Bright to Dim Oscillatory Response of the <i>Neurospora</i> Circadian Oscillator

Gooch, Van D.; Johnson, Alicia E.; Larrondo, Luis F.; Loros, Jennifer J.; Dunlap, Jay C.

doi:10.1177/0748730413517983

Cited by 4 publications

(2 citation statements)

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“…The morning-specific core circadian transcription factor WCC is rhythmically inactivated by clock-dependent phosphorylation [ 39 , 40 ]. When the function of WCC is compromised light- or clock-dependent transcription is essentially abolished [ 22 , 41 , 42 ]. To identify genes that are potentially regulated by WCC we analyzed the transcriptomes of light-grown cultures of wt and ∆ wc2 strains by RNA-seq.…”

Section: Resultsmentioning

confidence: 99%

Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora

Sancar

et al. 2015

BMC Biol

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BackgroundCircadian clocks control rhythmic expression of a large number of genes in coordination with the 24 hour day-night cycle. The mechanisms generating circadian rhythms, their amplitude and circadian phase are dependent on a transcriptional network of immense complexity. Moreover, the contribution of post-transcriptional mechanisms in generating rhythms in RNA abundance is not known.ResultsHere, we analyzed the clock-controlled transcriptome of Neurospora crassa together with temporal profiles of elongating RNA polymerase II. Our data indicate that transcription contributes to the rhythmic expression of the vast majority of clock-controlled genes (ccgs) in Neurospora. The ccgs accumulate in two main clusters with peak transcription and expression levels either at dawn or dusk. Dawn-phased genes are predominantly involved in catabolic and dusk-phased genes in anabolic processes, indicating a clock-controlled temporal separation of the physiology of Neurospora. Genes whose expression is strongly dependent on the core circadian activator WCC fall mainly into the dawn-phased cluster while rhythmic genes regulated by the glucose-dependent repressor CSP1 fall predominantly into the dusk-phased cluster. Surprisingly, the number of rhythmic transcripts increases about twofold in the absence of CSP1, indicating that rhythmic expression of many genes is attenuated by the activity of CSP1.ConclusionsThe data indicate that the vast majority of transcript rhythms in Neurospora are generated by dawn and dusk specific transcription. Our observations suggest a substantial plasticity of the circadian transcriptome with respect to the number of rhythmic genes as well as amplitude and phase of the expression rhythms and emphasize a major role of the circadian clock in the temporal organization of metabolism and physiology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-015-0126-4) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora

Sancar

et al. 2015

BMC Biol

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“…This phenomenon could be explained in two ways: RCO-1 participates in the control of circadian output pathways or it impairs core-clock function (and therefore output as well). To evaluate the latter proposal, the expression of a transcriptional reporter of the core clock (frq c-box -luc) (Gooch et al 2014b;Larrondo et al 2015; was analyzed along with overall levels of frq expression. Consistent with an earlier report (Zhou et al 2013) we found WC-1-independent and elevated expression of frq/FRQ in strains lacking RCO-1; however, in independent analyses conducted in two separate laboratories we were unable to reproduce the arrhythmicity previously reported for Drco-1 mutants (Zhou et al 2013; Liu et al 2015), using either stock strains from the Neurospora knockout project or the strain developed and utilized in the prior report (Zhou et al 2013).…”

Section: Discussionmentioning

confidence: 99%

Modulation of Circadian Gene Expression and Metabolic Compensation by the RCO-1 Corepressor of Neurospora crassa

et al. 2016

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Neurospora crassa is a model organism for the study of circadian clocks, molecular machineries that confer ∼24-hr rhythms to different processes at the cellular and organismal levels. The FREQUENCY (FRQ) protein is a central component of the Neurospora core clock, a transcription/translation negative feedback loop that controls genome-wide rhythmic gene expression. A genetic screen aimed at determining new components involved in the latter process identified regulation of conidiation 1 (rco-1), the ortholog of the Saccharomyces cerevisiae Tup1 corepressor, as affecting period length. By employing bioluminescent transcriptional and translational fusion reporters, we evaluated frq and FRQ expression levels in the rco-1 mutant background observing that, in contrast to prior reports, frq and FRQ expression are robustly rhythmic in the absence of RCO-1, although both amplitude and period length of the core clock are affected. Moreover, we detected a defect in metabolic compensation, such that high-glucose concentrations in the medium result in a significant decrease in period when RCO-1 is absent. Proteins physically interacting with RCO-1 were identified through co-immunoprecipitation and mass spectrometry; these include several components involved in chromatin remodeling and transcription, some of which, when absent, lead to a slight change in period. In the aggregate, these results indicate a dual role for RCO-1: although it is not essential for core-clock function, it regulates proper period and amplitude of core-clock dynamics and is also required for the rhythmic regulation of several clock-controlled genes.

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