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Najari-Hanjani P, Farazmandfar T, Golalipour M. PER3P1 pseudogene modulates PER3 oscillation: a new player in the molecular clock network. BIOL RHYTHM RES 2022. [DOI: 10.1080/09291016.2022.2050978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Parisa Najari-Hanjani
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
| | - Touraj Farazmandfar
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
- Cellular and Molecular Research Center, Golestan University of Medical Science, Gorgan, Iran
| | - Masoud Golalipour
- Department of Medical Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
- Cellular and Molecular Research Center, Golestan University of Medical Science, Gorgan, Iran
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Dysregulation of PER3 clock gene and its only pseudogene in colorectal cancer and type 2 diabetes. ARCH BIOL SCI 2022. [DOI: 10.2298/abs220223009n] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The period (PER) family genes (PER1, PER2, and PER3) play a fundamental role
in regulating the day/night cycle. PER3 has a pseudogene variant, PER3P1 or
PER4, whose role and expression pattern is unclear in human health and
diseases. This study was performed to evaluate the expression levels of
normal PER family members and the PER3P1 pseudogene in colorectal cancer
(CRC) and type 2 diabetes (T2D). Blood samples were taken from 50 diabetic
patients and analyzed using real-time PCR for quantification of PER3 and
PER3P1 expression. Colorectal tumor tissues of 50 individuals were also used
to evaluate the expression of PER members. All PER members, including
PER3P1, were found to be downregulated in colorectal tumor samples. Blood
samples collected from diabetic subjects revealed an opposite expression
pattern; both PER3 and its pseudogene were found to be upregulated when
compared to the control group. Our results reveal coordination between the
expression pattern of PER3P1 and normal PER family genes. Based on our
findings and the pathological importance of this pseudogene, it can be
suggested that PER3P1 may be one of the key regulators of the molecular
clock network and PER family expression. This hypothesis needs to be
confirmed by further studies.
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Mosig RA, Kojima S. Timing without coding: How do long non-coding RNAs regulate circadian rhythms? Semin Cell Dev Biol 2021; 126:79-86. [PMID: 34116930 DOI: 10.1016/j.semcdb.2021.04.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a new class of regulatory RNAs that play important roles in disease development and a variety of biological processes. Recent studies have underscored the importance of lncRNAs in the circadian clock system and demonstrated that lncRNAs regulate core clock genes and the core clock machinery in mammals. In this review, we provide an overview of our current understanding of how lncRNAs regulate the circadian clock without coding a protein. We also offer additional insights into the challenges in understanding the functions of lncRNAs and other unresolved questions in the field. We do not cover other regulatory ncRNAs even though they also play important roles; readers are highly encouraged to refer to other excellent reviews on this topic.
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Affiliation(s)
- Rebecca A Mosig
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech 1015 Life Science Circle, Blacksburg, VA 24061, USA.
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Bhadra U, Thakkar N, Das P, Pal Bhadra M. Evolution of circadian rhythms: from bacteria to human. Sleep Med 2017; 35:49-61. [DOI: 10.1016/j.sleep.2017.04.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/07/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022]
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Abstract
In considering the impact of the earth’s changing geophysical conditions during the history of life, it is surprising to learn that the earth’s rotational period may have been as short as 4 h, as recently as 1900 million years ago (or 1.9 billion years ago). The implications of such figures for the origin and evolution of clocks are considerable, and the authors speculate on how this short rotational period might have influenced the development of the “protoclock” in early microorganisms, such as the Cyanobacteria, during the geological periodsin which they arose and flourished. They then discuss the subsequent duplication of clock genes that took place around and after the Cambrian period, 543 million years ago, and its consequences. They compare the relative divergences of the canonical clock genes, which reveal the Per family to be the most rapidly evolving. In addition, the authors use a statistical test to predict which residues within the PER and CRY families may have undergone functional specialization.
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Affiliation(s)
- Eran Tauber
- Department of Genetics, University of Leicester, Leicester, UK
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Layeghifard M, Pirhaji L, Rabani R. Adaptive evolution in thePergene family of vertebrates: neofunctionalization by positive Darwinian selection after two major gene duplications. BIOL RHYTHM RES 2009. [DOI: 10.1080/09291010802553733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Comparative Analysis of Period Genes in Teleost Fish Genomes. J Mol Evol 2008; 67:29-40. [DOI: 10.1007/s00239-008-9121-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 02/26/2008] [Accepted: 05/06/2008] [Indexed: 10/22/2022]
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Abstract
The circadian clock percolates through every aspect of behaviour and physiology, and has wide implications for human and animal health. The molecular basis of the Drosophila circadian clock provides a model system that has remarkable similarities to that of mammals. The various cardinal clock molecules in the fly are outlined, and compared to those of their actual and 'functional' homologues in the mammal. We also focus on the evolutionary tinkering of these clock genes and compare and contrast the neuronal basis for behavioural rhythms between the two phyla.
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Affiliation(s)
- Ezio Rosato
- Department of Genetics, University of Leicester, Leicester, UK
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von Schantz M, Jenkins A, Archer SN. Evolutionary History of the Vertebrate Period Genes. J Mol Evol 2006; 62:701-7. [PMID: 16752210 DOI: 10.1007/s00239-005-0185-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 12/22/2005] [Indexed: 10/24/2022]
Abstract
Circadian clock genes are remarkably conserved between eucoelomates. Although Drosophila has one copy of each major component, vertebrates have two or (in the case of the Period genes) three paralogs (Per1-3). We investigated the possibility that the vertebrate Per genes arose through two genome duplications during the emergence of vertebrates. Phylogenetic trees have placed zebrafish and mammalian Per1 and 2 together in a separate branch from Per3. The positions of four coding region splice sites were conserved between Drosophila per and the human paralogs, the fifth one being unique to Drosophila. The human PER genes shared the positions of all coding region splice sites, except the first two in PER1 and PER2 (which PER3 lacks). The phases of all splice sites were conserved between all four genes with two exceptions. Analysis of all genes within 10 Mb of the human PER1-3 genes, which are located 7.8-8.8 Mb from the telomeres on chromosomes 17, 2, and 1, identified several orthologous neighbors shared by at least two PER genes. Two gene families, HES (hairy and Enhancer of Split) and KIF1 (kinesin-like protein 1), were represented in all three of these paralogons. Although no functional fourth human PER paralog exists, five representatives from the same gene families were found close to the telomer of chromosome 3. We conclude that the ancestral chordate Per gene underwent two duplication events, giving rise to Per1-3 and a lost fourth paralog.
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Affiliation(s)
- Malcolm von Schantz
- Centre for Chronobiology, School of Biomedical and Molecular Sciences, University of Surrey, Guildford, GU2 7XH, UK.
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Abstract
This article discusses a number of common methodologies used in the field of population genetics and evolution and reviews their application within circadian rhythm research. We examine the basic principles behind phylogenetic analysis and how these can be used to illuminate clock gene evolution. We then discuss genetic variation between and within species and show how neutrality tests can reveal the signatures of selection or drift on clock genes. These tests are particularly important for moving beyond "just so" stories when discussing the evolution of clock phenotypes, and we provide relevant circadian examples. We also focus on methods that can be used to study genetic variation, such as quantitative trait loci analysis. We discuss the various bootstrapping or resampling techniques that can be applied to generate confidence intervals in the various methodologies and then examine the use of interspecific transformation studies, which can, and have, provide some useful insights, not only into clock gene evolution in particular, but "behavioral" gene evolution in general. Finally, we assess gene/protein alignments and protein structure predictions and their implicit evolutionary bases.
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Avivi A, Oster H, Joel A, Beiles A, Albrecht U, Nevo E. Circadian genes in a blind subterranean mammal II: conservation and uniqueness of the three Period homologs in the blind subterranean mole rat, Spalax ehrenbergi superspecies. Proc Natl Acad Sci U S A 2002; 99:11718-23. [PMID: 12193657 PMCID: PMC129335 DOI: 10.1073/pnas.182423299] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2002] [Indexed: 11/18/2022] Open
Abstract
We demonstrated that a subterranean, visually blind mammal has a functional set of three Per genes that are important components of the circadian clockwork in mammals. The mole rat superspecies Spalax ehrenbergi is a blind subterranean animal that lives its entire life underground in darkness. It has degenerated eyes, but the retina and highly hypertrophic harderian gland are involved in photoperiodic perception. All three Per genes oscillate with a periodicity of 24 h in the suprachiasmatic nuclei, eye, and harderian gland and are expressed in peripheral organs. This oscillation is maintained under constant conditions. The light inducibility of sPer1 and sPer2, which are similar in structure to those of other mammals, indicates the role of these genes in clock resetting. However, sPer3 is unique in mammals and has two truncated isoforms, and its expressional analysis leaves its function unresolved. Per's expression analysis in the harderian gland suggests an important participation of this organ in the stabilization and resetting mechanism of the central pacemaker in the suprachiasmatic nuclei and in unique adaptation to life underground.
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Affiliation(s)
- Aaron Avivi
- Laboratory of Animal Molecular Evolution, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel.
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Abstract
Rhythmic variations in physiological and behavioural processes are mediated by both endogenous and exogenous factors. Endogenous factors include self-sustaining biological pacemakers or clocks which in the absence of strong external influences self-sustain periodic rhythms in such diverse physiological and psychological processes as core body temperature, food intake, cognitive performance and mood. Clocks with endogenous periods near or at 24 h (called circadian clocks from the Latin, circa dies, meaning about one day) have been documented from prokaryotes to single cell eukaryotes to multi-cellular, complex animals such as flies, rodents and humans. Over the past few years, a revolution in the understanding of the molecular basis of these clocks has led to the identification of a number of core clock genes and their proteins, and the development of elegant feedback models to explain the molecular gears of circadian clocks. At least eight human orthologs of mouse core clock genes have been identified, and polymorphisms in two of these, hClock and hPer2, have been implicated in human sleep disorders. Remarkably, knowledge of these core clock genes and the development of sophisticated reporter systems to monitor clock gene promoter activity have led to the astonishing observation that our body is actually composed of millions of cellular clocks and oscillators whose co-ordinated activity gives rise to pronounced daily, monthly, and seasonal rhythms in physiology and behaviour. An idea that is gaining favour is that our physical and mental well-being is probably determined by the appropriate phasing of these millions of cellular clocks with recurring, meaningful events in the environment.
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Affiliation(s)
- Hugh D Piggins
- School of Biological Sciences, University of Manchester, UK.
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