array of output rhythms, including photoperiodic growth. Furthermore, we uncover a role for PIFs in mediating light input to the circadian oscillator and show how their regulation by GI is required to set the pace of the clock in response to light-dark cycles.
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Affiliation(s)
- Maria A Nohales
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Wanlu Liu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Zhejiang University, University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Tomas Duffy
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Kazunari Nozue
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Mariko Sawa
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, La Jolla, CA 92093, USA
| | - Jose L Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, La Jolla, CA 92093, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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23
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Feke A, Liu W, Hong J, Li MW, Lee CM, Zhou EK, Gendron JM. Decoys provide a scalable platform for the identification of plant E3 ubiquitin ligases that regulate circadian function. eLife 2019; 8:44558. [PMID: 30950791 PMCID: PMC6483598 DOI: 10.7554/elife.44558] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/04/2019] [Indexed: 12/30/2022] Open
Abstract
The circadian clock relies on regulated degradation of clock proteins to maintain rhythmicity. Despite this, we know few components that mediate protein degradation. This is due to high levels of functional redundancy within plant E3 ubiquitin ligase families. In order to overcome this issue and discover E3 ubiquitin ligases that control circadian function, we generated a library of transgenic Arabidopsis plants expressing dominant-negative ‘decoy’ E3 ubiquitin ligases. We determined their effects on the circadian clock and identified dozens of new potential regulators of circadian function. To demonstrate the potency of the decoy screening methodology to overcome redundancy and identify bona fide clock regulators, we performed follow-up studies on MAC3A (PUB59) and MAC3B (PUB60). We show that they redundantly control circadian period by regulating splicing. This work demonstrates the viability of ubiquitin ligase decoys as a screening platform to overcome genetic challenges and discover E3 ubiquitin ligases that regulate plant development. Plants have an internal time keeper known as the circadian clock that operates in 24-hour cycles to coordinate the plants behaviors with the environment. The clock is made of many different proteins and plants carefully control when they make and destroy these proteins to regulate the cycle. Inside plant cells, enzymes known as E3 ubiquitin ligases determine which proteins are destroyed by labelling target proteins with a small tag. Plants have hundreds of different E3 ubiquitin ligases, leading to overlaps in the roles the different enzymes play. These overlaps make it difficult to identify the specific E3 ubiquitin ligases that are involved in a particular process. As a result, only few E3 ubiquitin ligases implicated in the circadian clock have been identified so far. A small weed known as Arabidopsis is often used in research studies because it grows quickly and the genes can be easily manipulated. Here, Feke et al. set out to develop a new tool to identify the specific E3 ubiquitin ligases involved in regulating the circadian clock in Arabidopsis. The team created a library of hundreds of Arabidopsis plants producing different decoy E3 ubiquitin ligases that retained their ability to bind to target proteins but were unable to degrade them. Nearly a quarter of the E3 ligases found in Arabidopsis were represented in this library. The decoy enzymes protected the target proteins from being degraded by the normal E3 ubiquitin ligases, resulting in the library plants having presumably higher levels of these target proteins compared to normal Arabidopsis plants. By tracking circadian rhythms in these plants, the team was able to identify the individual E3 ligases that control the circadian clock. The experiments revealed several E3 ligases that may regulate the circadian clock, including two enzymes called MAC3A and MAC3B. Further experiments demonstrated that MAC3A and MAC3B have similar roles in regulating the circadian clock and can compensate for the absence of the other. The library of Arabidopsis plants generated by Feke et al. is now available for other researchers to use in their studies. In the future this approach could be adapted to make similar libraries for crops and other plants that have even more E3 ligase enzymes than Arabidopsis.
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Affiliation(s)
- Ann Feke
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Wei Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Jing Hong
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Man-Wah Li
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Chin-Mei Lee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Elton K Zhou
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Joshua M Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
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24
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Translational switching of Cry1 protein expression confers reversible control of circadian behavior in arrhythmic Cry-deficient mice. Proc Natl Acad Sci U S A 2018; 115:E12388-E12397. [PMID: 30487216 PMCID: PMC6310849 DOI: 10.1073/pnas.1811438115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Circadian rhythms dominate our lives through our daily cycle of sleep and wakefulness. They are controlled by a brain master clock: the suprachiasmatic nucleus (SCN). SCN timekeeping pivots around a molecular loop incorporating Cryptochrome (Cry) proteins; global loss of these proteins disables the clock. We developed a biologically appropriate translational switch based on genetic code expansion to achieve reversible control of Cry1 expression. Cry1 translation in neurons of arrhythmic Cry-null SCN slices immediately, reversibly, and dose-dependently initiated circadian molecular rhythms. Cry1 translation in SCN neurons was sufficient to initiate circadian behavior rapidly and reversibly in arrhythmic Cry-null mice. This demonstrates control of mammalian behavior using translational switching, a method of broad applicability. The suprachiasmatic nucleus (SCN) is the principal circadian clock of mammals, coordinating daily rhythms of physiology and behavior. Circadian timing pivots around self-sustaining transcriptional–translational negative feedback loops (TTFLs), whereby CLOCK and BMAL1 drive the expression of the negative regulators Period and Cryptochrome (Cry). Global deletion of Cry1 and Cry2 disables the TTFL, resulting in arrhythmicity in downstream behaviors. We used this highly tractable biology to further develop genetic code expansion (GCE) as a translational switch to achieve reversible control of a biologically relevant protein, Cry1, in the SCN. This employed an orthogonal aminoacyl-tRNA synthetase/tRNACUA pair delivered to the SCN by adeno-associated virus (AAV) vectors, allowing incorporation of a noncanonical amino acid (ncAA) into AAV-encoded Cry1 protein carrying an ectopic amber stop codon. Thus, translational readthrough and Cry1 expression were conditional on the supply of ncAA via culture medium or drinking water and were restricted to neurons by synapsin-dependent expression of aminoacyl tRNA-synthetase. Activation of Cry1 translation by ncAA in neurons of arrhythmic Cry-null SCN slices immediately and dose-dependently initiated TTFL circadian rhythms, which dissipated rapidly after ncAA withdrawal. Moreover, genetic activation of the TTFL in SCN neurons rapidly and reversibly initiated circadian behavior in otherwise arrhythmic Cry-null mice, with rhythm amplitude being determined by the number of transduced SCN neurons. Thus, Cry1 does not specify the development of circadian circuitry and competence but is essential for its labile and rapidly reversible activation. This demonstrates reversible control of mammalian behavior using GCE-based translational switching, a method of potentially broad neurobiological interest.
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25
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Soengas P, Cartea ME, Velasco P, Francisco M. Endogenous Circadian Rhythms in Polyphenolic Composition Induce Changes in Antioxidant Properties in Brassica Cultivars. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5984-5991. [PMID: 29851489 DOI: 10.1021/acs.jafc.8b01732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
There is increasing evidence that the circadian clock is a significant driver of plant phytochemicals. However, little is known about the clock effect on antioxidant metabolites in edible crops. Thus, the aim of the present investigation was to study whether the antioxidant potential of Brassica cultivars is under circadian regulation and its relationship with polyphenol content. To accomplish that we entrain plants of four Brassica cultivars to light-dark cycles prior to release into continuous light. The antioxidant activity and phenolic content was monitored at four time points of the day during four consecutive days: 2 days under light-dark conditions followed by 2 days under continuous light. Results showed daily oscillation of antioxidant activity. In addition, those variations were related with endogenous circadian rhythms in polyphenolics and exhibit a species-specific pattern. Considered together, we determined that Brassica cultivars have an optimal time during a single day with increased levels of health phytochemicals.
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Affiliation(s)
- Pilar Soengas
- Group of Genetics, Breeding and Biochemistry of Brassicas , Misión Biológica de Galicia, Spanish Council for Scientific Research (CSIC) , Pontevedra , Spain
| | - M Elena Cartea
- Group of Genetics, Breeding and Biochemistry of Brassicas , Misión Biológica de Galicia, Spanish Council for Scientific Research (CSIC) , Pontevedra , Spain
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassicas , Misión Biológica de Galicia, Spanish Council for Scientific Research (CSIC) , Pontevedra , Spain
| | - Marta Francisco
- Group of Genetics, Breeding and Biochemistry of Brassicas , Misión Biológica de Galicia, Spanish Council for Scientific Research (CSIC) , Pontevedra , Spain
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26
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Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication. Proc Natl Acad Sci U S A 2018; 115:7135-7140. [PMID: 29789384 DOI: 10.1073/pnas.1801862115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Circadian period and phase of cultivated tomato (Solanum lycopersicum) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1, the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps. We reveal signatures of selection across the genomic region of LNK2 and different patterns of fixation of the mutant alleles. Strikingly, LNK2 and EID1 are both involved in light input to the circadian clock, indicating that domestication specifically targeted this input pathway. In line with this, we show that the clock deceleration in the cultivated tomato is light-dependent and requires the phytochrome B1 photoreceptor. Such conditional variation in circadian rhythms may be key for latitudinal adaptation in a variety of species, including crop plants and livestock.
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27
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Gould PD, Domijan M, Greenwood M, Tokuda IT, Rees H, Kozma-Bognar L, Hall AJ, Locke JC. Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression. eLife 2018; 7:31700. [PMID: 29697372 PMCID: PMC5988422 DOI: 10.7554/elife.31700] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
The Arabidopsis circadian clock orchestrates gene regulation across the day/night cycle. Although a multiple feedback loop circuit has been shown to generate the 24-hr rhythm, it remains unclear how robust the clock is in individual cells, or how clock timing is coordinated across the plant. Here we examine clock activity at the single cell level across Arabidopsis seedlings over several days under constant environmental conditions. Our data reveal robust single cell oscillations, albeit desynchronised. In particular, we observe two waves of clock activity; one going down, and one up the root. We also find evidence of cell-to-cell coupling of the clock, especially in the root tip. A simple model shows that cell-to-cell coupling and our measured period differences between cells can generate the observed waves. Our results reveal the spatial structure of the plant clock and suggest that unlike the centralised mammalian clock, the Arabidopsis clock has multiple coordination points.
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Affiliation(s)
- Peter D Gould
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Mirela Domijan
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom.,Department of Mathematical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Mark Greenwood
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom.,Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Isao T Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, Kusatsu, Japan
| | - Hannah Rees
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Laszlo Kozma-Bognar
- Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.,Department of Genetics, University of Szeged, Szeged, Hungary
| | - Anthony Jw Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - James Cw Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom.,Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Microsoft Research, Cambridge, United Kingdom
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28
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Poliner E, Takeuchi T, Du ZY, Benning C, Farré EM. Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, Nannochloropsis oceanica CCMP1779. ACS Synth Biol 2018; 99:112-127. [PMID: 29518315 PMCID: PMC6616531 DOI: 10.1111/tpj.14314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 04/25/2023]
Abstract
Utilization of microalgae has been hampered by limited tools for creating loss-of-function mutants. Furthermore, modified strains for deployment into the field must be free of antibiotic resistance genes and face fewer regulatory hurdles if they are transgene free. The oleaginous microalga, Nannochloropsis oceanica CCMP1779, is an emerging model for microalgal lipid metabolism. We present a one-vector episomal CRISPR/Cas9 system for N. oceanica that enables the generation of marker-free mutant lines. The CEN/ARS6 region from Saccharomyces cerevisiae was included in the vector to facilitate its maintenance as circular extrachromosal DNA. The vector utilizes a bidirectional promoter to produce both Cas9 and a ribozyme flanked sgRNA. This system efficiently generates targeted mutations, and allows the loss of episomal DNA after the removal of selection pressure, resulting in marker-free nontransgenic engineered lines. To test this system, we disrupted the nitrate reductase gene ( NR) and subsequently removed the CRISPR episome to generate nontransgenic marker-free nitrate reductase knockout lines (NR-KO).
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Affiliation(s)
- Eric Poliner
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
| | - Tomomi Takeuchi
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
| | - Zhi-Yan Du
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
| | - Christoph Benning
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
- Plant Biology Department, Michigan State University, East Lansing, Michigan
| | - Eva M. Farré
- Plant Biology Department, Michigan State University, East Lansing, Michigan
- Corresponding Author: Eva M. Farré (), Phone: +1-517-353-5215
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29
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Combined Pharmacological and Genetic Manipulations Unlock Unprecedented Temporal Elasticity and Reveal Phase-Specific Modulation of the Molecular Circadian Clock of the Mouse Suprachiasmatic Nucleus. J Neurosci 2017; 36:9326-41. [PMID: 27605609 DOI: 10.1523/jneurosci.0958-16.2016] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/15/2016] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED The suprachiasmatic nucleus (SCN) is the master circadian oscillator encoding time-of-day information. SCN timekeeping is sustained by a cell-autonomous transcriptional-translational feedback loop, whereby expression of the Period and Cryptochrome genes is negatively regulated by their protein products. This loop in turn drives circadian oscillations in gene expression that direct SCN electrical activity and thence behavior. The robustness of SCN timekeeping is further enhanced by interneuronal, circuit-level coupling. The aim of this study was to combine pharmacological and genetic manipulations to push the SCN clockwork toward its limits and, by doing so, probe cell-autonomous and emergent, circuit-level properties. Circadian oscillation of mouse SCN organotypic slice cultures was monitored as PER2::LUC bioluminescence. SCN of three genetic backgrounds-wild-type, short-period CK1ε(Tau/Tau) mutant, and long-period Fbxl3(Afh/Afh) mutant-all responded reversibly to pharmacological manipulation with period-altering compounds: picrotoxin, PF-670462 (4-[1-Cyclohexyl-4-(4-fluorophenyl)-1H-imidazol-5-yl]-2-pyrimidinamine dihydrochloride), and KNK437 (N-Formyl-3,4-methylenedioxy-benzylidine-gamma-butyrolactam). This revealed a remarkably wide operating range of sustained periods extending across 25 h, from ≤17 h to >42 h. Moreover, this range was maintained at network and single-cell levels. Development of a new technique for formal analysis of circadian waveform, first derivative analysis (FDA), revealed internal phase patterning to the circadian oscillation at these extreme periods and differential phase sensitivity of the SCN to genetic and pharmacological manipulations. For example, FDA of the CK1ε(Tau/Tau) mutant SCN treated with the CK1ε-specific inhibitor PF-4800567 (3-[(3-Chlorophenoxy)methyl]-1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine hydrochloride) revealed that period acceleration in the mutant is due to inappropriately phased activity of the CK1ε isoform. In conclusion, extreme period manipulation reveals unprecedented elasticity and temporal structure of the SCN circadian oscillation. SIGNIFICANCE STATEMENT The master circadian clock of the suprachiasmatic nucleus (SCN) encodes time-of-day information that allows mammals to predict and thereby adapt to daily environmental cycles. Using combined genetic and pharmacological interventions, we assessed the temporal elasticity of the SCN network. Despite having evolved to generate a 24 h circadian period, we show that the molecular clock is surprisingly elastic, able to reversibly sustain coherent periods between ≤17 and >42 h at the levels of individual cells and the overall circuit. Using quantitative techniques to analyze these extreme periodicities, we reveal that the oscillator progresses as a sequence of distinct stages. These findings reveal new properties of how the SCN functions as a network and should inform biological and mathematical analyses of circadian timekeeping.
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30
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Brancaccio M, Patton AP, Chesham JE, Maywood ES, Hastings MH. Astrocytes Control Circadian Timekeeping in the Suprachiasmatic Nucleus via Glutamatergic Signaling. Neuron 2017; 93:1420-1435.e5. [PMID: 28285822 PMCID: PMC5376383 DOI: 10.1016/j.neuron.2017.02.030] [Citation(s) in RCA: 291] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/25/2017] [Accepted: 02/16/2017] [Indexed: 12/02/2022]
Abstract
The suprachiasmatic nucleus (SCN) of the hypothalamus orchestrates daily rhythms of physiology and behavior in mammals. Its circadian (∼24 hr) oscillations of gene expression and electrical activity are generated intrinsically and can persist indefinitely in temporal isolation. This robust and resilient timekeeping is generally regarded as a product of the intrinsic connectivity of its neurons. Here we show that neurons constitute only one “half” of the SCN clock, the one metabolically active during circadian daytime. In contrast, SCN astrocytes are active during circadian nighttime, when they suppress the activity of SCN neurons by regulating extracellular glutamate levels. This glutamatergic gliotransmission is sensed by neurons of the dorsal SCN via specific pre-synaptic NMDA receptor assemblies containing NR2C subunits. Remarkably, somatic genetic re-programming of intracellular clocks in SCN astrocytes was capable of remodeling circadian behavioral rhythms in adult mice. Thus, SCN circuit-level timekeeping arises from interdependent and mutually supportive astrocytic-neuronal signaling. SCN neurons are active during circadian day, but SCN astrocytes are active at night Astrocytes direct circadian cycles of extracellular glutamate to inhibit SCN neurons Astrocyte-derived inhibition is mediated by NMDAR2C complexes on dorsal SCN neurons Genetic re-programming of the clock in SCN astrocytes reshapes circadian behavior
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Affiliation(s)
- Marco Brancaccio
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
| | - Andrew P Patton
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Johanna E Chesham
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Elizabeth S Maywood
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Michael H Hastings
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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31
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Abstract
This review summarizes various mathematical models of cell-autonomous mammalian circadian clock. We present the basics necessary for understanding of the cell-autonomous mammalian circadian oscillator, modern experimental data essential for its reconstruction and some special problems related to the validation of mathematical circadian oscillator models. This work compares existing mathematical models of circadian oscillator and the results of the computational studies of the oscillating systems. Finally, we discuss applications of the mathematical models of mammalian circadian oscillator for solving specific problems in circadian rhythm biology.
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32
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Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurley JM, Dunlap JC, Galagan JE, Freitag M, Sachs MS, Bell-Pedersen D. The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion. G3 (BETHESDA, MD.) 2017; 7:129-142. [PMID: 27856696 PMCID: PMC5217103 DOI: 10.1534/g3.116.034298] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Abstract
Light and the circadian clock have a profound effect on the biology of organisms through the regulation of large sets of genes. Toward understanding how light and the circadian clock regulate gene expression, we used genome-wide approaches to identify the direct and indirect targets of the light-responsive and clock-controlled transcription factor ADV-1 in Neurospora crassa A large proportion of ADV-1 targets were found to be light- and/or clock-controlled, and enriched for genes involved in development, metabolism, cell growth, and cell fusion. We show that ADV-1 is necessary for transducing light and/or temporal information to its immediate downstream targets, including controlling rhythms in genes critical to somatic cell fusion. However, while ADV-1 targets are altered in predictable ways in Δadv-1 cells in response to light, this is not always the case for rhythmic target gene expression. These data suggest that a complex regulatory network downstream of ADV-1 functions to generate distinct temporal dynamics of target gene expression relative to the central clock mechanism.
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Affiliation(s)
- Rigzin Dekhang
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Kristina M Smith
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Teresa M Lamb
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | | | - Erin L Bredeweg
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Oneida Ibarra
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Jillian M Emerson
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | | | | | - Elham Azizi
- Bioinformatics Program, Boston University, Massachusetts 02215
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jay C Dunlap
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - James E Galagan
- Bioinformatics Program, Boston University, Massachusetts 02215
- National Emerging Infectious Diseases Laboratories, Boston University, Massachusetts 02118
- Department of Microbiology, Boston University, Massachusetts 02215
- Department of Biomedical Engineering, Boston University, Massachusetts 02215
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843
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33
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Flis A, Fernández AP, Zielinski T, Mengin V, Sulpice R, Stratford K, Hume A, Pokhilko A, Southern MM, Seaton DD, McWatters HG, Stitt M, Halliday KJ, Millar AJ. Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure. Open Biol 2016; 5:rsob.150042. [PMID: 26468131 PMCID: PMC4632509 DOI: 10.1098/rsob.150042] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA quantification revealed low levels of PRR9 transcripts (peak approx. 50 copies cell−1) compared with other clock genes, and threefold higher levels of LHY RNA (more than 1500 copies cell−1) than of its close relative CCA1. The data are disseminated from BioDare, an online repository for focused timeseries data, which is expected to benefit mechanistic modelling. One data subset successfully constrained clock gene expression in a complex model, using publicly available software on parallel computers, without expert tuning or programming. We outline the empirical and mathematical justification for data aggregation in understanding highly interconnected, dynamic networks such as the clock, and the observed design constraints on the resources required to make this approach widely accessible.
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Affiliation(s)
- Anna Flis
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Aurora Piñas Fernández
- SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK
| | - Tomasz Zielinski
- SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK
| | - Virginie Mengin
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ronan Sulpice
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Kevin Stratford
- EPCC, University of Edinburgh, James Clerk Maxwell Building, Edinburgh EH9 3JZ, UK
| | - Alastair Hume
- SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK EPCC, University of Edinburgh, James Clerk Maxwell Building, Edinburgh EH9 3JZ, UK
| | - Alexandra Pokhilko
- SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Megan M Southern
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Daniel D Seaton
- SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK
| | - Harriet G McWatters
- SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Karen J Halliday
- SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK
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34
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Millar AJ. The Intracellular Dynamics of Circadian Clocks Reach for the Light of Ecology and Evolution. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:595-618. [PMID: 26653934 DOI: 10.1146/annurev-arplant-043014-115619] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A major challenge for biology is to extend our understanding of molecular regulation from the simplified conditions of the laboratory to ecologically relevant environments. Tractable examples are essential to make these connections for complex, pleiotropic regulators and, to go further, to link relevant genome sequences to field traits. Here, I review the case for the biological clock in higher plants. The gene network of the circadian clock drives pervasive, 24-hour rhythms in metabolism, behavior, and physiology across the eukaryotes and in some prokaryotes. In plants, the scope of chronobiology is now extending from the most tractable, intracellular readouts to the clock's many effects at the whole-organism level and across the life cycle, including biomass and flowering. I discuss five research areas where recent progress might be integrated in the future, to understand not only circadian functions in natural conditions but also the evolution of the clock's molecular mechanisms.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom;
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de Montaigu A, Berns MC, Coupland G. A Luciferase-Based Assay to Test Whether Gene Expression Responses to Environmental Inputs Are Temporally Restricted by the Circadian Clock. Methods Mol Biol 2016; 1398:93-106. [PMID: 26867618 DOI: 10.1007/978-1-4939-3356-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Gating is the mechanism by which the influence of an environmental signal on a particular output is temporally restricted by the circadian clock, so that the maximum response of the output to the signal occurs at a specific time. Gated regulation mechanisms have been described for several genes whose expression is strongly induced by light or temperature at certain times but repressed by the circadian clock at others. To reveal a gated pattern of expression in response to light, light pulses are applied in the dark at different times of the 24 h cycle and the transcriptional response of the gene of interest is then monitored with an appropriate technique. Luciferase (LUC) reporters have been the method of choice to study circadian rhythms in the past decades, but this methodology also provides an ideal platform for performing a gating assay. In this chapter, we describe a LUC imaging based protocol designed to test whether the influence of light on the expression of a gene of interest is gated by the circadian clock.
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Affiliation(s)
- Amaury de Montaigu
- Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D-50829, Cologne, Germany.
| | - Markus Christian Berns
- Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D-50829, Cologne, Germany
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D-50829, Cologne, Germany
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Greenham K, Lou P, Remsen SE, Farid H, McClung CR. TRiP: Tracking Rhythms in Plants, an automated leaf movement analysis program for circadian period estimation. PLANT METHODS 2015; 11:33. [PMID: 26019715 PMCID: PMC4445800 DOI: 10.1186/s13007-015-0075-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/12/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND A well characterized output of the circadian clock in plants is the daily rhythmic movement of leaves. This process has been used extensively in Arabidopsis to estimate circadian period in natural accessions as well as mutants with known defects in circadian clock function. Current methods for estimating circadian period by leaf movement involve manual steps throughout the analysis and are often limited to analyzing one leaf or cotyledon at a time. RESULTS In this study, we describe the development of TRiP (Tracking Rhythms in Plants), a new method for estimating circadian period using a motion estimation algorithm that can be applied to whole plant images. To validate this new method, we apply TRiP to a Recombinant Inbred Line (RIL) population in Arabidopsis using our high-throughput imaging platform. We begin imaging at the cotyledon stage and image through the emergence of true leaves. TRiP successfully tracks the movement of cotyledons and leaves without the need to select individual leaves to be analyzed. CONCLUSIONS TRiP is a program for analyzing leaf movement by motion estimation that enables high-throughput analysis of large populations of plants. TRiP is also able to analyze plant species with diverse leaf morphologies. We have used TRiP to estimate period for 150 Arabidopsis RILs as well as 5 diverse plant species, highlighting the broad applicability of this new method.
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Affiliation(s)
- Kathleen Greenham
- />Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, 03755 USA
| | - Ping Lou
- />Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, 03755 USA
| | - Sara E Remsen
- />Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, 03755 USA
| | - Hany Farid
- />Department of Computer Science, Dartmouth College, 6211 Sudikoff Lab, Hanover, 03755 USA
| | - C Robertson McClung
- />Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, 03755 USA
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Herzog ED, Kiss IZ, Mazuski C. Measuring synchrony in the mammalian central circadian circuit. Methods Enzymol 2014; 552:3-22. [PMID: 25707270 DOI: 10.1016/bs.mie.2014.10.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Circadian clocks control daily rhythms in physiology and behavior across all phyla. These rhythms are intrinsic to individual cells that must synchronize to their environment and to each other to anticipate daily events. Recent advances in recording from large numbers of cells for many circadian cycles have enabled researchers to begin to evaluate the mechanisms and consequences of intercellular circadian synchrony. Consequently, methods have been adapted to estimate the period, phase, and amplitude of individual circadian cells and calculate synchrony between cells. Stable synchronization requires that the cells share a common period. As a result, synchronized cells maintain constant phase relationships to each (e.g., with cell 1 peaking an hour before cell 2 each cycle). This chapter reviews how circadian rhythms are recorded from single mammalian cells and details methods for measuring their period and phase synchrony. These methods have been useful, for example, in showing that specific neuropeptides are essential to maintain synchrony among circadian cells.
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Affiliation(s)
- Erik D Herzog
- Department of Biology, Washington University, St. Louis, Missouri, USA.
| | - István Z Kiss
- Department of Chemistry, Saint Louis University, St. Louis, Missouri, USA
| | - Cristina Mazuski
- Department of Biology, Washington University, St. Louis, Missouri, USA
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Walter W, Striberny B, Gaquerel E, Baldwin IT, Kim SG, Heiland I. Improving the accuracy of expression data analysis in time course experiments using resampling. BMC Bioinformatics 2014; 15:352. [PMID: 25344112 PMCID: PMC4220062 DOI: 10.1186/s12859-014-0352-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 10/16/2014] [Indexed: 11/29/2022] Open
Abstract
Background As time series experiments in higher eukaryotes usually obtain data from different individuals collected at the different time points, a time series sample itself is not equivalent to a true biological replicate but is, rather, a combination of several biological replicates. The analysis of expression data derived from a time series sample is therefore often performed with a low number of replicates due to budget limitations or limitations in sample availability. In addition, most algorithms developed to identify specific patterns in time series dataset do not consider biological variation in samples collected at the same conditions. Results Using artificial time course datasets, we show that resampling considerably improves the accuracy of transcripts identified as rhythmic. In particular, the number of false positives can be greatly reduced while at the same time the number of true positives can be maintained in the range of other methods currently used to determine rhythmically expressed genes. Conclusions The resampling approach described here therefore increases the accuracy of time series expression data analysis and furthermore emphasizes the importance of biological replicates in identifying oscillating genes. Resampling can be used for any time series expression dataset as long as the samples are acquired from independent individuals at each time point. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0352-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wencke Walter
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany.
| | - Bernd Striberny
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Naturfagbygget, Dramsvegen 201, 9037, Tromsø, Norway.
| | - Emmanuel Gaquerel
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany. .,Center for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany.
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany.
| | - Sang-Gyu Kim
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany. .,Center for Genome Engineering, Institute for Basic Science, Gwanak-ro 1, Gwanak-gu, Seoul, 151-747, South Korea.
| | - Ines Heiland
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Naturfagbygget, Dramsvegen 201, 9037, Tromsø, Norway.
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Dixon LE, Hodge SK, van Ooijen G, Troein C, Akman OE, Millar AJ. Light and circadian regulation of clock components aids flexible responses to environmental signals. THE NEW PHYTOLOGIST 2014; 203:568-577. [PMID: 24842166 PMCID: PMC4286021 DOI: 10.1111/nph.12853] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 03/24/2014] [Indexed: 05/08/2023]
Abstract
The circadian clock measures time across a 24 h period, increasing fitness by phasing biological processes to the most appropriate time of day. The interlocking feedback loop mechanism of the clock is conserved across species; however, the number of loops varies. Mathematical and computational analyses have suggested that loop complexity affects the overall flexibility of the oscillator, including its responses to entrainment signals. We used a discriminating experimental assay, at the transition between different photoperiods, in order to test this proposal in a minimal circadian network (in Ostreococcus tauri) and a more complex network (in Arabidopsis thaliana). Transcriptional and translational reporters in O. tauri primarily tracked dawn or dusk, whereas in A. thaliana, a wider range of responses were observed, consistent with its more flexible clock. Model analysis supported the requirement for this diversity of responses among the components of the more complex network. However, these and earlier data showed that the O. tauri network retains surprising flexibility, despite its simple circuit. We found that models constructed from experimental data can show flexibility either from multiple loops and/or from multiple light inputs. Our results suggest that O. tauri has adopted the latter strategy, possibly as a consequence of genomic reduction.
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Affiliation(s)
- Laura E Dixon
- SynthSys, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JD, UK
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sarah K Hodge
- SynthSys, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JD, UK
| | - Gerben van Ooijen
- SynthSys, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JD, UK
| | - Carl Troein
- Department of Astronomy and Theoretical Physics, Lund University, 223 62, Lund, Sweden
| | - Ozgur E Akman
- SynthSys, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JD, UK
- Centre for Systems, Dynamics and Control, College of Engineering, Mathematics & Physical Sciences, University of Exeter, Exeter, EX4 4QF, UK
| | - Andrew J Millar
- SynthSys, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JD, UK
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Zielinski T, Moore AM, Troup E, Halliday KJ, Millar AJ. Strengths and limitations of period estimation methods for circadian data. PLoS One 2014; 9:e96462. [PMID: 24809473 PMCID: PMC4014635 DOI: 10.1371/journal.pone.0096462] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 04/08/2014] [Indexed: 11/18/2022] Open
Abstract
A key step in the analysis of circadian data is to make an accurate estimate of the underlying period. There are many different techniques and algorithms for determining period, all with different assumptions and with differing levels of complexity. Choosing which algorithm, which implementation and which measures of accuracy to use can offer many pitfalls, especially for the non-expert. We have developed the BioDare system, an online service allowing data-sharing (including public dissemination), data-processing and analysis. Circadian experiments are the main focus of BioDare hence performing period analysis is a major feature of the system. Six methods have been incorporated into BioDare: Enright and Lomb-Scargle periodograms, FFT-NLLS, mFourfit, MESA and Spectrum Resampling. Here we review those six techniques, explain the principles behind each algorithm and evaluate their performance. In order to quantify the methods' accuracy, we examine the algorithms against artificial mathematical test signals and model-generated mRNA data. Our re-implementation of each method in Java allows meaningful comparisons of the computational complexity and computing time associated with each algorithm. Finally, we provide guidelines on which algorithms are most appropriate for which data types, and recommendations on experimental design to extract optimal data for analysis.
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Affiliation(s)
| | - Anne M. Moore
- SynthSys, University of Edinburgh, Edinburgh, United Kingdom
| | - Eilidh Troup
- EPCC, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Andrew J. Millar
- SynthSys, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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