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      The core circadian component, Bmal1, is maintained in the pineal gland of old killifish brain

      research-article
      1 , 3 , 1 , 2 , , 1 , 3 , 4 , ∗∗
      iScience
      Elsevier
      Biological Sciences, Physiology, Molecular Biology, Chronobiology

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          Summary

          Circadian rhythm is altered during aging, although the underlying molecular mechanisms remain largely unknown. Here, we used the turquoise killifish as a short-lived vertebrate model to examine the effects of aging on the major circadian network comprising the four mammalian clock protein homologs, Bmal1, Clockb, Cry1b, and Per3, which are highly conserved in the killifish with 50%–85% amino acid sequence identity to their human counterparts. The amplitude of circadian rhythm was smaller in old fish (14 weeks) than in young fish (6 weeks). In old fish brain, the Bmal1 protein level was significantly downregulated. However, the Bmal1 interaction with Clockb and chromatin binding of Bmal1 to its downstream target promoters were retained. Furthermore, Bmal1 was relatively well maintained in the pineal gland compared with other regions of the old fish brain. The results suggest that the circadian clock system in the killifish becomes spatially confined to the pineal gland upon aging.

          Graphical Abstract

          Highlights

          • The amplitude of free-running circadian rhythms decreases during aging in killifish

          • Core clock genes are highly conserved in the turquoise killifish genome

          • Bmal1 protein expression decreases in whole brain tissue with aging

          • Bmal1 expression is relatively well maintained in the pineal gland with aging

          Abstract

          Biological Sciences; Physiology; Molecular Biology; Chronobiology

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          Most cited references59

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          Coordinated transcription of key pathways in the mouse by the circadian clock.

          In mammals, circadian control of physiology and behavior is driven by a master pacemaker located in the suprachiasmatic nuclei (SCN) of the hypothalamus. We have used gene expression profiling to identify cycling transcripts in the SCN and in the liver. Our analysis revealed approximately 650 cycling transcripts and showed that the majority of these were specific to either the SCN or the liver. Genetic and genomic analysis suggests that a relatively small number of output genes are directly regulated by core oscillator components. Major processes regulated by the SCN and liver were found to be under circadian regulation. Importantly, rate-limiting steps in these various pathways were key sites of circadian control, highlighting the fundamental role that circadian clocks play in cellular and organismal physiology.
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            Transcriptional architecture and chromatin landscape of the core circadian clock in mammals.

            The mammalian circadian clock involves a transcriptional feed back loop in which CLOCK and BMAL1 activate the Period and Cryptochrome genes, which then feedback and repress their own transcription. We have interrogated the transcriptional architecture of the circadian transcriptional regulatory loop on a genome scale in mouse liver and find a stereotyped, time-dependent pattern of transcription factor binding, RNA polymerase II (RNAPII) recruitment, RNA expression, and chromatin states. We find that the circadian transcriptional cycle of the clock consists of three distinct phases: a poised state, a coordinated de novo transcriptional activation state, and a repressed state. Only 22% of messenger RNA (mRNA) cycling genes are driven by de novo transcription, suggesting that both transcriptional and posttranscriptional mechanisms underlie the mammalian circadian clock. We also find that circadian modulation of RNAPII recruitment and chromatin remodeling occurs on a genome-wide scale far greater than that seen previously by gene expression profiling.
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              A circadian gene expression atlas in mammals: implications for biology and medicine.

              To characterize the role of the circadian clock in mouse physiology and behavior, we used RNA-seq and DNA arrays to quantify the transcriptomes of 12 mouse organs over time. We found 43% of all protein coding genes showed circadian rhythms in transcription somewhere in the body, largely in an organ-specific manner. In most organs, we noticed the expression of many oscillating genes peaked during transcriptional "rush hours" preceding dawn and dusk. Looking at the genomic landscape of rhythmic genes, we saw that they clustered together, were longer, and had more spliceforms than nonoscillating genes. Systems-level analysis revealed intricate rhythmic orchestration of gene pathways throughout the body. We also found oscillations in the expression of more than 1,000 known and novel noncoding RNAs (ncRNAs). Supporting their potential role in mediating clock function, ncRNAs conserved between mouse and human showed rhythmic expression in similar proportions as protein coding genes. Importantly, we also found that the majority of best-selling drugs and World Health Organization essential medicines directly target the products of rhythmic genes. Many of these drugs have short half-lives and may benefit from timed dosage. In sum, this study highlights critical, systemic, and surprising roles of the mammalian circadian clock and provides a blueprint for advancement in chronotherapy.
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                Author and article information

                Contributors
                Journal
                iScience
                iScience
                iScience
                Elsevier
                2589-0042
                09 December 2020
                22 January 2021
                09 December 2020
                : 24
                : 1
                : 101905
                Affiliations
                [1 ]Center for Plant Aging Research, Institute for Basic Science, Daegu, 42988, Republic of Korea
                Author notes
                []Corresponding author nam@ 123456dgist.ac.kr
                [∗∗ ]Corresponding author yumikim@ 123456ibs.re.kr
                [2]

                Present address: Department of New Biology, DGIST, Daegu, 42988, Republic of Korea

                [3]

                These authors contributed equally

                [4]

                Lead contact

                Article
                S2589-0042(20)31102-0 101905
                10.1016/j.isci.2020.101905
                7770606
                33385110
                06957888-3cca-4597-9226-1519493c59b9
                © 2020 The Author(s)

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 20 April 2020
                : 5 October 2020
                : 3 December 2020
                Categories
                Article

                biological sciences,physiology,molecular biology,chronobiology

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