Showing papers by "Hiroki R. Ueda published in 2007"

The 3' termini of mouse Piwi-interacting RNAs are 2'-O-methylated.

Abstract: Piwi-interacting RNAs (piRNAs) are a germline-specific class of small noncoding RNAs that are essential for spermatogenesis, but their function and biogenesis remain elusive Here we report a post-transcriptional modification of mouse piRNAs Mass spectrometric analysis reveals that the piRNAs tested are fully modified by 2'-O-methylation at their 3' termini This observation may provide a clue to the biogenesis and function of piRNAs in spermatogenesis

A functional genomics strategy reveals clockwork orange as a transcriptional regulator in the Drosophila circadian clock

Abstract: The Drosophila circadian clock consists of integrated autoregulatory feedback loops, making the clock difficult to elucidate without comprehensively identifying the network components in vivo. Previous studies have adopted genome-wide screening for clock-controlled genes using high-density oligonucleotide arrays that identified hundreds of clock-controlled genes. In an attempt to identify the core clock genes among these candidates, we applied genome-wide functional screening using an RNA interference (RNAi) system in vivo. Here we report the identification of novel clock gene candidates including clockwork orange (cwo), a transcriptional repressor belonging to the basic helix–loop–helix ORANGE family. cwo is rhythmically expressed and directly regulated by CLK–CYC through canonical E-box sequences. A genome-wide search for its target genes using the Drosophila genome tiling array revealed that cwo forms its own negative feedback loop and directly suppresses the expression of other clock genes through the E-box sequence. Furthermore, this negative transcriptional feedback loop contributes to sustaining a high-amplitude circadian oscillation in vivo. Based on these results, we propose that the competition between cyclic CLK–CYC activity and the adjustable threshold imposed by CWO keeps E-box-mediated transcription within the controllable range of its activity, thereby rendering a Drosophila circadian clock capable of generating high-amplitude oscillation.

Melanopsin-dependent photo-perturbation reveals desynchronization underlying the singularity of mammalian circadian clocks

Abstract: Singularity behaviour in circadian clocks--the loss of robust circadian rhythms following exposure to a stimulus such as a pulse of bright light--is one of the fundamental but mysterious properties of clocks. To quantitatively perturb and accurately measure the dynamics of cellular clocks, we synthetically produced photo-responsiveness within mammalian cells by exogenously introducing the photoreceptor melanopsin and continuously monitoring the effect of photo-perturbation on the state of cellular clocks. Here we report that a critical light pulse drives cellular clocks into singularity behaviour. Our theoretical analysis consistently predicts and subsequent single-cell level observation directly proves that desynchronization of individual cellular clocks underlies singularity behaviour. Our theoretical framework also explains why singularity behaviours have been experimentally observed in various organisms, and it suggests that desynchronization is a plausible mechanism for the observable singularity of circadian clocks. Importantly, these in vitro and in silico findings are further supported by in vivo observations that desynchronization underlies the multicell-level amplitude decrease in the rat suprachiasmatic nucleus induced by critical light pulses.

Systems biology of mammalian circadian clocks.

Abstract: Systems Biology is a natural extension of molecular biology and can be defined as biology after identification of key gene(s). Systems-biological research is hence seen as a multistage process, beginning with the comprehensive identification and quantitative analysis of individual system components and their networked interactions and leading to the ability to control existing systems toward the desired state and design new ones based on an understanding of structure and underlying dynamical principles. In this chapter, we take mammalian circadian clocks as a model system and describe systems-biological approaches, including the identification of clock-controlled genes, clock-controlled cis elements, and clock transcriptional circuits driven by functional genomics; the parameter change of clock components followed by quantitative measurement; and the dynamic and quantitative perturbation of the clock and its application to one of the fundamental but yet-unsolved questions: singularity behavior of clocks. As perspective for systems-biological investigations, we also introduce the system-level dynamical questions related to the core of clocks, including delay, nonlinearity, temperature-compensation and synchronization of mammalian circadian oscillator(s), and the system-level information problems related to clocks in the environment, including the internal representation of light change through perfect adaptation and internal representation of day length through photoperiodism in mammals.

Spiral spin structure in the Heisenberg pyrochlore magnet Cd Cr 2 O 4

Abstract: A frustrated spinel $\mathrm{Cd}{\mathrm{Cr}}_{2}{\mathrm{O}}_{4}$ undergoes a three-dimensional spin-Peierls transition at ${T}_{N}=7.8\phantom{\rule{0.3em}{0ex}}\mathrm{K}$ from a cubic paramagnetic to a tetragonal N\'eel state. The N\'eel state has a spiral magnetic structure with a characteristic wave vector of (0, $\ensuremath{\delta}$, 1) when the $c$ axis is elongated [J.-H. Chung et al., Phys. Rev. Lett. 95, 247204 (2005)]. Here, we report our spherical neutron polarimetry experiments to investigate the spiral spin structure in detail. Our results indicate that the spins lie in the $ac$ plane perpendicular to the direction of the spiral modulation. We also find that the spiral structure in the $ac$ plane is elliptical with the $c$ component larger by $\ensuremath{\sim}24%$ than the $a$ component, suggesting a strong coupling between the magnetic structure and the structural distortion. Unpolarized neutron diffraction under an external magnetic field has also been performed. The magnetic-field dependence suggests the existence of magnetic anisotropy in the N\'eel state, which is consistent with our previous inelastic studies [J.-H. Chung et al., Phys. Rev. Lett. 95, 247204 (2005)].

Microarrays: statistical methods for circadian rhythms.

Abstract: Microarrays are promising tools that are increasingly being applied to the study of circadian rhythms. The large and complex datasets they generate, however, mean they require a new approach on how to design experiments, handle datasets, translate results, and derive conclusions. This technology also requires statistical methods for the correct interpretation of data generated by the microarrays. In this chapter, we provide an overview of analytical methods applied to microarray experiments for the identification of genes with circadian expression.

Microarrays: quality control and hybridization protocol.

Abstract: Microarray technology is an exciting and promising tool, and is increasingly employed for studying circadian rhythms. To obtain optimal results from this technology, it is important to perform quality control experiments before engaging in genome-wide expression analysis. In this chapter, we provide an overview of quantitative polymerase chain reaction experiments using the ABI PRISM 7900HT system for quality control of samples, and microarray experiments using the Affymetrix GeneChip system for genome-wide expression analysis.

Desynchronization of Noisy Multi‐cellular Clocks Underlies the Population‐level Singularity Behavior of Mammalian Circadian Clock

Abstract: The singularity behavior of circadian clocks defined as the suppression of circadian oscillation by critical perturbation is one of the intriguing dynamical properties of circadian rhythms. Although the singularity behaviors have been observed in various organisms, its mechanism has not yet been elucidated, because the hierarchical structure of multi‐cell‐level circadian clocks exists behind the organism‐level circadian rhythm. In vitro light‐responsible circadian system is indispensable for extracting the underlying mechanism of the singularity behavior behind the hierarchical structure of multi‐cell organisms. To obtain such in vitro system, we synthetically constructed light‐responsible mammalian clock cells by exogenously introducing a photo‐responsible receptor. By using this synthetic system and population‐level high‐throughput promoter activity assay, we found that a light pulse with critical timing and strength can induce population‐level singularity behavior of the light‐responsible mammalian clo...