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Isomura A, Kageyama R. Ultradian oscillations and pulses: coordinating cellular responses and cell fate decisions. Development 2014; 141:3627-36. [PMID: 25249457 PMCID: PMC4197574 DOI: 10.1242/dev.104497] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Biological clocks play key roles in organismal development, homeostasis and function. In recent years, much work has focused on circadian clocks, but emerging studies have highlighted the existence of ultradian oscillators – those with a much shorter periodicity than 24 h. Accumulating evidence, together with recently developed optogenetic approaches, suggests that such ultradian oscillators play important roles during cell fate decisions, and analyzing the functional links between ultradian oscillation and cell fate determination will contribute to a deeper understanding of the design principle of developing embryos. In this Review, we discuss the mechanisms of ultradian oscillatory dynamics and introduce examples of ultradian oscillators in various biological contexts. We also discuss how optogenetic technology has been used to elucidate the biological significance of ultradian oscillations.
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Affiliation(s)
- Akihiro Isomura
- Institute for Virus Research, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (CREST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ryoichiro Kageyama
- Institute for Virus Research, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan Japan Science and Technology Agency, Core Research for Evolutional Science and Technology (CREST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan World Premier International Research Initiative-Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
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203
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Deng F, Chen X, Liao Z, Yan Z, Wang Z, Deng Y, Zhang Q, Zhang Z, Ye J, Qiao M, Li R, Denduluri S, Wang J, Wei Q, Li M, Geng N, Zhao L, Zhou G, Zhang P, Luu HH, Haydon RC, Reid RR, Yang T, He TC. A simplified and versatile system for the simultaneous expression of multiple siRNAs in mammalian cells using Gibson DNA Assembly. PLoS One 2014; 9:e113064. [PMID: 25398142 PMCID: PMC4232585 DOI: 10.1371/journal.pone.0113064] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/18/2014] [Indexed: 01/01/2023] Open
Abstract
RNA interference (RNAi) denotes sequence-specific mRNA degradation induced by short interfering double-stranded RNA (siRNA) and has become a revolutionary tool for functional annotation of mammalian genes, as well as for development of novel therapeutics. The practical applications of RNAi are usually achieved by expressing short hairpin RNAs (shRNAs) or siRNAs in cells. However, a major technical challenge is to simultaneously express multiple siRNAs to silence one or more genes. We previously developed pSOS system, in which siRNA duplexes are made from oligo templates driven by opposing U6 and H1 promoters. While effective, it is not equipped to express multiple siRNAs in a single vector. Gibson DNA Assembly (GDA) is an in vitro recombination system that has the capacity to assemble multiple overlapping DNA molecules in a single isothermal step. Here, we developed a GDA-based pSOK assembly system for constructing single vectors that express multiple siRNA sites. The assembly fragments were generated by PCR amplifications from the U6-H1 template vector pB2B. GDA assembly specificity was conferred by the overlapping unique siRNA sequences of insert fragments. To prove the technical feasibility, we constructed pSOK vectors that contain four siRNA sites and three siRNA sites targeting human and mouse β-catenin, respectively. The assembly reactions were efficient, and candidate clones were readily identified by PCR screening. Multiple β-catenin siRNAs effectively silenced endogenous β-catenin expression, inhibited Wnt3A-induced β-catenin/Tcf4 reporter activity and expression of Wnt/β-catenin downstream genes. Silencing β-catenin in mesenchymal stem cells inhibited Wnt3A-induced early osteogenic differentiation and significantly diminished synergistic osteogenic activity between BMP9 and Wnt3A in vitro and in vivo. These findings demonstrate that the GDA-based pSOK system has been proven simplistic, effective and versatile for simultaneous expression of multiple siRNAs. Thus, the reported pSOK system should be a valuable tool for gene function studies and development of novel therapeutics.
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Affiliation(s)
- Fang Deng
- Department of Cell Biology, Third Military Medical University, Chongqing, 400038, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
| | - Xiang Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
| | - Zhan Liao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Department of Orthopaedic Surgery, the Affiliated Xiang-Ya Hospital of Central South University, Changsha, 410008, China
| | - Zhengjian Yan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, 400016, China
| | - Zhongliang Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, 400016, China
| | - Youlin Deng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, 400016, China
| | - Qian Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, 400016, China
| | - Zhonglin Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Department of Surgery, the Affiliated Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jixing Ye
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- School of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Min Qiao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Department of Orthopaedic Surgery, the Affiliated Xiang-Ya Hospital of Central South University, Changsha, 410008, China
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, 400016, China
| | - Ruifang Li
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Department of Surgery, the Affiliated Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Sahitya Denduluri
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
| | - Jing Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, 400016, China
| | - Qiang Wei
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, 400016, China
| | - Melissa Li
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
| | - Nisha Geng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
| | - Lianggong Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Department of Orthopaedic Surgery, the Second Affiliated Hospital of Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Guolin Zhou
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
| | - Penghui Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, 400016, China
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
| | - Russell R. Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- The Laboratory of Craniofacial Biology, Department of Surgery, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
| | - Tian Yang
- Department of Cell Biology, Third Military Medical University, Chongqing, 400038, China
- * E-mail: (TCH); (TY)
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, United States of America
- Department of Orthopaedic Surgery, the Affiliated Xiang-Ya Hospital of Central South University, Changsha, 410008, China
- * E-mail: (TCH); (TY)
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204
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Abstract
There have been considerable advances in uncovering the complex genetic mechanisms that underlie nervous system disease pathogenesis, particularly with the advent of exome and whole genome sequencing techniques. The emerging field of epigenetics is also providing further insights into these mechanisms. Here, we discuss our understanding of the interplay that exists between genetic and epigenetic mechanisms in these disorders, highlighting the nascent field of epigenetic epidemiology-which focuses on analyzing relationships between the epigenome and environmental exposures, development and aging, other health-related phenotypes, and disease states-and next-generation research tools (i.e., those leveraging synthetic and chemical biology and optogenetics) for examining precisely how epigenetic modifications at specific genomic sites affect disease processes.
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Affiliation(s)
- Irfan A. Qureshi
- />Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461 USA
| | - Mark F. Mehler
- />Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461 USA
- />Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Ruth L. and David S. Gottesman Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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206
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Fujita Y, Furushima R, Ohno H, Sagawa F, Inoue T. Cell-surface receptor control that depends on the size of a synthetic equilateral-triangular RNA-protein complex. Sci Rep 2014; 4:6422. [PMID: 25234354 PMCID: PMC4168268 DOI: 10.1038/srep06422] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/26/2014] [Indexed: 01/29/2023] Open
Abstract
A human cell surface displays many complex-structured receptors for receiving extracellular signals to regulate cellular functions. The use of precisely regulated signal-controls of the receptors could have possibilities beyond the current synthetic biology research that begins with the transfection of exogenous molecules to rewire intracellular circuits. However, by using a current ligand-receptor technique, the configuration of the artificially assembled cell surface molecules has been undefined because the assemblage is an unsystematic molecular clustering. Thus, the system bears improvements for precisely regulating receptor functions. We report here a new tool that refines stereochemically-controlled positioning of an assembled surface receptor. The tool performs rationally as an ON/OFF switch and is finely tunable so that a 3 to 6 nm size difference of the device precisely distinguishes the efficiency of apoptosis induced via cell-surface receptor binding. We discuss the potential use of the device in next-generation synthetic biology and in cell surface studies.
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Affiliation(s)
- Yoshihiko Fujita
- Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Rie Furushima
- 1] Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan [2]
| | - Hirohisa Ohno
- Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Fumihiko Sagawa
- Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tan Inoue
- Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
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209
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Torella JP, Lienert F, Boehm CR, Chen JH, Way JC, Silver PA. Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications. Nat Protoc 2014; 9:2075-89. [PMID: 25101822 DOI: 10.1038/nprot.2014.145] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies--for example, repeated terminator and insulator sequences--that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.
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Affiliation(s)
- Joseph P Torella
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Florian Lienert
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christian R Boehm
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jan-Hung Chen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey C Way
- 1] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. [2] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Pamela A Silver
- 1] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. [2] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
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