Neurospora. EMBO J 28:1029–1042. https://doi.
org/10.1038/emboj.2009.54
Chen C-H, DeMay BS, Gladfelter AS et al (2010) Physical interaction between VIVID and white collar
complex regulates photoadaptation in Neurospora.
Proc Natl Acad Sci 107:16715–16720
Cheng P, Yang Y, Heintzen C, Liu Y (2001a) Coiled-coil
domain-mediated FRQ-FRQ interaction is essential for its circadian clock function in Neurospora.
EMBO J 20:101–108. https://doi.org/10.1093/
emboj/20.1.101
Cheng P, Yang Y, Liu Y (2001b) Interlocked feedback
loops contribute to the robustness of the Neurospora
circadian clock. Proc Natl Acad Sci U S A 98:7408–
7413. https://doi.org/10.1073/pnas.121170298
Cheng P, Yang Y, Gardner KH, Liu Y (2002) PAS
domain-mediated WC-1/WC-2 interaction is
essential for maintaining the steady-state level of
WC-1 and the function of both proteins in circadian clock and light responses of Neurospora. Mol
Cell Biol 22:517–524. https://doi.org/10.1128/
MCB.22.2.517-524.2002
Cheng P, Yang Y, Wang L et al (2003) WHITE
COLLAR-1, a multifunctional Neurospora protein
involved in the circadian feedback loops, light
sensing, and transcription repression of wc-2. J
Biol Chem 278:3801–3808. https://doi.org/
10.1074/jbc.M209592200
Cheng P, He Q, He Q et al (2005) Regulation of the
Neurospora circadian clock by an RNA helicase.
Genes Dev 19:234–241. https://doi.org/10.1101/
gad.1266805.234
Chiu JC, Ko HW, Edery I (2011) NEMO/NLK phosphorylates PERIOD to initiate a time-delay phosphorylation circuit that sets circadian clock speed. Cell
145:357–370.
https://doi.org/10.1016/j.
cell.2011.04.002
Collett MA, Garceau N, Dunlap JC, Loros JJ (2002) Light
and clock expression of the Neurospora clock gene
frequency is differentially driven by but dependent
on WHITE COLLAR-2. Genetics 160:149–158
Colot HV, Loros JJ, Dunlap JC (2005) Temperaturemodulated alternative splicing and promoter use
in the circadian clock gene frequency. Mol Biol
Cell 16:5563–5571. https://doi.org/10.1091/mbc.
E05-08-0756
Conrad KS, Hurley JM, Widom J et al (2016) Structure
of the frequency – interacting RNA helicase : a
protein interaction hub for the circadian clock.
EMBO
J
35:4–7.
https://doi.org/10.15252/
embj.201694327
Crosthwaite SK, Dunlap JC, Loros JJ (1997) Neurospora
wc-1 and wc-2: transcription, Photoresponses, and
the origins of circadian rhythmicity. Science 276
(80):763–769
Cupertino FB, Virgilio S, Freitas FZ et al (2015) Regulation of glycogen metabolism by the CRE-1, RCO-1
and RCM-1 proteins in Neurospora crassa. The
role of CRE-1 as the central transcriptional regulator. Fungal Genet Biol 77:82–94. https://doi.org/
10.1016/j.fgb.2015.03.011
Dasgupta A, Chen C-H, Lee C et al (2015) Biological
significance of photoreceptor photocycle length:
VIVID photocycle governs the dynamic VIVIDwhite collar complex pool mediating photoadaptation and response to changes in light intensity. PLoS Genet 11:e1005215
De los Santos H, Collins EJ, Hurley JM, Bennett KP
(2017) Circadian rhythms in Neurospora exhibit
biologically relevant driven and damped harmonic
oscillations. In: Proceedings of the 8th ACM international conference on bioinformatics, computational biology, and health informatics. ACM, New
York, NY, pp 455–463
DeCoursey PJ (2014) Survival value of suprachiasmatic
nuclei (SCN) in four wild sciurid rodents. Behav
Neurosci 128:240–249
DeCoursey PJ, Krulas JR, Mele G, Holley DC (1997)
Circadian performance of suprachiasmatic nuclei
(SCN)-lesioned antelope ground squirrels in a desert enclosure. Physiol Behav 62:1099–1108. https://
doi.org/10.1016/S0031-9384(97)00263-1
DeCoursey PJ, Walker JK, Smith SA (2000) A circadian
pacemaker in free-living chipmunks: essential for
survival? J Comp Physiol A 186:169–180. https://
doi.org/10.1007/s003590050017
Denault DL, Loros JJ, Dunlap JC (2001) WC-2 mediates
WC-1–FRQ interaction within the PAS proteinlinked circadian feedback loop of Neurospora.
EMBO J 20:109
Diernfellner ACR, Schafmeier T, Merrow MW, Brunner
M (2005) Molecular mechanism of temperature
sensing by the circadian clock of Neurospora
crassa. Genes Dev 19:1968–1973. https://doi.org/
10.1101/gad.345905
Diernfellner A, Colot HV, Dintsis O et al (2007) Long
and short isoforms of Neurospora clock protein
FRQ support temperature-compensated circadian
rhythms. FEBS Lett 581:5759–5764. https://doi.
org/10.1016/j.febslet.2007.11.043
Dovzhenok AA, Baek M, Lim S, Hong CI (2015) Mathematical modeling and validation of glucose compensation of the Neurospora circadian clock.
Biophys J 108:1830–1839. https://doi.org/10.1016/
j.bpj.2015.01.043
Dunlap JC (1999) Molecular bases for circadian clocks.
Cell 96:271–290. https://doi.org/10.1016/S00928674(00)80566-8
Dunlap JC (2008) Salad days in the rhythms trade.
Genetics 178:1–13
Dunlap JC, Loros JJ (2016) Yes, circadian rhythms
actually do affect almost everything. Cell Res
26:759–760. https://doi.org/10.1038/cr.2016.65
Dunlap JC, Loros JJ (2017) Making time: conservation
of biological clocks from fungi to animals. Microbiol Spectr 5(3). https://doi.org/10.1128/microbiolspec.FUNK-0039-2016
Dunlap JC, Loros JJ (2018) Just-so stories and origin
myths: phosphorylation and structural disorder in
circadian clock proteins. Mol Cell 69:165–168.
https://doi.org/10.1016/j.molcel.2017.11.028
4 From Genetics to Molecular Oscillations: The Circadian Clock in Neurospora crassa
97
org/10.1038/emboj.2009.54
Chen C-H, DeMay BS, Gladfelter AS et al (2010) Physical interaction between VIVID and white collar
complex regulates photoadaptation in Neurospora.
Proc Natl Acad Sci 107:16715–16720
Cheng P, Yang Y, Heintzen C, Liu Y (2001a) Coiled-coil
domain-mediated FRQ-FRQ interaction is essential for its circadian clock function in Neurospora.
EMBO J 20:101–108. https://doi.org/10.1093/
emboj/20.1.101
Cheng P, Yang Y, Liu Y (2001b) Interlocked feedback
loops contribute to the robustness of the Neurospora
circadian clock. Proc Natl Acad Sci U S A 98:7408–
7413. https://doi.org/10.1073/pnas.121170298
Cheng P, Yang Y, Gardner KH, Liu Y (2002) PAS
domain-mediated WC-1/WC-2 interaction is
essential for maintaining the steady-state level of
WC-1 and the function of both proteins in circadian clock and light responses of Neurospora. Mol
Cell Biol 22:517–524. https://doi.org/10.1128/
MCB.22.2.517-524.2002
Cheng P, Yang Y, Wang L et al (2003) WHITE
COLLAR-1, a multifunctional Neurospora protein
involved in the circadian feedback loops, light
sensing, and transcription repression of wc-2. J
Biol Chem 278:3801–3808. https://doi.org/
10.1074/jbc.M209592200
Cheng P, He Q, He Q et al (2005) Regulation of the
Neurospora circadian clock by an RNA helicase.
Genes Dev 19:234–241. https://doi.org/10.1101/
gad.1266805.234
Chiu JC, Ko HW, Edery I (2011) NEMO/NLK phosphorylates PERIOD to initiate a time-delay phosphorylation circuit that sets circadian clock speed. Cell
145:357–370.
https://doi.org/10.1016/j.
cell.2011.04.002
Collett MA, Garceau N, Dunlap JC, Loros JJ (2002) Light
and clock expression of the Neurospora clock gene
frequency is differentially driven by but dependent
on WHITE COLLAR-2. Genetics 160:149–158
Colot HV, Loros JJ, Dunlap JC (2005) Temperaturemodulated alternative splicing and promoter use
in the circadian clock gene frequency. Mol Biol
Cell 16:5563–5571. https://doi.org/10.1091/mbc.
E05-08-0756
Conrad KS, Hurley JM, Widom J et al (2016) Structure
of the frequency – interacting RNA helicase : a
protein interaction hub for the circadian clock.
EMBO
J
35:4–7.
https://doi.org/10.15252/
embj.201694327
Crosthwaite SK, Dunlap JC, Loros JJ (1997) Neurospora
wc-1 and wc-2: transcription, Photoresponses, and
the origins of circadian rhythmicity. Science 276
(80):763–769
Cupertino FB, Virgilio S, Freitas FZ et al (2015) Regulation of glycogen metabolism by the CRE-1, RCO-1
and RCM-1 proteins in Neurospora crassa. The
role of CRE-1 as the central transcriptional regulator. Fungal Genet Biol 77:82–94. https://doi.org/
10.1016/j.fgb.2015.03.011
Dasgupta A, Chen C-H, Lee C et al (2015) Biological
significance of photoreceptor photocycle length:
VIVID photocycle governs the dynamic VIVIDwhite collar complex pool mediating photoadaptation and response to changes in light intensity. PLoS Genet 11:e1005215
De los Santos H, Collins EJ, Hurley JM, Bennett KP
(2017) Circadian rhythms in Neurospora exhibit
biologically relevant driven and damped harmonic
oscillations. In: Proceedings of the 8th ACM international conference on bioinformatics, computational biology, and health informatics. ACM, New
York, NY, pp 455–463
DeCoursey PJ (2014) Survival value of suprachiasmatic
nuclei (SCN) in four wild sciurid rodents. Behav
Neurosci 128:240–249
DeCoursey PJ, Krulas JR, Mele G, Holley DC (1997)
Circadian performance of suprachiasmatic nuclei
(SCN)-lesioned antelope ground squirrels in a desert enclosure. Physiol Behav 62:1099–1108. https://
doi.org/10.1016/S0031-9384(97)00263-1
DeCoursey PJ, Walker JK, Smith SA (2000) A circadian
pacemaker in free-living chipmunks: essential for
survival? J Comp Physiol A 186:169–180. https://
doi.org/10.1007/s003590050017
Denault DL, Loros JJ, Dunlap JC (2001) WC-2 mediates
WC-1–FRQ interaction within the PAS proteinlinked circadian feedback loop of Neurospora.
EMBO J 20:109
Diernfellner ACR, Schafmeier T, Merrow MW, Brunner
M (2005) Molecular mechanism of temperature
sensing by the circadian clock of Neurospora
crassa. Genes Dev 19:1968–1973. https://doi.org/
10.1101/gad.345905
Diernfellner A, Colot HV, Dintsis O et al (2007) Long
and short isoforms of Neurospora clock protein
FRQ support temperature-compensated circadian
rhythms. FEBS Lett 581:5759–5764. https://doi.
org/10.1016/j.febslet.2007.11.043
Dovzhenok AA, Baek M, Lim S, Hong CI (2015) Mathematical modeling and validation of glucose compensation of the Neurospora circadian clock.
Biophys J 108:1830–1839. https://doi.org/10.1016/
j.bpj.2015.01.043
Dunlap JC (1999) Molecular bases for circadian clocks.
Cell 96:271–290. https://doi.org/10.1016/S00928674(00)80566-8
Dunlap JC (2008) Salad days in the rhythms trade.
Genetics 178:1–13
Dunlap JC, Loros JJ (2016) Yes, circadian rhythms
actually do affect almost everything. Cell Res
26:759–760. https://doi.org/10.1038/cr.2016.65
Dunlap JC, Loros JJ (2017) Making time: conservation
of biological clocks from fungi to animals. Microbiol Spectr 5(3). https://doi.org/10.1128/microbiolspec.FUNK-0039-2016
Dunlap JC, Loros JJ (2018) Just-so stories and origin
myths: phosphorylation and structural disorder in
circadian clock proteins. Mol Cell 69:165–168.
https://doi.org/10.1016/j.molcel.2017.11.028
4 From Genetics to Molecular Oscillations: The Circadian Clock in Neurospora crassa
97