Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale

Wang, Guang Zhong; Hickey, Stephanie L.; Shi, Lei; Huang, Hung Chung; Nakashe, Prachi; Koike, Nobuya; Tu, Benjamin P.; Takahashi, Joseph S.; Konopka, Genevieve

doi:10.1016/j.celrep.2015.10.043

Cited by 58 publications

(94 citation statements)

References 71 publications

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“…Interestingly, the aAMPs of all of these four genes were more reduced than the Mean, which typically resulted from the increased troughs and decreased peaks. This independence was also confirmed by that the number of rhythmic genes that increased ~40% with increasing amplitude, although the mean level of gene expression did not change (G. Z. Wang et al, ). Recently, amplitude was found to correlate with soil composition in populations of wild barley ( Hordeum vulgare ssp.…”

Section: Discussionmentioning

confidence: 82%

OsPRR37confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice

Liu

Zhou

et al. 2018

Plant Cell & Environment

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The circadian clock enables organisms to rapidly adapt to the ever-changing environmental conditions that are caused by daily light/dark cycles. Circadian clock genes universally affect key agricultural traits, particularly flowering time. Here, we show that OsPRR37, a circadian clock gene, delays rice flowering time in an expression level-dependent manner. Using high-throughput mRNA sequencing on an OsPRR37 overexpressing transgenic line (OsPRR37-OE5) and the recipient parent Guangluai4 that contains the loss-of-function Osprr37, we identify 14,992 genes that display diurnal rhythms, which account for 52.9% of the transcriptome. Overexpressing OsPRR37 weakens the transcriptomic rhythms and alters the phases of rhythmic genes. In total, 3,210 differentially expressed genes (DEGs) are identified, among which 1,863 rhythmic DEGs show a correlation between the change of absolute amplitudes and the mean expression levels. We further reveal that OsPRR37 functions as a transcriptional repressor to repress the expression levels and amplitudes of day-phased clock genes. More importantly, OsPRR37 confers expanded regulation on the evening-phased rhythmic DEGs by repressing the morning-phased rhythmic DEGs. Further study shows that OsPRR37 expands its regulation on flowering pathways by repressing Ehd1. Thus, our results demonstrate an expanded regulation mechanism of the circadian clock on the diurnal rhythms of the transcriptome.

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Section: Discussionmentioning

confidence: 82%

OsPRR37confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice

Liu

Zhou

et al. 2018

Plant Cell & Environment

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“…The circadian clock in the liver regulates RNAPII occupancy on a genome-wide basis and drives genome-wide circadian modulation of chromatin states. These circadian rhythms in chromatin state poise the genome for transcription on a daily basis to coincide with the daily metabolic demands of the organism and to optimize the energy utilization of gene expression 143 . In addition to the circadian modulation of chromatin states, the three-dimensional architecture of the nucleus and the interaction of active and repressive chromosomal domains undergo circadian oscillations (Box 3) 144–148 .…”

Section: Discussionmentioning

confidence: 99%

Transcriptional architecture of the mammalian circadian clock

2016

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Circadian clocks are endogenous oscillators that control 24-hour physiological and behavioral processes in organisms. These cell-autonomous clocks are composed of a transcription–translation-based autoregulatory feedback loop. With the development of next-generation sequencing approaches, biochemical and genomic insights into circadian function have recently come into focus. Genome-wide analyses of the clock transcriptional feedback loop have revealed a global circadian regulation of transcription factor occupancy, RNA polymerase II recruitment and initiation, nascent transcription and chromatin remodelling. The genomic targets of the circadian clock are pervasive and are intimately linked to the regulation of metabolism, cell growth and physiology.

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“…These programs of periodic genes include cyclin mRNAs, DNA replication factors, APC activators, and other cellular components that are utilized at specific times during the cell cycle. Our group and others have proposed that this “just-in-time transcription” mechanism is an important aspect of energy-efficient and faithful cell divisions [23,24]. In S .…”

Section: Introductionmentioning

confidence: 99%

Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans

et al. 2016

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The pathogenic yeast Cryptococcus neoformans causes fungal meningitis in immune-compromised patients. Cell proliferation in the budding yeast form is required for C. neoformans to infect human hosts, and virulence factors such as capsule formation and melanin production are affected by cell-cycle perturbation. Thus, understanding cell-cycle regulation is critical for a full understanding of virulence factors for disease. Our group and others have demonstrated that a large fraction of genes in Saccharomyces cerevisiae is expressed periodically during the cell cycle, and that proper regulation of this transcriptional program is important for proper cell division. Despite the evolutionary divergence of the two budding yeasts, we found that a similar percentage of all genes (~20%) is periodically expressed during the cell cycle in both yeasts. However, the temporal ordering of periodic expression has diverged for some orthologous cell-cycle genes, especially those related to bud emergence and bud growth. Genes regulating DNA replication and mitosis exhibited a conserved ordering in both yeasts, suggesting that essential cell-cycle processes are conserved in periodicity and in timing of expression (i.e. duplication before division). In S. cerevisiae cells, we have proposed that an interconnected network of periodic transcription factors (TFs) controls the bulk of the cell-cycle transcriptional program. We found that temporal ordering of orthologous network TFs was not always maintained; however, the TF network topology at cell-cycle commitment appears to be conserved in C. neoformans. During the C. neoformans cell cycle, DNA replication genes, mitosis genes, and 40 genes involved in virulence are periodically expressed. Future work toward understanding the gene regulatory network that controls cell-cycle genes is critical for developing novel antifungals to inhibit pathogen proliferation.

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Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale

Cited by 58 publications

References 71 publications

OsPRR37confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice

OsPRR37confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice

Transcriptional architecture of the mammalian circadian clock

Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans

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