Positive Autoregulation Delays the Expression Phase of Mammalian Clock Gene Per2

In mammals, cellular circadian rhythms are generated by a transcriptional-translational autoregulatory network that consists of clock genes that encode transcriptional regulators. Of these clock genes, Period1 (Per1) and Period2 (Per2) are essential for sustainable circadian rhythmicity and photic entrainment. Intriguingly, Per1 and Per2 mRNAs exhibit circadian oscillations with a 4-hour phase difference, but they are similarly transactivated by CLOCK-BMAL1. In this study, we investigated the mechanism underlying the phase difference between Per1 and Per2 through a combination of mathematical simulations and molecular experiments. Mathematical analyses of a model for the mammalian circadian oscillator demonstrated that the slow synthesis and fast degradation of mRNA tend to advance the oscillation phase of mRNA expression. However, the phase difference between Per1 and Per2 was not reproduced by the model, which implemented a 1.1-fold difference in degradation rates and a 3-fold difference in CLOCK-BMAL1 mediated inductions of Per1 and Per2 as estimated in cultured mammalian cells. Thus, we hypothesized the existence of a novel transcriptional activation of Per2 by PER1/2 such that the Per2 oscillation phase was delayed. Indeed, only the Per2 promoter, but not Per1, was strongly induced by both PER1 and PER2 in the presence of CLOCK-BMAL1 in a luciferase reporter assay. Moreover, a 3-hour advance was observed in the transcriptional oscillation of the delta-Per2 reporter gene lacking cis-elements required for the induction by PER1/2. These results indicate that the Per2 positive feedback regulation is a significant factor responsible for generating the phase difference between Per1 and Per2 gene expression

Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale

SummaryGenes expressing circadian RNA rhythms are enriched for metabolic pathways, but the adaptive significance of cyclic gene expression remains unclear. We estimated the genome-wide synthetic and degradative cost of transcription and translation in three organisms and found that the cost of cycling genes is strikingly higher compared to non-cycling genes. Cycling genes are expressed at high levels and constitute the most costly proteins to synthesize in the genome. We demonstrate that metabolic cycling is accelerated in yeast grown under higher nutrient flux and the number of cycling genes increases ∼40%, which are achieved by increasing the amplitude and not the mean level of gene expression. These results suggest that rhythmic gene expression optimizes the metabolic cost of global gene expression and that highly expressed genes have been selected to be downregulated in a cyclic manner for energy conservation

Guidelines for Genome-Scale Analysis of Biological Rhythms

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them

Guidelines for Genome-Scale Analysis of Biological Rhythms

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding ‘big data’ that is conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them

Early stage growth process of dinaphtho[2, 3-b:2\u27, 3\u27-f]thieno[3, 2-b]thiophene (DNTT) thin film

Early stage growth process of Dinaphtho[2, 3-b:2\u27, 3\u27-f]thieno[3, 2-b]thiophenes (DNTTs) thin film was investigated using grazing incidence X-ray diffraction (GIXD) and surface morphology analysis using atomic force microscopy (AFM). The thin film growth conditions were controlled by the slow deposition method. The vertical orientation of DNTT was confirmed from the first layer growth by GIXD. The morphologies of first layer grains were universal in the growth rate range of 0.155 ML/min - 0.017 ML/min. In addition, the dependence of the nuclei density on the deposition flow rate indicates that the number of molecules required for nucleation is 2 molecules (dimers). This result indicates that fewer molecules are sufficient for nucleation in the case of DNTT compared to the pentacene thin film growth on SiO2

Mechanical Stability Evaluation of Water-sealed Type Underground Rock Cavern Using Tilt Response to Gas Pressure Change in Cavern

In addition to hydrological characterization of water-sealed type underground rock caverns, their mechanical stability is constantly monitored by measuring several properties, such as earthquake-induced vibration, strain, and tilt. Among them, tilt measurement is the most accurate monitoring method for rock deformation because of the tiltmeter's high resolution of 10-9 rad, which enables the detection of minute deformations caused by earth tide, rock responses to earthquake, change in atmospheric pressure, and artificial disturbance by operation. This study aimed to correctly extract these responses from long-term tilt data measured by a high precision tiltmeter at the Kushikino station and clarify the mechanism of tilt change as a result of deformation of rock mass. Tilt changes due to a small change in the gas phase pressure at the top of the rock cavern, approximately 10 kPa pressure fluctuation, were analyzed and discussed. The gradient response due to the gas pressure change was extracted from the measurement data by BAYTAP-G, and its magnitude was identified as 2 to 8 nrad, which was almost the same tilt response magnitude observed at an issuance of stored crude oil. This tilt response to the increase in tank gas pressure was numerically confirmed to originate from minute elastic deformation of rock masses, by using finite element method. Because fluctuation of the gas phase pressure can be continuously monitored, the effectiveness of tilt measurement was proved as a minute strain sensor for deformation of the water-sealed type underground rock cavern

Non-coding cis-element of Period2 is essential for maintaining organismal circadian behaviour and body temperature rhythmicity

体内リズムの発現に必要なDNAのスイッチを発見 --蛋白質をコードしないノンコーディング領域のDNA配列が活躍--. 京都大学プレスリリース. 2019-06-12.Non-coding cis-regulatory elements are essential determinants of development, but their exact impacts on behavior and physiology in adults remain elusive. Cis-element-based transcriptional regulation is believed to be crucial for generating circadian rhythms in behavior and physiology. However, genetic evidence supporting this model is based on mutations in the protein-coding sequences of clock genes. Here, we report generation of mutant mice carrying a mutation only at the E′-box cis-element in the promoter region of the core clock gene Per2. The Per2 E′-box mutation abolishes sustainable molecular clock oscillations and renders circadian locomotor activity and body temperature rhythms unstable. Without the E′-box, Per2 messenger RNA and protein expression remain at mid-to-high levels. Our work delineates the Per2 E′-box as a critical nodal element for keeping sustainable cell-autonomous circadian oscillation and reveals the extent of the impact of the non-coding cis-element in daily maintenance of animal locomotor activity and body temperature rhythmicity

Involvement of posttranscriptional regulation of Clock in the emergence of circadian clock oscillation during mouse development

Significance Circadian clocks reside in each cell level throughout the body in mammals. Intrinsic cellular circadian clocks develop cell autonomously during the cellular differentiation process. However, mechanisms controlling the emergence of cellular circadian clock oscillation in vivo are not fully understood. Here, we show that Dicer/Dgcr8-mediated posttranscriptional mechanisms control the CLOCK protein expression in both mouse fetal hearts and in vitro differentiating ES cells, which contributes to the emergence of circadian clock in mammalian cells. This event occurs after cell lineage determination into hearts or loss of pluripotent stem cell markers in differentiating ES cells, suggesting the cellular differentiation-coupled clock development may be conducted by a two-step program consisting of cellular differentiation and subsequent establishment of circadian transcriptional/translational feedback loops.</jats:p

Prediction of the Clinical Outcomes of Sigmoid Volvulus by Abdominal X-Ray: AXIS Classification System

Aim. Early diagnosis and evaluation of the severity of sigmoid volvulus are necessary for management and early intervention. We developed a new predictive classification system for sigmoid volvulus based on X-ray findings. Methods. We retrospectively analyzed 66 patients diagnosed with sigmoid volvulus using the electronic medical records at the Osaki Citizen’s Hospital and the University of Tokyo Hospital from 2008–2015. We classified patients according to the coffee-bean sign mesenteric axis on X-ray (AXIS classification: group A, 0–90°; group B, 90–135°; and group C, >135°). We examined the association between AXIS classification and severe sigmoid volvulus, intestinal necrosis, need for surgery, 30-day mortality, and length of stay using the Cochran–Armitage trend test. Results. In total, 66 patients were analyzed. They had a mean age of 76.9 years, and 47 (71.0%) were male. They were classified into three groups according to the AXIS classification system (group A, 40 patients; group B, 23 patients; and group C, 3 patients). Group C had a significantly higher frequency of severe sigmoid volvulus (100%) compared to group B (30%) and group A (15%). AXIS classification was significantly associated with the severity of sigmoid volvulus (p=0.003), necrosis (p=0.004), and need for surgery (p=0.001), but not with the 30-day mortality or the length of stay. Conclusions. We developed the AXIS classification system to predict the severity of sigmoid volvulus. This new classification system may facilitate triage and therapeutic decision-making for sigmoid volvulus patients