The circadian clock a system of coupled oscillators · 2019-09-05 · The circadian clock – a...
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The circadian clock –
a system of coupled oscillators
Hanspeter Herzel Institute for Theoretical Biology (ITB)
Charité and Humboldt University Berlin
together with
Patrick Pett, Grigory Bordyugov, Bharath Ananthasubramaniam,
Christoph Schmal (ITB), Achim Kramer group (Charite), Anja
Korencic (Ljubljana), Isao Tokuda (Kyoto), Adrian Granada (Harvard)
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The environmental external oscillator entrains our internal oscillator
(the circadian clock)
Zeitgeber
Light
Temperature
Food
…
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Light synchronizes
the clock
Regulation of
physiology and behavior
Clock genes
(e.g. Period2)
Positive
elements
activation
nucleus
SCN-neuron
Negative
elements
inhibition
Synchronization of
peripheral clocks
The system
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3rd ventricle
optic chiasm
Synchronization
clock-genes
(e.g. Period2)
positive
elements
activation
nucleus
SCN-neuron
negative
elements
inhibition
Oscillation
Molecular Chronobiology
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The circadian oscillator
Circadian rhythm
Oster et al., 2002
Feedback loops Oscillations
Reppert and Weaver, 2001
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Molecular Chronobiology
Vanselow et al., Genes & Dev, 2006
mass spec.
Entrainment
6 days 35/39° C
Constant
37° C
0 1 2 3
Rel. lu
min
esce
nce
PER2 wt
FASPS
Time (days)
live cell imaging
+CHX
PER2 wt
β-Actin
FASPS
β-Actin
0 0.5 1 2 3 4 6 8 h
bio- chemistry
Measurements
cell biology
wild-type
q1 = 0
q12 = 0.75
Time (days)
0 1 2 3 4 Norm
aliz
ed c
oncentr
atio
n
Model prediction Test of prediction Mathematical Model
Time (days)
1 2 3 4 5 6
Rel. lu
min
escence
solvent
CKI-7 (50 µM)
CKI-7 (200 µM)
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Coupled oscillators
1. Synergy of feedback loops
2. Oscillator networks
3. Entrainment phase (chronotypes)
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Clock genes and feedback loops
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E-boxes, ROR-elements and D-boxes drive clock genes
H Ukai, HR Ueda: Annu Rev Physiol 72: 579-603 (2010)
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Science 19, 349-354, 2012
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Construction of a core clock model using
• representative genes: activators (Bmal1, Dbp)+
early inhibitors (Per2, Rev-Erb)+late inhibitor (Cry1)
• experimentally verified binding sites
• known degradation rates
• reasonable delays
• fitted transcriptional parameters
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Anja Korencic et al., Scientific Reports 2014
Core-clock model from expression profiles and promoters
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Model design and global optimization
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5 DDE model can reproduce expression profiles
Pett et al., submitted
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Global optimization finds
multiple parameter sets
P. Pett et al.: Co-existing feedback loops generate
tissue-specific circadian rhythms, submitted
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P. Pett et al., submitted
Synergy of feedback loops allows tissue specificity
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Large tissue diversity of peripheral clocks
R. Zhang PNAS 2014
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Clock-controlled genes in peripheral organs
Korencic 2014
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Summary Part 1
How to design a minimal core clock model?
- Five genes represent most regulations
- DDEs require few parameters
- Transcriptional regulations remain heuristic
- Per/Cry loops, Rev-Erba loop and repressilator possible
- Peripheral tissues: comparable core clock but different
clock-controlled genes and tissue-specific timing
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Outline
1. Synergy of feedback loops
2. Oscillator networks
3. Entrainment phase (chronotypes)
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Paradigm 2004: single cells are self-sustained,
periods vary from 20 to 28 hours, weak coupling
Nonlinear dynamics: tori, chaos … expected
Observations: - 20000 neurons in the SCN are
robustly synchronized
- „splitting“ rare
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Gonze et al. Biophysical J. 2005
Bifurcation diagram of coupled Goodwin models
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Sloppy oscillators synchronize well
independent of specific coupling scheme
S. Bernard, D. Gonze, B. Cajavec, H. Herzel, and A.
Kramer: Synchronization-Induced Rhythmicity of Circadian
Oscillators in the Suprachiasmatic Nucleus, PLoS Comp.
Biol. (2007) 3:e68.
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Damped oscillators synchronize well
independent of specific coupling scheme
S. Bernard, D. Gonze, B. Cajavec, H. Herzel, and A. Kramer:
Synchronization-Induced Rhythmicity of Circadian
Oscillators in the Suprachiasmatic Nucleus, PLoS Comp.
Biol. (2007) 3:e68.
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Coupling can even synchronize Cry-DKO neonatal SCN
D. Ono, S. Honma, K. Honma
Nature Communications 2013
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B. Ananthasubramaniam, E. D. Herzog, H. Herzel. PLoS Comp. Biol. 2014
Coupling phase controls synchronization
Implications for dual role of GABA (J. Evans, Neuron 2013) and
synchrony of neonatal versus adult SCN slices (Honma, Nature
Communications 2013)
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SCN slice data from wildtype and knockouts
Network simulations with varying coupling phases
Isao Tokuda et al.
Biophys. J. 2015
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I.T.Tokuda et al. Biophys. J. 2015
Synchronization of noisy oscillators (WT and DKO)
CV about 1
CV above 1
Better sync for WT
Coupling strength
enhances sync
Coupling phase
matters strongly
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Part 2: Summary and outlook
• Many SCN neurons might be noisy weakly
damped oscillators
• Ensembles of damped oscillators are easily
synchronized and entrained
• Coupling phase as essential as coupling strength
Outlook: - Dominant coupling mechanisms?
- Quantification of coupling strength?
- Role of spatial heterogeneities?
- Control of entrainment phases („chronotypes“)
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Outline
1. Synergy of feedback loops
2. Oscillator networks
3. Entrainment phase (chronotypes)
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Hallmarks of entrainment
Period of the entrained oscillator becomes equal to the Zeitgeber period
The phase-angle between Zeitgeber cycle and entrained oscillator is constant
(i.e. the phase of entrainment <-> chronotype)
T
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human volunteers, 05-03-04 raw
10000
11000
12000
13000
14000
15000
16000
17000
18000
0 20 40 60 80 100 120 140
hours
coun
ts/5
min
CH
hours
cp
m
circadian promoter luciferase
biopsy
skin fibroblasts
lentiviral infection
23,5
24
24,5
25
25,5
0 20 40 60 80 100
HO score
Hu
man
perio
d l
en
gth
Direct measurement
of human circadian period!
SAD
Brown et al., PNAS 2008
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Brown et al., PNAS 2008
Fibroblast Period Length and Fibroblast Transcriptional Phase
Correlate Under Entrained Conditions
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Circadian period τ, phase of entrainment ψ in humans
small variations in τ (+- 0.2 hrs) and wide range of chronotypes (+- 1.5 hrs)
7-fold ratio of Δψ to Δτ
Phase of entrainment ψ
Duffy et al., and Czeisler, 2011
Period τ
Roenneberg (2004)
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Small entrainment range implies
large phase variability
A. Granada et al. 2013
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modified Goodwin model (3 ODEs)
Gonze et al. Biophys. J. 89 (2005)
two-loop model (19 ODEs) Relogio
et al. PLoS Comp. Biol. 7 (2011)
Test of theory using genetic network models
Katharina Imkeller, Master thesis 2013
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Entrainment phase as a function of mismatch
large phase variations smaller phase variability
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K. Hoffmann Z. vergl. Physiologie 62, 93-100 (1969)
Increasing entrainment range and phase variability
with Zeitgeber strength in lizards
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PRC/PTC as iterated map: stable entrainment phase varies by 12 hours
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Periodically driven damped oscillators exhibit
phase jump of 180° around resonance
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Uncoupled circadian systems have a smaller ratio of Δψ to Δτ
Aschoff and Pohl, 1978
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Circadian period τ, phase of entrainment ψ in humans
small variations in τ (+- 0.2 hrs) lead to wide range of chronotypes (+- 1.5 hrs)
since the SCN is a „strong oscillator“ due to coupling
Phase of entrainment ψ
Duffy et al., and Czeisler, 2011
Period τ
Roenneberg (2004)
Granada et al. PLoS One 2013
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Photoperiod (day length) effects entrainment range
Simulations of amplitude-phase oscillator (C. Schmal et al. 2015)
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Arnold onion quantifies seasonality
C. Schmal et al.: A theoretical study on seasonality (2015)
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Summary Part 3
• Coupling leads to „strong oscillators“ with small
PRC, narrow entrainment range and variable phases
• Models predict dependencies of entrainment phases
on period mismatch, Zeitgeber strength/amplitude
and photoperiods
• Theory explains wide range of chronotypes
(see also Wever 1964)
• Mammals: Robust oscillator implies flexible phase