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Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network

Dorjsuren Battogtokh, Shihoko Kojima, John J. Tyson, Joerg Stelling
2018 PLoS Computational Biology  
The circadian clock is no exception: an antisense transcript of the mammalian core-clock gene PERIOD2 (PER2), which we shall refer to as Per2AS RNA, oscillates with a circadian period and a nearly 12 h  ...  In this paper, we ask whether Per2AS plays a regulatory role in the mammalian circadian clock by studying in silico the potential effects of interactions between Per2 and Per2AS RNAs on circadian rhythms  ...  Angela Relogio for her explanations of the model and results reported in Ref. [18] . Author Contributions Conceptualization: Dorjsuren Battogtokh, Shihoko Kojima, John J. Tyson.  ... 
doi:10.1371/journal.pcbi.1005957 pmid:29447160 pmcid:PMC5831635 fatcat:nm3b5clbcbcxrilg27qz4otoru

Circadian Oscillators: Around the Transcription–Translation Feedback Loop and on to Output

Jennifer M. Hurley, Jennifer J. Loros, Jay C. Dunlap
2016 TIBS -Trends in Biochemical Sciences. Regular ed  
These include roles for antisense transcription, intrinsically disordered proteins, codon bias in clock genes, and a more focused discussion of post-transcriptional and translational regulation as a part  ...  The function of qrf, the prototypic circadian antisense molecule, is currently an area of much interest and discussion.  ...  Acknowledgments The authors regret that space considerations precluded the discussion and citation of much additional work of interest.  ... 
doi:10.1016/j.tibs.2016.07.009 pmid:27498225 pmcid:PMC5045794 fatcat:bvmlmqbk4vcl5fphsikpbfgmjm

Deciphering the Dynamics of Interlocked Feedback Loops in a Model of the Mammalian Circadian Clock [article]

Dorjsuren Battogtokh, John J. Tyson
2018 bioRxiv   pre-print
In this work, we report a detailed bifurcation analysis of a mathematical model of the mammalian circadian clock network developed by Relogio et al. [16], noteworthy for its consistency with available  ...  The bifurcation diagrams reported here can be used for predicting how the core-clock network responds - in terms of period, amplitude and phases of oscillations - to different perturbations.  ...  Acknowledgements Financial Assistance from the Department of Biological Sciences and the College of Science at Virginia Tech is gratefully acknowledged.  ... 
doi:10.1101/306852 fatcat:wc52bsag4zamhoeisfqrecot7q

Natural antisense transcript of Period2, Per2AS, regulates the amplitude of the mouse circadian clock

Rebecca A Mosig, Allison N Castaneda, Jacob C Deslauriers, Landon P Frazier, Kevin L He, Naseem Maghzian, Aarati Pokharel, Camille T Schrier, Lily Zhu, Nobuya Koike, John J Tyson, Carla B Green (+2 others)
2021 Genes & Development  
Our work also supports the idea that antisense transcripts of core clock genes constitute a common feature of circadian clocks, as they are found in other organisms.  ...  Overall, our data indicate that Per2AS is an important regulatory molecule in the mammalian circadian clock machinery.  ...  J.S.T. is an Investigator in the Howard Hughes Medical Institute.  ... 
doi:10.1101/gad.343541.120 pmid:34016691 pmcid:PMC8168560 fatcat:e4wxdzedejglpaubcis2q6rapq

Transcriptional Regulation of Circadian Clocks [chapter]

Jürgen A. Ripperger, Steven A. Brown
2009 The Circadian Clock  
In it, similarities and differences among circadian systems in metazoans, in plants, in simple eukaryotes like the bread mold Neurospora crassa, and in the evolutionarily ancient clocks of photosynthetic  ...  The first chapter of this book has introduced the historical background of the circadian clock, as well as its anatomical organization.  ...  From the observation of Hardin, Hall, and Rosbash in 1990 that the product of the circadian clock protein PERIOD regulates its own transcription, a model was proposed that has become the cornerstone of  ... 
doi:10.1007/978-1-4419-1262-6_2 fatcat:byfwfa5rabdj7gaj3gxjwf6qdm

Entrainment of breast (cancer) epithelial cells detects distinct circadian oscillation patterns for clock and hormone receptor genes

Stefano Rossetti, Joseph Esposito, Francesca Corlazzoli, Alex Gregorski, Nicoletta Sacchi
2012 Cell Cycle  
Disclosure of potential conflicts of interest No potential conflicts of interest were disclosed.  ...  The mammalian circadian clock.  ...  The cellular clock is based on a network of core clock genes, which drive the circadian expression of non-clock genes involved in many cellular processes.  ... 
doi:10.4161/cc.11.2.18792 pmid:22193044 pmcid:PMC3293384 fatcat:a7egfyycy5a4pekq3q73er5ily

Thefrequencynatural antisense transcript first promotes, then represses,frequencygene expression via facultative heterochromatin

Na Li, Tammy M. Joska, Catherine E. Ruesch, Samuel J. Coster, William J. Belden
2015 Proceedings of the National Academy of Sciences of the United States of America  
The circadian clock is controlled by a network of interconnected feedback loops that require histone modifications and chromatin remodeling.  ...  Long noncoding natural antisense transcripts (NATs) originate from Period in mammals and frequency (frq) in Neurospora.  ...  Eric Selker for providing the HP1-GFP used in the ChIP experiments. We also thank Dr. Wendie Cohick for comments. This work was supported by NIH Grant R01GM101378 (to W.J.B.).  ... 
doi:10.1073/pnas.1406130112 pmid:25831497 pmcid:PMC4394252 fatcat:mikwalkxpzh4jcq4depzfk4pq4

Genetics of Circadian Rhythms in Mammalian Model Organisms [chapter]

Phillip L. Lowrey, Joseph S. Takahashi
2011 Advances in Genetics  
The mammalian circadian system is a complex hierarchical temporal network which is organized around an ensemble of uniquely coupled cells comprising the principal circadian pacemaker in the suprachiasmatic  ...  Here we will explore the genetics of the mammalian circadian system from cell-autonomous molecular oscillations, to interactions among central and peripheral oscillators and ultimately, to the daily rhythms  ...  J.S.T. is an Investigator in the Howard Hughes Medical Institute.  ... 
doi:10.1016/b978-0-12-387690-4.00006-4 pmid:21924978 pmcid:PMC3709251 fatcat:iv5ruutdjjhvxddhblty2hihqi

Suprachiasmatic Nucleus: Cell Autonomy and Network Properties

David K. Welsh, Joseph S. Takahashi, Steve A. Kay
2010 Annual Review of Physiology  
Individual SCN neurons in dispersed culture can generate independent circadian oscillations of clock gene expression and neuronal firing.  ...  The suprachiasmatic nucleus (SCN) is the primary circadian pacemaker in mammals.  ...  To serve this purpose, mammalian cells contain circadian clocks composed of genes that interact in oscillatory transcriptional networks within cells (1, 2) and regulate the expression of many other genes  ... 
doi:10.1146/annurev-physiol-021909-135919 pmid:20148688 pmcid:PMC3758475 fatcat:gnfavo3yzzcf5lprwdsdj3dmkm

Regulated DNA Methylation and the Circadian Clock: Implications in Cancer

Tammy Joska, Riasat Zaman, William Belden
2014 Biology  
In recent years, it has become evident that dynamic DNA methylation accompanies the circadian clock and is found at clock genes in Neurospora, mice and cancer cells.  ...  In this capacity, aberrant DNA methylation may serve as a readout of misregulated clock genes and not as the causative agent.  ...  Conflicts of Interest The authors declare no conflict of interest.  ... 
doi:10.3390/biology3030560 pmid:25198253 pmcid:PMC4192628 fatcat:d64qyjd7b5b47l2bpt5i4navda

Non-coding Vibration in Circadian Oscillation

Utpal Bhadra, Pradipta Patra, Manika Pal Bhadra
2017 Advanced Techniques in Biology & Medicine  
Here, we sum up the basic role of small regulatory RNA and their epigenetic circuits in brain clock activity.  ...  Multiple epigenetic events including post-transcriptional regulation, splicing, polyadenylation, mature mRNA editing and stability of translation products are the main vibrators for circadian oscillation  ...  Figure 2 : 2 The figure shows mammalian circadian clock and other three layers of its control. (a) Suprachiasmatic nucleus possess master circadian pacemaker.  ... 
doi:10.4172/2379-1764.1000236 fatcat:el2j4upegrea7g4fbhg3btisrm

Chromatin landscape and circadian dynamics: Spatial and temporal organization of clock transcription

Lorena Aguilar-Arnal, Paolo Sassone-Corsi
2014 Proceedings of the National Academy of Sciences of the United States of America  
Work in the Center for Epigenetics and Metabolism is supported by the National Institutes of Health, Merieux Research Grants, King Abdullah University of Science and Technology, and INSERM. L.A.  ...  We thank all the members of the P.S.-C. laboratory for discussions and insights.  ...  In the absence of environmental zeitgebers, the clock "free runs" in periods close to 24 h long.  ... 
doi:10.1073/pnas.1411264111 pmid:25378702 pmcid:PMC4460512 fatcat:4orz35mz35fspizojdgltgy23m

The pedestrian watchmaker: Genetic clocks from engineered oscillators

Natalie A. Cookson, Lev S. Tsimring, Jeff Hasty
2009 FEBS Letters  
These biological clocks have long been a focus of research; however, a clear understanding of how they maintain oscillations in the face of unpredictable environments and the inherent noise of biological  ...  The crucial role of time-keeping has required organisms to develop sophisticated regulatory networks to ensure the reliable propagation of periodic behavior.  ...  Acknowledgements Support was provided by a DOE CSGF Grant (DE-FG02-97ER25308) and the NIH (GM69811-01).  ... 
doi:10.1016/j.febslet.2009.10.089 pmid:19903483 pmcid:PMC2921805 fatcat:7pseb2rzovhrpmbmdixwpco54y

A role for Timeless in epithelial morphogenesis during kidney development

Z. Li, R. O. Stuart, J. Qiao, A. Pavlova, K. T. Bush, M. Pohl, H. Sakurai, S. K. Nigam
2000 Proceedings of the National Academy of Sciences of the United States of America  
By employing a targeted screen to identify transcription factors involved early in the morphogenetic program leading to UB branching, we identified the mammalian ortholog of Timeless (mTim) as a potential  ...  In the kidney, this can be modeled by a very simple system consisting of isolated ureteric bud (UB) cells, which undergo branching morphogenesis in response to soluble factors present in the conditioned  ...  Although antisense ODN were designed to interact with the target mRNA, sense and missense ODN also may interact with either the target or other mRNA.  ... 
doi:10.1073/pnas.97.18.10038 pmid:10963667 pmcid:PMC27664 fatcat:2jzwxzwuzndhlgjyjrytu54pnu

Flies, clocks and evolution

2001 Philosophical Transactions of the Royal Society of London. Biological Sciences  
The conservation of function of clock molecules is illustrated by comparison with the mammalian circadian system, and the apparent swapping of roles between various canonical clock gene components is highlighted  ...  However, this is not borne out because the expression of clock molecules in the brain of the giant silk moth, Antheraea pernyi, is not easy to reconcile with the negative feedback roles of the period and  ...  B (2001) Table 1 . 1 Circadian clock genes in the £y and mammals. Note that for the mammalian clock there is controversy about the expression and function of several genes. Drosophila Phil.  ... 
doi:10.1098/rstb.2001.0961 pmid:11710984 pmcid:PMC1088553 fatcat:3qt7dac2jrbltin5svwsbclaza
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