Transcriptional architecture of the mammalian circadian clock

Nature Reviews Genetics, Journal Year: 2016, Volume and Issue: 18(3), P. 164 - 179

Published: Dec. 19, 2016

Language: Английский

---

A circadian gene expression atlas in mammals: Implications for biology and medicine

Proceedings of the National Academy of Sciences, Journal Year: 2014, Volume and Issue: 111(45), P. 16219 - 16224

Published: Oct. 27, 2014

Significance We generated high-resolution multiorgan expression data showing that nearly half of all genes in the mouse genome oscillate with circadian rhythm somewhere body. Such widespread transcriptional oscillations have not been previously reported mammals. Applying pathway analysis, we observed new clock-mediated spatiotemporal relationships. Moreover, found a majority best-selling drugs United States target gene products. Many these relatively short half-lives, and our predict which may benefit from timed dosing.

Language: Английский

---

Central and Peripheral Circadian Clocks in Mammals

Annual Review of Neuroscience, Journal Year: 2012, Volume and Issue: 35(1), P. 445 - 462

Published: May 20, 2012

The circadian system of mammals is composed a hierarchy oscillators that function at the cellular, tissue, and systems levels. A common molecular mechanism underlies cell-autonomous oscillator throughout body, yet this clock adapted to different functional contexts. In central suprachiasmatic nucleus (SCN) hypothalamus, coupled population neuronal acts as master pacemaker for organism drive rhythms in activity rest, feeding, body temperature, hormones. Coupling within SCN network confers robustness pacemaker, which turn provides stability overall temporal architecture organism. Throughout majority cells clocks are intimately enmeshed metabolic pathways. Thus, an emerging view adaptive significance their fundamental role orchestrating metabolism.

Language: Английский

---

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

Science, Journal Year: 2012, Volume and Issue: 338(6105), P. 349 - 354

Published: Sept. 1, 2012

Transcription Around the Clock The biological clock that controls daily rhythms in mammalian physiology and behavior is thought to be regulated large part by transcriptional events (see Perspective Doherty Kay ). Koike et al. (p. 349 ; published online 30 August) produced a comprehensive analysis of these across entire mouse liver genome over 24-hour period. Only ∼22% cycling messenger RNA transcripts were driven de novo transcription, suggesting posttranscriptional also play an important regulatory role clock. Biological timing organisms can respond rhythmic cues from environment. Morf 379 , 23 explored how one such cue, cycles ambient temperature, influence circadian cells. Cold-inducible RNA–binding protein (CIRP) accumulates when body temperature low. A systematic search for binding partners CIRP identified encoding core components Loss decreased amplitude gene expression cells lacking adapted more quickly cycles.

Language: Английский

---

Molecular Components of the Mammalian Circadian Clock

Handbook of experimental pharmacology, Journal Year: 2013, Volume and Issue: unknown, P. 3 - 27

Published: Jan. 1, 2013

Language: Английский

---

The Sinocyclocheilus cavefish genome provides insights into cave adaptation

BMC Biology, Journal Year: 2016, Volume and Issue: 14(1)

Published: Jan. 4, 2016

An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to massive southwestern karst area adjacent Qinghai-Tibetan Plateau of China. In order understand whether orogeny influenced evolution these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing comparative analyses three species this genus, S. grahami, rhinocerous anshuiensis. These are surface-dwelling, semi-cave-dwelling cave-restricted, respectively. The assembled genome sizes anshuiensis 1.75 Gb, 1.73 Gb 1.68 Divergence time population history reveal that their speciation dynamics correlated with different stages uplifting Plateau. We carried out found many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes crystallin mutations melanogenesis-related deletions scale-related genes) down-regulation circadian rhythm pathway possibly associated regressive features (such eye degeneration, albinism, rudimentary scales lack rhythms), some expansion taste-related transcription factor gene) may point constructive enhanced taste buds) which evolved cave fishes. As first report on among distinct our work provides not only insights into mechanisms adaptation, but also represents a fundamental resource for better understanding biology.

Language: Английский

---

Mutation of the Human Circadian Clock Gene CRY1 in Familial Delayed Sleep Phase Disorder

Cell, Journal Year: 2017, Volume and Issue: 169(2), P. 203 - 215.e13

Published: April 1, 2017

Language: Английский

---

Strengths and Limitations of Period Estimation Methods for Circadian Data

PLoS ONE, Journal Year: 2014, Volume and Issue: 9(5), P. e96462 - e96462

Published: May 8, 2014

A key step in the analysis of circadian data is to make an accurate estimate underlying period. There are many different techniques and algorithms for determining period, all with assumptions differing levels complexity. Choosing which algorithm, implementation measures accuracy use can offer pitfalls, especially non-expert. We have developed BioDare system, online service allowing data-sharing (including public dissemination), data-processing analysis. Circadian experiments main focus hence performing period a major feature system. Six methods been incorporated into BioDare: Enright Lomb-Scargle periodograms, FFT-NLLS, mFourfit, MESA Spectrum Resampling. Here we review those six techniques, explain principles behind each algorithm evaluate their performance. In order quantify methods' accuracy, examine against artificial mathematical test signals model-generated mRNA data. Our re-implementation method Java allows meaningful comparisons computational complexity computing time associated algorithm. Finally, provide guidelines on most appropriate types, recommendations experimental design extract optimal

Language: Английский

---

Competing E3 Ubiquitin Ligases Govern Circadian Periodicity by Degradation of CRY in Nucleus and Cytoplasm

Cell, Journal Year: 2013, Volume and Issue: 152(5), P. 1091 - 1105

Published: Feb. 1, 2013

Language: Английский

---

Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptional Activator Complex

Science, Journal Year: 2012, Volume and Issue: 337(6091), P. 189 - 194

Published: June 1, 2012

The circadian clock in mammals is driven by an autoregulatory transcriptional feedback mechanism that takes approximately 24 hours to complete. A key component of this a heterodimeric activator consisting two basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) domain protein subunits, CLOCK and BMAL1. Here, we report the crystal structure complex containing mouse CLOCK:BMAL1 bHLH-PAS domains at 2.3 Å resolution. reveals unusual asymmetric heterodimer with three each subunits--bHLH, PAS-A, PAS-B--tightly intertwined involved dimerization interactions, resulting distinct interfaces. Mutations perturb observed interfaces affect stability activity as well periodicity oscillator. starting point for understanding atomic level driving mammalian clock.

Language: Английский

---