Genomes and Genes
Summary: Biological mechanism that controls CIRCADIAN RHYTHM. Circadian clocks exist in the simplest form in cyanobacteria and as more complex systems in fungi, plants, and animals. In humans the system includes photoresponsive RETINAL GANGLION CELLS and the SUPRACHIASMATIC NUCLEUS that acts as the central oscillator.
- Shinohara Y, Koyama Y, Ukai Tadenuma M, Hirokawa T, Kikuchi M, Yamada R, et al. Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock. Mol Cell. 2017;67:783-798.e20 pubmed publisher..Surprisingly, this domain can confer temperature compensation on a temperature-sensitive TTBK1. These findings suggest the temperature-sensitive substrate- and product-binding mechanisms underlie temperature compensation. ..
- Solanas G, Peixoto F, Perdiguero E, Jardi M, Ruiz Bonilla V, Datta D, et al. Aged Stem Cells Reprogram Their Daily Rhythmic Functions to Adapt to Stress. Cell. 2017;170:678-692.e20 pubmed publisher..Thus, stem cells rewire their diurnal timed functions to adapt to metabolic cues and to tissue-specific age-related traits. ..
- Shostak A. Circadian Clock, Cell Division, and Cancer: From Molecules to Organism. Int J Mol Sci. 2017;18: pubmed publisher..Therefore, a better understanding of the molecular links regulating the physiological balance between the two cycles will have potential significance for the treatment of cancer and associated disorders. ..
- Paijmans J, Lubensky D, ten Wolde P. Period Robustness and Entrainability of the Kai System to Changing Nucleotide Concentrations. Biophys J. 2017;113:157-173 pubmed publisherb>Circadian clocks must be able to entrain to time-varying signals to keep their oscillations in phase with the day-night rhythm...
- Wee P, Loy S, Toh J, Tham E, Cheung Y, Godfrey K, et al. Circadian feeding patterns of 12-month-old infants. Br J Nutr. 2017;117:1702-1710 pubmed publisher..Our findings indicated that the timing of feeding at 12 months was associated with daily energy and macronutrient intakes, and feeding mode during early infancy...
- Narasimamurthy R, Virshup D. A Flick of the Tail Keeps the Circadian Clock in Line. Mol Cell. 2017;66:437-438 pubmed publisherb>Circadian clocks signal and adapt to an ever-changing world by juggling a panoply of transcriptional and post-translational modifications. In this issue of Molecular Cell, Gustafson et al...
- Snijder J, Schuller J, Wiegard A, Lössl P, Schmelling N, Axmann I, et al. Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state. Science. 2017;355:1181-1184 pubmed publisher..Our data reveal details of the interactions between the Kai proteins and provide a structural basis to understand periodic assembly of the protein oscillator. ..
- Ezer D, Jung J, Lan H, Biswas S, Grégoire L, Box M, et al. The evening complex coordinates environmental and endogenous signals in Arabidopsis. Nat Plants. 2017;3:17087 pubmed publisher..Hence, our results show that the EC plays a central role in coordinating endogenous and environmental signals in Arabidopsis. ..
- Lin R, Mo Y, Zha H, Qu Z, Xie P, Zhu Z, et al. CLOCK Acetylates ASS1 to Drive Circadian Rhythm of Ureagenesis. Mol Cell. 2017;68:198-209.e6 pubmed publisher..Taken together, CLOCK modulates metabolic rhythmicity by acting as a rhythmic acetyl-transferase for metabolic enzymes. ..
- Riestra P, Gebreab S, Xu R, Khan R, Gaye A, Correa A, et al. Circadian CLOCK gene polymorphisms in relation to sleep patterns and obesity in African Americans: findings from the Jackson heart study. BMC Genet. 2017;18:58 pubmed publisher..In this work, CLOCK gene variants were associated with sleep duration and BMI suggesting that the effects of these polymorphisms on circadian rhythmicity may affect sleep duration and body weight regulation in Africans Americans. ..
- Krishnaiah S, Wu G, Altman B, Growe J, Rhoades S, Coldren F, et al. Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism. Cell Metab. 2017;25:961-974.e4 pubmed publisher..These results provide the first comprehensive views of circadian liver and cell-autonomous metabolism. ..
- Rivera Zavala J, Molina Aguilar C, Pérez Mendoza M, Olguín Martínez M, Hernández Muñoz R, Báez Ruiz G, et al. Daytime restricted feeding modifies the daily regulation of fatty acid ?-oxidation and the lipoprotein profile in rats. Br J Nutr. 2017;117:930-941 pubmed publisher..These adaptations could be part of the metabolic input that underlies the expression of the food-entrained oscillator. ..
- Frederick A, Goldsmith J, de Zavalía N, Amir S. Mapping the co-localization of the circadian proteins PER2 and BMAL1 with enkephalin and substance P throughout the rodent forebrain. PLoS ONE. 2017;12:e0176279 pubmed publisher..These results indicate that clock genes are not unique to specific cell types, and further studies will be required to determine the factors that contribute to the regulation of clock gene expression throughout the brain. ..
- Aryal R, Kwak P, Tamayo A, Gebert M, Chiu P, Walz T, et al. Macromolecular Assemblies of the Mammalian Circadian Clock. Mol Cell. 2017;67:770-782.e6 pubmed publisher..Our results define the macromolecular assemblies comprising the circadian feedback loop and provide an initial structural view of endogenous eukaryotic clock machinery. ..
- Thu Le H, Nakamura Y, Oh oka K, Ishimaru K, Nakajima S, Nakao A. The frequency of Th17 cells in the small intestine exhibits a day-night variation dependent on circadian clock activity. Biochem Biophys Res Commun. 2017;490:290-295 pubmed publisher..The findings provide novel insight into the regulation of the Th17 cell population in the small intestine at steady state, which may have translational potential for mucosal vaccination strategies. ..
- Rybakowski J, Dmitrzak Weglar M, Kliwicki S, Hauser J. Polymorphism of circadian clock genes and prophylactic lithium response. Bipolar Disord. 2014;16:151-8 pubmed..Of special interest may be polymorphisms of these genes involved both in the predisposition to bipolar mood disorder and the lithium response. ..
- PreuÃŸner M, Goldammer G, Neumann A, Haltenhof T, Rautenstrauch P, MÃ¼ller McNicoll M, et al. Body Temperature Cycles Control Rhythmic Alternative Splicing in Mammals. Mol Cell. 2017;67:433-446.e4 pubmed publisher..Together our data establish body temperature-driven AS as a core clock-independent oscillator in mammalian peripheral clocks. ..
- Wegner S, Belle M, Hughes A, Diekman C, Piggins H. Delayed Cryptochrome Degradation Asymmetrically Alters the Daily Rhythm in Suprachiasmatic Clock Neuron Excitability. J Neurosci. 2017;37:7824-7836 pubmed publisher..Therefore, post-translational modification shapes SCN neuronal state and network properties. ..
- Staiger D, Shin J, Johansson M, Davis S. The circadian clock goes genomic. Genome Biol. 2013;14:208 pubmed publisher..Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing system in plants. ..
- Ricci S, Bohnenstiehl D, Eggleston D, Kellogg M, Lyon R. Oyster toadfish (Opsanus tau) boatwhistle call detection and patterns within a large-scale oyster restoration site. PLoS ONE. 2017;12:e0182757 pubmed publisher..This type of non-invasive acoustic monitoring provides long-term, semi-continuous information on animal behavior and abundance, and operates effectively in settings that are otherwise difficult to sample. ..
- Brown L, Williams J, Taylor L, Thomson R, Nolan P, Foster R, et al. Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker. Nucleic Acids Res. 2017;45:9860-9873 pubmed publisher..SCN-enriched transcripts identified in this study provide novel insights into SCN function, including identifying genes which may play key roles in SCN physiology or provide SCN-specific drivers...
- Cyr K, Avaldi O, Wikswo J. Circadian hormone control in a human-on-a-chip: In vitro biology's ignored component?. Exp Biol Med (Maywood). 2017;242:1714-1731 pubmed publisher..This will help translate OoC work into pharmaceutical applications and connect the OoC community with the greater pharmacology and physiology communities...
- Taylor S, Wang T, Granados Fuentes D, Herzog E. Resynchronization Dynamics Reveal that the Ventral Entrains the Dorsal Suprachiasmatic Nucleus. J Biol Rhythms. 2017;32:35-47 pubmed publisher..Taken together, these results provide direct evidence that the ventral SCN entrains the dorsal SCN in constant conditions. ..
- Minas G, Momiji H, Jenkins D, Costa M, Rand D, Finkenstädt B. ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data. BMC Bioinformatics. 2017;18:316 pubmed publisher..The output from this software provides a useful analysis of time series data and can be incorporated into further modelling approaches or in hypothesis generation. ..
- Gustafson C, Parsley N, Asimgil H, Lee H, Ahlbach C, Michael A, et al. A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms. Mol Cell. 2017;66:447-457.e7 pubmed publisher..Furthermore, isomerization is regulated by the cyclophilin family of peptidyl-prolyl isomerases, highlighting the potential for regulation of BMAL1 protein dynamics in period determination. ..
- Kiessling S, Ucar A, Chowdhury K, Oster H, Eichele G. Genetic background-dependent effects of murine micro RNAs on circadian clock function. PLoS ONE. 2017;12:e0176547 pubmed publisher..Together, our results reveal a strain and light regimen-specific function of miR-132/212 in the circadian clock machinery suggesting that miR-132 and miR-212 act as background-dependent circadian rhythm modulators. ..
- Gan S, O Shea E. An Unstable Singularity Underlies Stochastic Phasing of the Circadian Clock in Individual Cyanobacterial Cells. Mol Cell. 2017;67:659-672.e12 pubmed publisher..Our findings and approach can be applied to other biological oscillators. ..
- Schibler U. Mammalian Circadian Cogwheels Are Parts of Macromolecular Machines. Mol Cell. 2017;67:727-729 pubmed publisher..2017) and a mechanism rendering this molecular timekeeper temperature-compensated (Shinohara et al., 2017). ..
- Liu X, Dang Y, Matsu ura T, He Y, He Q, Hong C, et al. DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition. Mol Cell. 2017;67:203-213.e4 pubmed publisherAlthough the coupling between circadian and cell cycles allows circadian clocks to gate cell division and DNA replication in many organisms, circadian clocks were thought to function independently of cell cycle...
- Dhillon T, Morohashi K, Stockinger E. CBF2A-CBF4B genomic region copy numbers alongside the circadian clock play key regulatory mechanisms driving expression of FR-H2 CBFs. Plant Mol Biol. 2017;94:333-347 pubmed publisher..These data support a scenario in which CBF2A-CBF4B genomic region copy numbers affect expression of other FR-H2 CBFs through a mechansim in which these other FR-H2 CBFs are activated by those in the copy number variable unit. ..
- Lee J, Yoo E, Lee H, Park K, Hur J, Lim C. LSM12 and ME31B/DDX6 Define Distinct Modes of Posttranscriptional Regulation by ATAXIN-2 Protein Complex in Drosophila Circadian Pacemaker Neurons. Mol Cell. 2017;66:129-140.e7 pubmed publisher..Taken together, these data suggest that the ATX2 complex may switch distinct modes of posttranscriptional regulation through its associating factors to control circadian clocks and ATX2-related physiology.
- Co A, Lagomarsino M, Caselle M, Osella M. Stochastic timing in gene expression for simple regulatory strategies. Nucleic Acids Res. 2017;45:1069-1078 pubmed publisher..is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression...
- Gibbs J, Ray D. The role of the circadian clock in rheumatoid arthritis. Arthritis Res Ther. 2013;15:205 pubmed publisher..Furthermore, a full understanding of the mechanisms by which the clock couples to the immune system may provide novel therapeutic targets for the treatment of this debilitating disease. ..