1
|
Millius A, Yamada RG, Fujishima H, Maeda K, Standley DM, Sumiyama K, Perrin D, Ueda HR. Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep. Proc Natl Acad Sci U S A 2023; 120:e2214636120. [PMID: 37769257 PMCID: PMC10556633 DOI: 10.1073/pnas.2214636120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
Many mammalian proteins have circadian cycles of production and degradation, and many of these rhythms are altered posttranscriptionally. We used ribosome profiling to examine posttranscriptional control of circadian rhythms by quantifying RNA translation in the liver over a 24-h period from circadian-entrained mice transferred to constant darkness conditions and by comparing ribosome binding levels to protein levels for 16 circadian proteins. We observed large differences in ribosome binding levels compared to protein levels, and we observed delays between peak ribosome binding and peak protein abundance. We found extensive binding of ribosomes to upstream open reading frames (uORFs) in circadian mRNAs, including the core clock gene Period2 (Per2). An increase in the number of uORFs in the 5'UTR was associated with a decrease in ribosome binding in the main coding sequence and a reduction in expression of synthetic reporter constructs. Mutation of the Per2 uORF increased luciferase and fluorescence reporter expression in 3T3 cells and increased luciferase expression in PER2:LUC MEF cells. Mutation of the Per2 uORF in mice increased Per2 mRNA expression, enhanced ribosome binding on Per2, and reduced total sleep time compared to that in wild-type mice. These results suggest that uORFs affect mRNA posttranscriptionally, which can impact physiological rhythms and sleep.
Collapse
Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Kazuhiko Maeda
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Daron M. Standley
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Kenta Sumiyama
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya464-8601, Japan
| | - Dimitri Perrin
- School of Computer Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
- Centre for Data Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| |
Collapse
|
2
|
Tone D, Ode KL, Zhang Q, Fujishima H, Yamada RG, Nagashima Y, Matsumoto K, Wen Z, Yoshida SY, Mitani TT, Arisato Y, Ohno RI, Ukai-Tadenuma M, Yoshida Garçon J, Kaneko M, Shi S, Ukai H, Miyamichi K, Okada T, Sumiyama K, Kiyonari H, Ueda HR. Distinct phosphorylation states of mammalian CaMKIIβ control the induction and maintenance of sleep. PLoS Biol 2022; 20:e3001813. [PMID: 36194579 PMCID: PMC9531794 DOI: 10.1371/journal.pbio.3001813] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
The reduced sleep duration previously observed in Camk2b knockout mice revealed a role for Ca2+/calmodulin-dependent protein kinase II (CaMKII)β as a sleep-promoting kinase. However, the underlying mechanism by which CaMKIIβ supports sleep regulation is largely unknown. Here, we demonstrate that activation or inhibition of CaMKIIβ can increase or decrease sleep duration in mice by almost 2-fold, supporting the role of CaMKIIβ as a core sleep regulator in mammals. Importantly, we show that this sleep regulation depends on the kinase activity of CaMKIIβ. A CaMKIIβ mutant mimicking the constitutive-active (auto)phosphorylation state promotes the transition from awake state to sleep state, while mutants mimicking subsequent multisite (auto)phosphorylation states suppress the transition from sleep state to awake state. These results suggest that the phosphorylation states of CaMKIIβ differently control sleep induction and maintenance processes, leading us to propose a "phosphorylation hypothesis of sleep" for the molecular control of sleep in mammals.
Collapse
Affiliation(s)
- Daisuke Tone
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Koji L. Ode
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Qianhui Zhang
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Yoshiki Nagashima
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Thermo Fisher Scientific K.K., Yokohama, Kanagawa, Japan
| | - Katsuhiko Matsumoto
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Zhiqing Wen
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shota Y. Yoshida
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Graduate school of Medicine, Osaka University, Suita, Osaka, Japan
| | - Tomoki T. Mitani
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Graduate school of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yuki Arisato
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Rei-ichiro Ohno
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Maki Ukai-Tadenuma
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Junko Yoshida Garçon
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo, Japan
| | - Shoi Shi
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hideki Ukai
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Kazunari Miyamichi
- Laboratory for Comparative Connections, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo, Japan
| | - Takashi Okada
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, the University of Tokyo, Minato-city, Tokyo, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail:
| |
Collapse
|
3
|
Abstract
Organoids are self-organizing in vitro 3D cultures that are histologically similar to a variety of human organs. A recent study by Rosselot et al (2021) shows that mature intestinal organoids possess species-specific circadian clocks similar to their respective in vivo context, suggesting organoids as promising platforms to study circadian medicine.
Collapse
Affiliation(s)
- Rikuhiro G Yamada
- Laboratory for Synthetic BiologyRIKEN Center for Biosystems Dynamics ResearchSuitaJapan
| | - Hiroki R Ueda
- Laboratory for Synthetic BiologyRIKEN Center for Biosystems Dynamics ResearchSuitaJapan,Department of Systems PharmacologyGraduate School of MedicineThe University of TokyoTokyoJapan
| |
Collapse
|
4
|
Mano T, Murata K, Kon K, Shimizu C, Ono H, Shi S, Yamada RG, Miyamichi K, Susaki EA, Touhara K, Ueda HR. CUBIC-Cloud provides an integrative computational framework toward community-driven whole-mouse-brain mapping. Cell Rep Methods 2021; 1:100038. [PMID: 35475238 PMCID: PMC9017177 DOI: 10.1016/j.crmeth.2021.100038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/17/2021] [Accepted: 05/20/2021] [Indexed: 01/18/2023]
Abstract
Recent advancements in tissue clearing technologies have offered unparalleled opportunities for researchers to explore the whole mouse brain at cellular resolution. With the expansion of this experimental technique, however, a scalable and easy-to-use computational tool is in demand to effectively analyze and integrate whole-brain mapping datasets. To that end, here we present CUBIC-Cloud, a cloud-based framework to quantify, visualize, and integrate mouse brain data. CUBIC-Cloud is a fully automated system where users can upload their whole-brain data, run analyses, and publish the results. We demonstrate the generality of CUBIC-Cloud by a variety of applications. First, we investigated the brain-wide distribution of five cell types. Second, we quantified Aβ plaque deposition in Alzheimer's disease model mouse brains. Third, we reconstructed a neuronal activity profile under LPS-induced inflammation by c-Fos immunostaining. Last, we show brain-wide connectivity mapping by pseudotyped rabies virus. Together, CUBIC-Cloud provides an integrative platform to advance scalable and collaborative whole-brain mapping.
Collapse
Affiliation(s)
- Tomoyuki Mano
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Ken Murata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuhiro Kon
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chika Shimizu
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Hiroaki Ono
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shoi Shi
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Kazunari Miyamichi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Etsuo A. Susaki
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroki R. Ueda
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
5
|
Niwa Y, Kanda GN, Yamada RG, Shi S, Sunagawa GA, Ukai-Tadenuma M, Fujishima H, Matsumoto N, Masumoto KH, Nagano M, Kasukawa T, Galloway J, Perrin D, Shigeyoshi Y, Ukai H, Kiyonari H, Sumiyama K, Ueda HR. Muscarinic Acetylcholine Receptors Chrm1 and Chrm3 Are Essential for REM Sleep. Cell Rep 2020; 24:2231-2247.e7. [PMID: 30157420 DOI: 10.1016/j.celrep.2018.07.082] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/03/2018] [Accepted: 07/25/2018] [Indexed: 01/30/2023] Open
Abstract
Sleep regulation involves interdependent signaling among specialized neurons in distributed brain regions. Although acetylcholine promotes wakefulness and rapid eye movement (REM) sleep, it is unclear whether the cholinergic pathway is essential (i.e., absolutely required) for REM sleep because of redundancy from neural circuits to molecules. First, we demonstrate that synaptic inhibition of TrkA+ cholinergic neurons causes a severe short-sleep phenotype and that sleep reduction is mostly attributable to a shortened sleep duration in the dark phase. Subsequent comprehensive knockout of acetylcholine receptor genes by the triple-target CRISPR method reveals that a similar short-sleep phenotype appears in the knockout of two Gq-type acetylcholine receptors Chrm1 and Chrm3. Strikingly, Chrm1 and Chrm3 double knockout chronically diminishes REM sleep to an almost undetectable level. These results suggest that muscarinic acetylcholine receptors, Chrm1 and Chrm3, are essential for REM sleep.
Collapse
Affiliation(s)
- Yasutaka Niwa
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; International Institute for Integrative Sleep Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Genki N Kanda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Rikuhiro G Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shoi Shi
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Genshiro A Sunagawa
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Maki Ukai-Tadenuma
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naomi Matsumoto
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Koh-Hei Masumoto
- Department of Anatomy and Neurobiology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osakasayama City, Osaka 589-8511, Japan; Center for Medical Science, International University of Health and Welfare, 2600-1 Kitakanemaru, Ohtawara, Tochigi 324-8501, Japan; Division of Neuroanatomy, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Mianmi-Kogushi, Ube, Yamaguchi 755-8505, Japan
| | - Mamoru Nagano
- Department of Anatomy and Neurobiology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osakasayama City, Osaka 589-8511, Japan
| | - Takeya Kasukawa
- Large Scale Data Managing Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - James Galloway
- School of Electrical Engineering and Computer Science, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Dimitri Perrin
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; School of Electrical Engineering and Computer Science, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Yasufumi Shigeyoshi
- Department of Anatomy and Neurobiology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osakasayama City, Osaka 589-8511, Japan
| | - Hideki Ukai
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroshi Kiyonari
- Animal Resource Development Unit and Genetic Engineering Team, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| |
Collapse
|
6
|
Abstract
Rapid-eye movement (REM) sleep is a paradoxical sleep state characterized by brain activity similar to wakefulness, rapid-eye-movement, and lack of muscle tone. REM sleep is a fundamental brain function, evolutionary conserved across species, including human, mouse, bird, and even reptiles. The physiological importance of REM sleep is highlighted by severe sleep disorders incurred by a failure in REM sleep regulation. Despite the intense interest in the mechanism of REM sleep regulation, the molecular machinery is largely left to be investigated. In models of REM sleep regulation, acetylcholine has been a pivotal component. However, even newly emerged techniques such as pharmacogenetics and optogenetics have not fully clarified the function of acetylcholine either at the cellular level or neural-circuit level. Recently, we discovered that the Gq type muscarinic acetylcholine receptor genes, Chrm1 and Chrm3, are essential for REM sleep. In this review, we develop the perspective of current knowledge on REM sleep from a molecular viewpoint. This should be a starting point to clarify the molecular and cellular machinery underlying REM sleep regulation and will provide insights to explore physiological functions of REM sleep and its pathological roles in REM-sleep-related disorders such as depression, PTSD, and neurodegenerative diseases.
Collapse
Affiliation(s)
- Rikuhiro G Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.,Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
7
|
Honda KK, Kawamoto T, Ueda HR, Nakashima A, Ueshima T, Yamada RG, Nishimura M, Oda R, Nakamura S, Kojima T, Noshiro M, Fujimoto K, Hashimoto S, Kato Y. Different circadian expression of major matrix-related genes in various types of cartilage: modulation by light-dark conditions. J Biochem 2013; 154:373-81. [PMID: 23940085 DOI: 10.1093/jb/mvt068] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We screened circadian-regulated genes in rat cartilage by using a DNA microarray analysis. In rib growth-plate cartilage, numerous genes showed statistically significant circadian mRNA expression under both 12:12 h light-dark and constant darkness conditions. Type II collagen and aggrecan genes--along with several genes essential for post-translational modifications of collagen and aggrecan, including prolyl 4-hydroxylase 1, lysyl oxidase, lysyl oxidase-like 2 and 3'-phosphoadenosine 5'-phosphosulphate synthase 2--showed the same circadian phase. In addition, the mRNA level of SOX9, a master transcription factor for the synthesis of type II collagen and aggrecan, has a similar phase of circadian rhythms. The circadian expression of the matrix-related genes may be critical in the development and the growth of various cartilages, because similar circadian expression of the matrix-related genes was observed in hip joint cartilage. However, the circadian phase of the major matrix-related genes in the rib permanent cartilage was almost the converse of that in the rib growth-plate cartilage under light-dark conditions. We also found that half of the oscillating genes had conserved clock-regulatory elements, indicating contribution of the elements to the clock outputs. These findings suggest that the synthesis of the cartilage matrix macromolecules is controlled by cell-autonomous clocks depending upon the in vivo location of cartilage.
Collapse
Affiliation(s)
- Kiyomasa K Honda
- Department of Dental and Medical Biochemistry, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima 734-8553; Laboratory for Systems Biology, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047; Department of Prosthetic Dentistry, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588; and Molecular Medicine Laboratories, Institute for Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Watanabe T, Suzuki T, Ishikawa A, Yokota Y, Ueda HR, Yamada RG, Tei H, Imai S, Tomida S, Kobayashi J, Naito E, Yasuo S, Nakao N, Namikawa T, Yoshimura T, Ebihara S. Genetic and molecular analysis of wild-derived arrhythmic mice. PLoS One 2009; 4:e4301. [PMID: 19173005 PMCID: PMC2628734 DOI: 10.1371/journal.pone.0004301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 12/03/2008] [Indexed: 11/18/2022] Open
Abstract
A new circadian variant was isolated by screening the intercross offspring of wild-caught mice (Mus musculus castaneus). This variant was characterized by an initial maintenance of damped oscillations and subsequent loss of rhythmicity after being transferred from light-dark (LD) cycles to constant darkness (DD). To map the genes responsible for the persistence of rhythmicity (circadian ratio) and the length of free-running period (tau), quantitative trait locus (QTL) analysis was performed using F(2) mice obtained from an F(1) cross between the circadian variant and C57BL/6J mice. As a result, a significant QTL with a main effect for circadian ratio (Arrhythmicity; Arrh-1) was mapped on Chromosome (Chr) 8. For tau, four significant QTLs, Short free-running period (Sfp-1) (Chr 1), Sfp-2 (Chr 6), Sfp-3 (Chr 8), Sfp-4 (Chr 11) were determined. An epistatic interaction was detected between Chr 3 (Arrh-2) and Chr 5 (Arrh-3). An in situ hybridization study of clock genes and mouse Period1::luciferase (mPer1::luc) real-time monitoring analysis in the suprachiasmatic nucleus (SCN) suggested that arrhythmicity in this variant might not be attributed to core circadian mechanisms in the SCN neurons. Our strategy using wild-derived variant mice may provide a novel opportunity to evaluate circadian and its related disorders in human that arise from the interaction between multiple variant genes.
Collapse
Affiliation(s)
- Tsuyoshi Watanabe
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tohru Suzuki
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Infectious Disease, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Akira Ishikawa
- Division of Applied Genetics and Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yuki Yokota
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hiroki R. Ueda
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, Hyogo, Japan
- Functional Genomics Subunit, Center for Developmental Biology, RIKEN, Hyogo, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, Hyogo, Japan
| | - Hajime Tei
- Research Group of Chronogenomics, Mitsubishi Kagaku Institute of Life Sciences, Tokyo, Japan
| | - Saki Imai
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shigeru Tomida
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Junya Kobayashi
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Emiko Naito
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shinobu Yasuo
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Nobuhiro Nakao
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takao Namikawa
- Division of Applied Genetics and Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takashi Yoshimura
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shizufumi Ebihara
- Division of Biomodeling, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- * E-mail: .
| |
Collapse
|
9
|
Matsumoto A, Ukai-Tadenuma M, Yamada RG, Houl J, Uno KD, Kasukawa T, Dauwalder B, Itoh TQ, Takahashi K, Ueda R, Hardin PE, Tanimura T, Ueda HR. A functional genomics strategy reveals clockwork orange as a transcriptional regulator in the Drosophila circadian clock. Genes Dev 2007; 21:1687-700. [PMID: 17578908 PMCID: PMC1899476 DOI: 10.1101/gad.1552207] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Drosophila circadian clock consists of integrated autoregulatory feedback loops, making the clock difficult to elucidate without comprehensively identifying the network components in vivo. Previous studies have adopted genome-wide screening for clock-controlled genes using high-density oligonucleotide arrays that identified hundreds of clock-controlled genes. In an attempt to identify the core clock genes among these candidates, we applied genome-wide functional screening using an RNA interference (RNAi) system in vivo. Here we report the identification of novel clock gene candidates including clockwork orange (cwo), a transcriptional repressor belonging to the basic helix-loop-helix ORANGE family. cwo is rhythmically expressed and directly regulated by CLK-CYC through canonical E-box sequences. A genome-wide search for its target genes using the Drosophila genome tiling array revealed that cwo forms its own negative feedback loop and directly suppresses the expression of other clock genes through the E-box sequence. Furthermore, this negative transcriptional feedback loop contributes to sustaining a high-amplitude circadian oscillation in vivo. Based on these results, we propose that the competition between cyclic CLK-CYC activity and the adjustable threshold imposed by CWO keeps E-box-mediated transcription within the controllable range of its activity, thereby rendering a Drosophila circadian clock capable of generating high-amplitude oscillation.
Collapse
Affiliation(s)
- Akira Matsumoto
- Center for Research and Advancement in Higher Education, Kyushu University, Ropponmatu, Fukuoka 810-8560, Japan
- E-MAIL ; FAX 81-92-726-4641
| | - Maki Ukai-Tadenuma
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Jerry Houl
- Department of Biology and Center for Research on Biological Clocks, Texas A&M University, College Station, Texas 77843, USA
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - Kenichiro D. Uno
- Functional Genomics Unit, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takeya Kasukawa
- Functional Genomics Unit, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Brigitte Dauwalder
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - Taichi Q. Itoh
- Department of Biology, Faculty of Science, Kyushu University, Ropponmatu, Fukuoka 810-8560, Japan
| | - Kuniaki Takahashi
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Ryu Ueda
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Paul E. Hardin
- Department of Biology and Center for Research on Biological Clocks, Texas A&M University, College Station, Texas 77843, USA
| | - Teiichi Tanimura
- Department of Biology, Faculty of Science, Kyushu University, Ropponmatu, Fukuoka 810-8560, Japan
| | - Hiroki R. Ueda
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Functional Genomics Unit, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Department of Bioscience, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Corresponding authors.E-MAIL ; FAX 81-78-306-3194
| |
Collapse
|
10
|
Kurimoto K, Yabuta Y, Ohinata Y, Ono Y, Uno KD, Yamada RG, Ueda HR, Saitou M. An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res 2006; 34:e42. [PMID: 16547197 PMCID: PMC1409679 DOI: 10.1093/nar/gkl050] [Citation(s) in RCA: 320] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A systems-level understanding of a small but essential population of cells in development or adulthood (e.g. somatic stem cells) requires accurate quantitative monitoring of genome-wide gene expression, ideally from single cells. We report here a strategy to globally amplify mRNAs from single cells for highly quantitative high-density oligonucleotide microarray analysis that combines a small number of directional PCR cycles with subsequent linear amplification. Using this strategy, both the representation of gene expression profiles and reproducibility between individual experiments are unambiguously improved from the original method, along with high coverage and accuracy. The immediate application of this method to single cells in the undifferentiated inner cell masses of mouse blastocysts at embryonic day (E) 3.5 revealed the presence of two populations of cells, one with primitive endoderm (PE) expression and the other with pluripotent epiblast-like gene expression. The genes expressed differentially between these two populations were well preserved in morphologically differentiated PE and epiblast in the embryos one day later (E4.5), demonstrating that the method successfully detects subtle but essential differences in gene expression at the single-cell level among seemingly homogeneous cell populations. This study provides a strategy to analyze biophysical events in medicine as well as in neural, stem cell and developmental biology, where small numbers of distinctive or diseased cells play critical roles.
Collapse
Affiliation(s)
- Kazuki Kurimoto
- Laboratory for Mammalian Germ Cell Biology, Center for Developmental Biology, RIKEN Kobe Institute2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yukihiro Yabuta
- Laboratory for Mammalian Germ Cell Biology, Center for Developmental Biology, RIKEN Kobe Institute2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasuhide Ohinata
- Laboratory for Mammalian Germ Cell Biology, Center for Developmental Biology, RIKEN Kobe Institute2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yukiko Ono
- Laboratory for Mammalian Germ Cell Biology, Center for Developmental Biology, RIKEN Kobe Institute2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Department of BioScience, Tokyo University of AgricultureSetagaya-ku, Tokyo 156-8502, Japan
| | - Kenichiro D. Uno
- Functional Genomics Subunit, Center for Developmental Biology, RIKEN Kobe Institute2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN Kobe Institute2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hiroki R. Ueda
- Functional Genomics Subunit, Center for Developmental Biology, RIKEN Kobe Institute2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory for Systems Biology, Center for Developmental Biology, RIKEN Kobe Institute2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Mitinori Saitou
- Laboratory for Mammalian Germ Cell Biology, Center for Developmental Biology, RIKEN Kobe Institute2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto UniversityOiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
- To whom correspondence should be addressed. Tel: +81 78 306 3376; Fax: +81 78 306 3377;
| |
Collapse
|
11
|
Sato TK, Yamada RG, Ukai H, Baggs JE, Miraglia LJ, Kobayashi TJ, Welsh DK, Kay SA, Ueda HR, Hogenesch JB. Feedback repression is required for mammalian circadian clock function. Nat Genet 2006; 38:312-9. [PMID: 16474406 PMCID: PMC1994933 DOI: 10.1038/ng1745] [Citation(s) in RCA: 280] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Accepted: 01/09/2006] [Indexed: 11/09/2022]
Abstract
Direct evidence for the requirement of transcriptional feedback repression in circadian clock function has been elusive. Here, we developed a molecular genetic screen in mammalian cells to identify mutants of the circadian transcriptional activators CLOCK and BMAL1, which were uncoupled from CRYPTOCHROME (CRY)-mediated transcriptional repression. Notably, mutations in the PER-ARNT-SIM domain of CLOCK and the C terminus of BMAL1 resulted in synergistic insensitivity through reduced physical interactions with CRY. Coexpression of these mutant proteins in cultured fibroblasts caused arrhythmic phenotypes in population and single-cell assays. These data demonstrate that CRY-mediated repression of the CLOCK/BMAL1 complex activity is required for maintenance of circadian rhythmicity and provide formal proof that transcriptional feedback is required for mammalian clock function.
Collapse
Affiliation(s)
- Trey K Sato
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|