Such second tier circadian transcription factors may generate different phases of circadian gene expression. We, in collaboration with colleagues, recently presented evidence that the WCC controls expression of about 24 transcription factors, which have the potential to transduce circadian information to downstream genes. Most ccgs identified previously had maximum expression levels around dawn, that is, at a time when the WCC is highly active and also at dusk. WCC is activated by light and required for the synchronization of the circadian clock with exogenous light–dark cycles. WC1 is the main blue-light photo-receptor of Neurospora. It is composed of two GATA type transcription factors, white collar-1 (WC1) and white collar-2 (WC2). The white collar complex (WCC) is the core transcription activator of the circadian oscillator of Neurospora crassa. Moreover, recent genome-wide studies in animals suggest that post-transcriptional processes contribute substantially to the generation of rhythmic transcript levels in addition to rhythmic transcription. Circadian chromatin modifications and transcribing RNA polymerase II (RNAPII) profiles indicate a crucial role of circadian transcription in the orchestration of rhythmic gene expression. Gene expression analyses in a variety of organisms suggested that 2% to 15% of their transcriptomes are expressed in a circadian fashion with different phases throughout the day. It is therefore important to identify in a comprehensive manner the genes that are controlled by the circadian clock and understand the molecular mechanisms underlying rhythmic gene expression. The mechanisms generating circadian expression rhythms and circadian phase are complex. In plants, misalignment of the circadian clock with the external light–dark cycle results in lower chlorophyll production and slower growth. Disruption of the circadian oscillator in mammals is associated with metabolic pathologies, premature aging and cancer. In mammals, the circadian clock coordinates metabolic pathways, such as glycolysis, gluconeogenesis, fatty acid oxidation and xenobiotic detoxification. These circadian oscillators drive rhythmic expression of clock-controlled genes (ccgs) in various organisms. In eukaryotes, the robustness of circadian oscillations is dependent on cell-autonomous interconnected transcriptional-translational feedback loops. Ĭircadian clocks are molecular oscillators that coordinate metabolism, physiology and behavior of organisms with daily environmental changes. 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. The data indicate that the vast majority of transcript rhythms in Neurospora are generated by dawn and dusk specific transcription. 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. 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. 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. The ccgs accumulate in two main clusters with peak transcription and expression levels either at dawn or dusk. Our data indicate that transcription contributes to the rhythmic expression of the vast majority of clock-controlled genes (ccgs) in Neurospora. Here, we analyzed the clock-controlled transcriptome of Neurospora crassa together with temporal profiles of elongating RNA polymerase II. Moreover, the contribution of post-transcriptional mechanisms in generating rhythms in RNA abundance is not known. The mechanisms generating circadian rhythms, their amplitude and circadian phase are dependent on a transcriptional network of immense complexity. Circadian clocks control rhythmic expression of a large number of genes in coordination with the 24 hour day-night cycle.
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