1
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Kim SH, Haynes KA. Reader-Effectors as Actuators of Epigenome Editing. Methods Mol Biol 2024; 2842:103-127. [PMID: 39012592 DOI: 10.1007/978-1-0716-4051-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Epigenome editing applications are gaining broader use for targeted transcriptional control as more enzymes with diverse chromatin-modifying functions are being incorporated into fusion proteins. Development of these fusion proteins, called epigenome editors, has outpaced the study of proteins that interact with edited chromatin. One type of protein that acts downstream of chromatin editing is the reader-effector, which bridges epigenetic marks with biological effects like gene regulation. As the name suggests, a reader-effector protein is generally composed of a reader domain and an effector domain. Reader domains directly bind epigenetic marks, while effector domains often recruit protein complexes that mediate transcription, chromatin remodeling, and DNA repair. In this chapter, we discuss the role of reader-effectors in driving the outputs of epigenome editing and highlight instances where abnormal and context-specific reader-effectors might impair the effects of epigenome editing. Lastly, we discuss how engineered reader-effectors may complement the epigenome editing toolbox to achieve robust and reliable gene regulation.
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Affiliation(s)
- Seong Hu Kim
- Wallace H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA.
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2
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Lam C. Design and mathematical analysis of activating transcriptional amplifiers that enable modular temporal control in synthetic juxtacrine circuits. Synth Syst Biotechnol 2023; 8:654-672. [PMID: 37868744 PMCID: PMC10587772 DOI: 10.1016/j.synbio.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/09/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
The ability to control mammalian cells such that they self-organize or enact therapeutic effects as desired has incredible implications. Not only would it further our understanding of native processes such as development and the immune response, but it would also have powerful applications in medical fields such as regenerative medicine and immunotherapy. This control is typically obtained by synthetic circuits that use synthetic receptors, but control remains incomplete. The synthetic juxtacrine receptors (SJRs) are widely used as they are fully modular and enable spatial control, but they have limited gene expression amplification and temporal control. As these are integral facets to cell control, I therefore designed transcription factor based amplifiers that amplify gene expression and enable unidirectional temporal control by prolonging duration of target gene expression. Using a validated in silico framework for SJR signaling, I combined these amplifiers with SJRs and show that these SJR amplifier circuits can direct spatiotemporal patterning and improve the quality of self-organization. I then show that these circuits can improve chimeric antigen receptor (CAR) T cell tumor killing against various heterogenous antigen expression tumors. These amplifiers are flexible tools that improve control over SJR based circuits with both basic and therapeutic applications.
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3
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Martin RM, de Almeida MR, Gameiro E, de Almeida SF. Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics. Nucleic Acids Res 2023; 51:11010-11023. [PMID: 37819055 PMCID: PMC10639055 DOI: 10.1093/nar/gkad812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
We have developed RHINO, a genetically encoded sensor that selectively binds RNA:DNA hybrids enabling live-cell imaging of cellular R-loops. RHINO comprises a tandem array of three copies of the RNA:DNA hybrid binding domain of human RNase H1 connected by optimized linker segments and fused to a fluorescent protein. This tool allows the measurement of R-loop abundance and dynamics in live cells with high specificity and sensitivity. Using RHINO, we provide a kinetic framework for R-loops at nucleoli, telomeres and protein-coding genes. Our findings demonstrate that R-loop dynamics vary significantly across these regions, potentially reflecting the distinct roles R-loops play in different chromosomal contexts. RHINO is a powerful tool for investigating the role of R-loops in cellular processes and their contribution to disease development and progression.
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Affiliation(s)
- Robert M Martin
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Madalena R de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Eduardo Gameiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
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4
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Yang L, Zhang P, Wang Y, Hu G, Guo W, Gu X, Pu L. Plant synthetic epigenomic engineering for crop improvement. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2191-2204. [PMID: 35851940 DOI: 10.1007/s11427-021-2131-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Efforts have been directed to redesign crops with increased yield, stress adaptability, and nutritional value through synthetic biology-the application of engineering principles to biology. A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops, thus heralding the promise of "synthetic epigenetics." In this review, we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques, epigenetic editing, and deep learning-driven predictive tools can rapidly extend these insights. We also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.
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Affiliation(s)
- Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guihua Hu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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5
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Gyenis L, Menyhart D, Cruise ES, Jurcic K, Roffey SE, Chai DB, Trifoi F, Fess SR, Desormeaux PJ, Núñez de Villavicencio Díaz T, Rabalski AJ, Zukowski SA, Turowec JP, Pittock P, Lajoie G, Litchfield DW. Chemical Genetic Validation of CSNK2 Substrates Using an Inhibitor-Resistant Mutant in Combination with Triple SILAC Quantitative Phosphoproteomics. Front Mol Biosci 2022; 9:909711. [PMID: 35755813 PMCID: PMC9225150 DOI: 10.3389/fmolb.2022.909711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Casein Kinase 2 (CSNK2) is an extremely pleiotropic, ubiquitously expressed protein kinase involved in the regulation of numerous key biological processes. Mapping the CSNK2-dependent phosphoproteome is necessary for better characterization of its fundamental role in cellular signalling. While ATP-competitive inhibitors have enabled the identification of many putative kinase substrates, compounds targeting the highly conserved ATP-binding pocket often exhibit off-target effects limiting their utility for definitive kinase-substrate assignment. To overcome this limitation, we devised a strategy combining chemical genetics and quantitative phosphoproteomics to identify and validate CSNK2 substrates. We engineered U2OS cells expressing exogenous wild type CSNK2A1 (WT) or a triple mutant (TM, V66A/H160D/I174A) with substitutions at residues important for inhibitor binding. These cells were treated with CX-4945, a clinical-stage inhibitor of CSNK2, and analyzed using large-scale triple SILAC (Stable Isotope Labelling of Amino Acids in Cell Culture) quantitative phosphoproteomics. In contrast to wild-type CSNK2A1, CSNK2A1-TM retained activity in the presence of CX-4945 enabling identification and validation of several CSNK2 substrates on the basis of their increased phosphorylation in cells expressing CSNK2A1-TM. Based on high conservation within the kinase family, we expect that this strategy can be broadly adapted for identification of other kinase-substrate relationships.
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Affiliation(s)
- Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Daniel Menyhart
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Edward S Cruise
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Kristina Jurcic
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Scott E Roffey
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Darren B Chai
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Flaviu Trifoi
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Sam R Fess
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Paul J Desormeaux
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | | | - Adam J Rabalski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Stephanie A Zukowski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Jacob P Turowec
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Paula Pittock
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Gilles Lajoie
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - David W Litchfield
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
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6
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Franklin KA, Shields CE, Haynes KA. Beyond the marks: reader-effectors as drivers of epigenetics and chromatin engineering. Trends Biochem Sci 2022; 47:417-432. [PMID: 35427480 PMCID: PMC9074927 DOI: 10.1016/j.tibs.2022.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
Chromatin is a system of proteins and DNA that regulates chromosome organization and gene expression in eukaryotes. Essential features that support these processes include biochemical marks on histones and DNA, 'writer' enzymes that generate or remove these marks and proteins that translate the marks into transcriptional regulation: reader-effectors. Here, we review recent studies that reveal how reader-effectors drive chromatin-mediated processes. Advances in proteomics and epigenomics have accelerated the discovery of chromatin marks and their correlation with gene states, outpacing our understanding of the corresponding reader-effectors. Therefore, we summarize the current state of knowledge and open questions about how reader-effectors impact cellular function and human disease and discuss how synthetic biology can deepen our knowledge of reader-effector activity.
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Affiliation(s)
- Kierra A Franklin
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Cara E Shields
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA.
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7
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Yamaguchi N. The epigenetic mechanisms regulating floral hub genes and their potential for manipulation. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1277-1287. [PMID: 34752611 DOI: 10.1093/jxb/erab490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Gene regulatory networks formed by transcription factors play essential roles in the regulation of gene expression during plant reproductive development. These networks integrate endogenous, phytohormonal, and environmental cues. Molecular genetic, biochemical, and chemical analyses performed mainly in Arabidopsis have identified network hub genes and revealed the contributions of individual components to these networks. Here, I outline current understanding of key epigenetic regulatory circuits identified by research on plant reproduction, and highlight significant recent examples of genetic engineering and chemical applications to modulate the epigenetic regulation of gene expression. Furthermore, I discuss future prospects for applying basic plant science to engineer useful floral traits in a predictable manner as well as the potential side effects.
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Affiliation(s)
- Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
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8
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Pei WD, Zhang Y, Yin TL, Yu Y. Epigenome editing by CRISPR/Cas9 in clinical settings: possibilities and challenges. Brief Funct Genomics 2021; 19:215-228. [PMID: 31819946 DOI: 10.1093/bfgp/elz035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/24/2019] [Accepted: 11/05/2019] [Indexed: 12/26/2022] Open
Abstract
Epigenome editing is a promising approach for both basic research and clinical application. With the convergence of techniques from different fields, regulating gene expression artificially becomes possible. From a clinical point of view, targeted epigenome editing by CRISPR/Cas9 of disease-related genes offers novel therapeutic avenues for many diseases. In this review, we summarize the EpiEffectors used in epigenome editing by CRISPR/Cas9, current applications of epigenome editing and progress made in this field. Moreover, application challenges such as off-target effects, inefficient delivery, stability and immunogenicity are discussed. In conclusion, epigenome editing by CRISPR/Cas9 has broad prospects in the clinic, and future work will promote the application of this technology.
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Affiliation(s)
- Wen-Di Pei
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191 China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, PR China
| | - Tai-Lang Yin
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Yang Yu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191 China.,Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing, 100191 China
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9
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Di Blasi R, Blyuss O, Timms JF, Conole D, Ceroni F, Whitwell HJ. Non-Histone Protein Methylation: Biological Significance and Bioengineering Potential. ACS Chem Biol 2021; 16:238-250. [PMID: 33411495 DOI: 10.1021/acschembio.0c00771] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein methylation is a key post-translational modification whose effects on gene expression have been intensively studied over the last two decades. Recently, renewed interest in non-histone protein methylation has gained momentum for its role in regulating important cellular processes and the activity of many proteins, including transcription factors, enzymes, and structural complexes. The extensive and dynamic role that protein methylation plays within the cell also highlights its potential for bioengineering applications. Indeed, while synthetic histone protein methylation has been extensively used to engineer gene expression, engineering of non-histone protein methylation has not been fully explored yet. Here, we report the latest findings, highlighting how non-histone protein methylation is fundamental for certain cellular functions and is implicated in disease, and review recent efforts in the engineering of protein methylation.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, U.K
- Imperial College Centre for Synthetic Biology, Imperial College London, London, U.K
| | - Oleg Blyuss
- School of Physics, Astronomy and Mathematics, University of Hertfordshire, Hatfield, U.K
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - John F Timms
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, U.K
| | - Daniel Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, U.K
| | - Francesca Ceroni
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, U.K
- Imperial College Centre for Synthetic Biology, Imperial College London, London, U.K
| | - Harry J Whitwell
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, U.K
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Sir Alexander Fleming Building, Imperial College London, Hammersmith Campus, London, SW7 2AZ, U.K
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10
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Wells CI, Drewry DH, Pickett JE, Tjaden A, Krämer A, Müller S, Gyenis L, Menyhart D, Litchfield DW, Knapp S, Axtman AD. Development of a potent and selective chemical probe for the pleiotropic kinase CK2. Cell Chem Biol 2021; 28:546-558.e10. [PMID: 33484635 DOI: 10.1016/j.chembiol.2020.12.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/30/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
Abstract
Building on the pyrazolopyrimidine CK2 (casein kinase 2) inhibitor scaffold, we designed a small targeted library. Through comprehensive evaluation of inhibitor selectivity, we identified inhibitor 24 (SGC-CK2-1) as a highly potent and cell-active CK2 chemical probe with exclusive selectivity for both human CK2 isoforms. Remarkably, despite years of research pointing to CK2 as a key driver in cancer, our chemical probe did not elicit a broad antiproliferative phenotype in >90% of >140 cell lines when tested in dose-response. While many publications have reported CK2 functions, CK2 biology is complex and an available high-quality chemical tool such as SGC-CK2-1 will be indispensable in deciphering the relationships between CK2 function and phenotypes.
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Affiliation(s)
- Carrow I Wells
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC 27599, USA
| | - David H Drewry
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC 27599, USA
| | - Julie E Pickett
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC 27599, USA
| | - Amelie Tjaden
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchman Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchman Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchman Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Daniel Menyhart
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - David W Litchfield
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada; Department of Oncology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchman Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Alison D Axtman
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC 27599, USA.
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11
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Optogenetic control of mRNA localization and translation in live cells. Nat Cell Biol 2020; 22:341-352. [PMID: 32066905 DOI: 10.1038/s41556-020-0468-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
Despite efforts to visualize the spatio-temporal dynamics of single messenger RNAs, the ability to precisely control their function has lagged. This study presents an optogenetic approach for manipulating the localization and translation of specific mRNAs by trapping them in clusters. This clustering greatly amplified reporter signals, enabling endogenous RNA-protein interactions to be clearly visualized in single cells. Functionally, this sequestration reduced the ability of mRNAs to access ribosomes, markedly attenuating protein synthesis. A spatio-temporally resolved analysis indicated that sequestration of endogenous β-actin mRNA attenuated cell motility through the regulation of focal-adhesion dynamics. These results suggest a mechanism highlighting the indispensable role of newly synthesized β-actin protein for efficient cell migration. This platform may be broadly applicable for use in investigating the spatio-temporal activities of specific mRNAs in various biological processes.
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12
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Mathur M, Kim CM, Munro SA, Rudina SS, Sawyer EM, Smolke CD. Programmable mutually exclusive alternative splicing for generating RNA and protein diversity. Nat Commun 2019; 10:2673. [PMID: 31209208 PMCID: PMC6572816 DOI: 10.1038/s41467-019-10403-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/01/2019] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing performs a central role in expanding genomic coding capacity and proteomic diversity. However, programming of splicing patterns in engineered biological systems remains underused. Synthetic approaches thus far have predominantly focused on controlling expression of a single protein through alternative splicing. Here, we describe a modular and extensible platform for regulating four programmable exons that undergo a mutually exclusive alternative splicing event to generate multiple functionally-distinct proteins. We present an intron framework that enforces the mutual exclusivity of two internal exons and demonstrate a graded series of consensus sequence elements of varying strengths that set the ratio of two mutually exclusive isoforms. We apply this framework to program the DNA-binding domains of modular transcription factors to differentially control downstream gene activation. This splicing platform advances an approach for generating diverse isoforms and can ultimately be applied to program modular proteins and increase coding capacity of synthetic biological systems.
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Affiliation(s)
- Melina Mathur
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Cameron M Kim
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Sarah A Munro
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Joint Initiative for Metrology in Biology, Stanford, CA, 94305, USA
- Genome-scale Measurements Group, National Institute of Standards and Technology, Stanford, CA, 94305, USA
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Shireen S Rudina
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Eric M Sawyer
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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13
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Engineering Epigenetic Regulation Using Synthetic Read-Write Modules. Cell 2018; 176:227-238.e20. [PMID: 30528434 DOI: 10.1016/j.cell.2018.11.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 08/31/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022]
Abstract
Chemical modifications to DNA and histone proteins are involved in epigenetic programs underlying cellular differentiation and development. Regulatory networks involving molecular writers and readers of chromatin marks are thought to control these programs. Guided by this common principle, we established an orthogonal epigenetic regulatory system in mammalian cells using N6-methyladenine (m6A), a DNA modification not commonly found in metazoan epigenomes. Our system utilizes synthetic factors that write and read m6A and consequently recruit transcriptional regulators to control reporter loci. Inspired by models of chromatin spreading and epigenetic inheritance, we used our system and mathematical models to construct regulatory circuits that induce m6A-dependent transcriptional states, promote their spatial propagation, and maintain epigenetic memory of the states. These minimal circuits were able to program epigenetic functions de novo, conceptually validating "read-write" architectures. This work provides a toolkit for investigating models of epigenetic regulation and encoding additional layers of epigenetic information in cells.
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14
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Yamatsugu K, Kawashima SA, Kanai M. Leading approaches in synthetic epigenetics for novel therapeutic strategies. Curr Opin Chem Biol 2018; 46:10-17. [DOI: 10.1016/j.cbpa.2018.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/12/2018] [Accepted: 03/17/2018] [Indexed: 12/20/2022]
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15
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Olney KC, Nyer DB, Vargas DA, Wilson Sayres MA, Haynes KA. The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells. BMC SYSTEMS BIOLOGY 2018; 12:83. [PMID: 30253781 PMCID: PMC6156859 DOI: 10.1186/s12918-018-0608-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023]
Abstract
Background Mounting evidence from genome-wide studies of cancer shows that chromatin-mediated epigenetic silencing at large cohorts of genes is strongly linked to a poor prognosis. This mechanism is thought to prevent cell differentiation and enable evasion of the immune system. Drugging the cancer epigenome with small molecule inhibitors to release silenced genes from the repressed state has emerged as a powerful approach for cancer research and drug development. Targets of these inhibitors include chromatin-modifying enzymes that can acquire drug-resistant mutations. In order to directly target a generally conserved feature, elevated trimethyl-lysine 27 on histone H3 (H3K27me3), we developed the Polycomb-based Transcription Factor (PcTF), a fusion activator that targets methyl-histone marks via its N-terminal H3K27me3-binding motif, and co-regulates sets of silenced genes. Results Here, we report transcriptome profiling analyses of PcTF-treated breast cancer model cell lines. We identified a set of 19 PcTF-upregulated genes, or PUGs, that were consistent across three distinct breast cancer cell lines. These genes are associated with the interferon response pathway. Conclusions Our results demonstrate for the first time a chromatin-mediated interferon-related transcriptional response driven by an engineered fusion protein that physically links repressive histone marks with active transcription. Electronic supplementary material The online version of this article (10.1186/s12918-018-0608-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kimberly C Olney
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, 85287-4501, AZ, USA
| | - David B Nyer
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA
| | - Daniel A Vargas
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, 85287-4501, AZ, USA.,Center for Evolution and Medicine, Arizona State University, 427 E Tyler Mall, Tempe, 85287-1701, AZ, USA
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA.
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16
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Tekel SJ, Barrett C, Vargas D, Haynes KA. Design, Construction, and Validation of Histone-Binding Effectors in Vitro and in Cells. Biochemistry 2018; 57:4707-4716. [PMID: 29791133 DOI: 10.1021/acs.biochem.8b00327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chromatin is a system of nuclear proteins and nucleic acids that plays a pivotal role in gene expression and cell behavior and is therefore the subject of intense study for cell development and cancer research. Biochemistry, crystallography, and reverse genetics have elucidated the macromolecular interactions that drive chromatin regulation. One of the central mechanisms is the recognition of post-translational modifications (PTMs) on histone proteins by a family of nuclear proteins known as "readers". This knowledge has launched a wave of activity around the rational design of proteins that interact with histone PTMs. Useful molecular tools have emerged from this work, enabling researchers to probe and manipulate chromatin states in live cells. Chromatin-based proteins represent a vast design space that remains underexplored. Therefore, we have developed a rapid prototyping platform to identify engineered fusion proteins that bind histone PTMs in vitro and regulate genes near the same histone PTMs in living cells. We have used our system to build gene activators with strong avidity for the gene silencing-associated histone PTM H3K27me3. Here, we describe procedures and data for cell-free production of fluorescently tagged fusion proteins, enzyme-linked immunosorbent assay-based measurement of histone PTM binding, and a live cell assay to demonstrate that the fusion proteins modulate transcriptional activation at a site that carries the target histone PTM. This pipeline will be useful for synthetic biologists who are interested in designing novel histone PTM-binding actuators and probes.
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Affiliation(s)
- Stefan J Tekel
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Cassandra Barrett
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Daniel Vargas
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
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17
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Tekel SJ, Vargas DA, Song L, LaBaer J, Caplan MR, Haynes KA. Tandem Histone-Binding Domains Enhance the Activity of a Synthetic Chromatin Effector. ACS Synth Biol 2018; 7:842-852. [PMID: 29429329 DOI: 10.1021/acssynbio.7b00281] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fusion proteins that specifically interact with biochemical marks on chromosomes represent a new class of synthetic transcriptional regulators that decode cell state information rather than DNA sequences. In multicellular organisms, information relevant to cell state, tissue identity, and oncogenesis is often encoded as biochemical modifications of histones, which are bound to DNA in eukaryotic nuclei and regulate gene expression states. We have previously reported the development and validation of the "polycomb-based transcription factor" (PcTF), a fusion protein that recognizes histone modifications through a protein-protein interaction between its polycomb chromodomain (PCD) motif and trimethylated lysine 27 of histone H3 (H3K27me3) at genomic sites. We demonstrated that PcTF activates genes at methyl-histone-enriched loci in cancer-derived cell lines. However, PcTF induces modest activation of a methyl-histone associated reporter compared to a DNA-binding activator. Therefore, we modified PcTF to enhance its binding avidity. Here, we demonstrate the activity of a modified regulator called Pc2TF, which has two tandem copies of the H3K27me3-binding PCD at the N-terminus. Pc2TF has a smaller apparent dissociation constant value in vitro and shows enhanced gene activation in HEK293 cells compared to PcTF. These results provide compelling evidence that the intrinsic histone-binding activity of the PCD motif can be used to tune the activity of synthetic histone-binding transcriptional regulators.
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Affiliation(s)
- Stefan J. Tekel
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287-9709, United States
| | - Daniel A. Vargas
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287-9709, United States
| | - Lusheng Song
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287-9709, United States
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287-9709, United States
| | - Michael R. Caplan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287-9709, United States
| | - Karmella A. Haynes
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287-9709, United States
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18
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Engineered Multivalent Sensors to Detect Coexisting Histone Modifications in Living Stem Cells. Cell Chem Biol 2018; 25:51-56.e6. [DOI: 10.1016/j.chembiol.2017.10.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/18/2017] [Accepted: 10/18/2017] [Indexed: 02/08/2023]
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19
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Tekel SJ, Haynes KA. Molecular structures guide the engineering of chromatin. Nucleic Acids Res 2017; 45:7555-7570. [PMID: 28609787 PMCID: PMC5570049 DOI: 10.1093/nar/gkx531] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/07/2017] [Indexed: 12/28/2022] Open
Abstract
Chromatin is a system of proteins, RNA, and DNA that interact with each other to organize and regulate genetic information within eukaryotic nuclei. Chromatin proteins carry out essential functions: packing DNA during cell division, partitioning DNA into sub-regions within the nucleus, and controlling levels of gene expression. There is a growing interest in manipulating chromatin dynamics for applications in medicine and agriculture. Progress in this area requires the identification of design rules for the chromatin system. Here, we focus on the relationship between the physical structure and function of chromatin proteins. We discuss key research that has elucidated the intrinsic properties of chromatin proteins and how this information informs design rules for synthetic systems. Recent work demonstrates that chromatin-derived peptide motifs are portable and in some cases can be customized to alter their function. Finally, we present a workflow for fusion protein design and discuss best practices for engineering chromatin to assist scientists in advancing the field of synthetic epigenetics.
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Affiliation(s)
- Stefan J Tekel
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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20
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Daer RM, Cutts JP, Brafman DA, Haynes KA. The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells. ACS Synth Biol 2017; 6:428-438. [PMID: 27783893 DOI: 10.1021/acssynbio.5b00299] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to efficiently edit eukaryotic genomes, it is critical to test the impact of chromatin dynamics on CRISPR/Cas9 function and develop strategies to adapt the system to eukaryotic contexts. So far, research has extensively characterized the relationship between the CRISPR endonuclease Cas9 and the composition of the RNA-DNA duplex that mediates the system's precision. Evidence suggests that chromatin modifications and DNA packaging can block eukaryotic genome editing by custom-built DNA endonucleases like Cas9; however, the underlying mechanism of Cas9 inhibition is unclear. Here, we demonstrate that closed, gene-silencing-associated chromatin is a mechanism for the interference of Cas9-mediated DNA editing. Our assays use a transgenic cell line with a drug-inducible switch to control chromatin states (open and closed) at a single genomic locus. We show that closed chromatin inhibits binding and editing at specific target sites and that artificial reversal of the silenced state restores editing efficiency. These results provide new insights to improve Cas9-mediated editing in human and other mammalian cells.
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Affiliation(s)
- René M. Daer
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - Josh P. Cutts
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - David A. Brafman
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - Karmella A. Haynes
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
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21
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Nyer DB, Daer RM, Vargas D, Hom C, Haynes KA. Regulation of cancer epigenomes with a histone-binding synthetic transcription factor. NPJ Genom Med 2017; 2. [PMID: 28919981 PMCID: PMC5600530 DOI: 10.1038/s41525-016-0002-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin proteins have expanded the mammalian synthetic biology toolbox by enabling control of active and silenced states at endogenous genes. Others have reported synthetic proteins that bind DNA and regulate genes by altering chromatin marks, such as histone modifications. Previously, we reported the first synthetic transcriptional activator, the "Polycomb-based transcription factor" (PcTF) that reads histone modifications through a protein-protein interaction between the polycomb chromodomain motif and trimethylated lysine 27 of histone H3 (H3K27me3). Here, we describe the genome-wide behavior of the polycomb-based transcription factor fusion protein. Transcriptome and chromatin profiling revealed several polycomb-based transcription factor-sensitive promoter regions marked by distal H3K27me3 and proximal fusion protein binding. These results illuminate a mechanism in which polycomb-based transcription factor interactions bridge epigenomic marks with the transcription initiation complex at target genes. In three cancer-derived human cell lines tested here, some target genes encode developmental regulators and tumor suppressors. Thus, the polycomb-based transcription factor represents a powerful new fusion protein-based method for cancer research and treatment where silencing marks are translated into direct gene activation.
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Affiliation(s)
- David B Nyer
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Box 9709, Tempe, AZ 85287, USA
| | - Rene M Daer
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Box 9709, Tempe, AZ 85287, USA
| | - Daniel Vargas
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Box 9709, Tempe, AZ 85287, USA
| | - Caroline Hom
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Box 9709, Tempe, AZ 85287, USA
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Box 9709, Tempe, AZ 85287, USA
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22
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Mathur M, Xiang JS, Smolke CD. Mammalian synthetic biology for studying the cell. J Cell Biol 2016; 216:73-82. [PMID: 27932576 PMCID: PMC5223614 DOI: 10.1083/jcb.201611002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/25/2022] Open
Abstract
Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology.
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Affiliation(s)
- Melina Mathur
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Joy S Xiang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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23
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Abstract
We are entering an era of epigenome engineering. The precision manipulation of chromatin and epigenetic modifications provides new ways to interrogate their influence on genome and cell function and to harness these changes for applications. We review the design and state of epigenome editing tools, highlighting the unique regulatory properties afforded by these systems.
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Affiliation(s)
- Minhee Park
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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24
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Wei KY, Smolke CD. Engineering dynamic cell cycle control with synthetic small molecule-responsive RNA devices. J Biol Eng 2015; 9:21. [PMID: 26594238 PMCID: PMC4654890 DOI: 10.1186/s13036-015-0019-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/27/2015] [Indexed: 01/08/2023] Open
Abstract
Background The cell cycle plays a key role in human health and disease, including development and cancer. The ability to easily and reversibly control the mammalian cell cycle could mean improved cellular reprogramming, better tools for studying cancer, more efficient gene therapy, and improved heterologous protein production for medical or industrial applications. Results We engineered RNA-based control devices to provide specific and modular control of gene expression in response to exogenous inputs in living cells. Specifically, we identified key regulatory nodes that arrest U2-OS cells in the G0/1 or G2/M phases of the cycle. We then optimized the most promising key regulators and showed that, when these optimized regulators are placed under the control of a ribozyme switch, we can inducibly and reversibly arrest up to ~80 % of a cellular population in a chosen phase of the cell cycle. Characterization of the reliability of the final cell cycle controllers revealed that the G0/1 control device functions reproducibly over multiple experiments over several weeks. Conclusions To our knowledge, this is the first time synthetic RNA devices have been used to control the mammalian cell cycle. This RNA platform represents a general class of synthetic biology tools for modular, dynamic, and multi-output control over mammalian cells. Electronic supplementary material The online version of this article (doi:10.1186/s13036-015-0019-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathy Y Wei
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA 94305 USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA 94305 USA
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25
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Kabadi AM, Thakore PI, Vockley CM, Ousterout DG, Gibson TM, Guilak F, Reddy TE, Gersbach CA. Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain. ACS Synth Biol 2015; 4:689-99. [PMID: 25494287 PMCID: PMC4475448 DOI: 10.1021/sb500322u] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Genetic reprogramming holds great potential for disease modeling, drug screening, and regenerative medicine. Genetic reprogramming of mammalian cells is typically achieved by forced expression of natural transcription factors that control master gene networks and cell lineage specification. However, in many instances, the natural transcription factors do not induce a sufficiently robust response to completely reprogram cell phenotype. In this study, we demonstrate that protein engineering of the master transcription factor MyoD can enhance the conversion of human dermal fibroblasts and adult stem cells to a skeletal myocyte phenotype. Fusion of potent transcriptional activation domains to MyoD led to increased myogenic gene expression, myofiber formation, cell fusion, and global reprogramming of the myogenic gene network. This work supports a general strategy for synthetically enhancing the direct conversion between cell types that can be applied in both synthetic biology and regenerative medicine.
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Affiliation(s)
| | | | | | | | | | - Farshid Guilak
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | | | - Charles A. Gersbach
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
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26
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Abou El Hassan M, Huang K, Eswara MBK, Zhao M, Song L, Yu T, Liu Y, Liu JC, McCurdy S, Ma A, Wither J, Jin J, Zacksenhaus E, Wrana JL, Bremner R. Cancer Cells Hijack PRC2 to Modify Multiple Cytokine Pathways. PLoS One 2015; 10:e0126466. [PMID: 26030458 PMCID: PMC4450877 DOI: 10.1371/journal.pone.0126466] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/03/2015] [Indexed: 01/21/2023] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is an epigenetic regulator induced in many cancers. It is thought to drive tumorigenesis by repressing division, stemness, and/or developmental regulators. Cancers evade immune detection, and diverse immune regulators are perturbed in different tumors. It is unclear how such cell-specific effects are coordinated. Here, we show a profound and cancer-selective role for PRC2 in repressing multiple cytokine pathways. We find that PRC2 represses hundreds of IFNγ stimulated genes (ISGs), cytokines and cytokine receptors. This target repertoire is significantly broadened in cancer vs non-cancer cells, and is distinct in different cancer types. PRC2 is therefore a higher order regulator of the immune program in cancer cells. Inhibiting PRC2 with either RNAi or EZH2 inhibitors activates cytokine/cytokine receptor promoters marked with bivalent H3K27me3/H3K4me3 chromatin, and augments responsiveness to diverse immune signals. PRC2 inhibition rescues immune gene induction even in the absence of SWI/SNF, a tumor suppressor defective in ~20% of human cancers. This novel PRC2 function in tumor cells could profoundly impact the mechanism of action and efficacy of EZH2 inhibitors in cancer treatment.
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Affiliation(s)
| | - Katherine Huang
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Manoja B. K. Eswara
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Michael Zhao
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Lan Song
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Tao Yu
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Yu Liu
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Jeffrey C. Liu
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Sean McCurdy
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
- Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Anqi Ma
- Department of Structural and Chemical Biology, Icahn School of Medicine, Mt Sinai Hospital, New York, New York, United States of America
| | - Joan Wither
- Toronto Western Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Jian Jin
- Department of Structural and Chemical Biology, Icahn School of Medicine, Mt Sinai Hospital, New York, New York, United States of America
| | - Eldad Zacksenhaus
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey L. Wrana
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
- Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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27
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Risca VI, Greenleaf WJ. Unraveling the 3D genome: genomics tools for multiscale exploration. Trends Genet 2015; 31:357-72. [PMID: 25887733 DOI: 10.1016/j.tig.2015.03.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/16/2015] [Accepted: 03/24/2015] [Indexed: 12/15/2022]
Abstract
A decade of rapid method development has begun to yield exciting insights into the 3D architecture of the metazoan genome and the roles it may play in regulating transcription. Here we review core methods and new tools in the modern genomicist's toolbox at three length scales, ranging from single base pairs to megabase-scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation.
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Affiliation(s)
- Viviana I Risca
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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28
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Abstract
As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including 'epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication.
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29
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Attention deficits and hyperactivity-impulsivity: what have we learned, what next? Dev Psychopathol 2014; 25:1489-503. [PMID: 24342852 DOI: 10.1017/s0954579413000734] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The domains of self-regulation, self-control, executive function, inattention, and impulsivity cut across broad swathes of normal and abnormal development. Attention-deficit/hyperactivity disorder is a common syndrome that encompasses a portion of these domains. In the past 25 years research on attention-deficit/hyperactivity disorder has been characterized by dramatic advances in genetic, neural, and neuropsychological description of the syndrome as well as clarification of its multidimensional phenotypic structure. The limited clinical applicability of these research findings poses the primary challenge for the next generation. It is likely that clinical breakthroughs will require further refinement in describing heterogeneity or clinical/biological subgroups, renewed focus on the environment in the form of etiological events as well as psychosocial contexts of development, and integration of both with biological understanding.
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30
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Pick H, Kilic S, Fierz B. Engineering chromatin states: chemical and synthetic biology approaches to investigate histone modification function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:644-56. [PMID: 24768924 DOI: 10.1016/j.bbagrm.2014.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/26/2014] [Accepted: 04/16/2014] [Indexed: 01/11/2023]
Abstract
Patterns of histone post-translational modifications (PTMs) and DNA modifications establish a landscape of chromatin states with regulatory impact on gene expression, cell differentiation and development. These diverse modifications are read out by effector protein complexes, which ultimately determine their functional outcome by modulating the activity state of underlying genes. From genome-wide studies employing high-throughput ChIP-Seq methods as well as proteomic mass spectrometry studies, a large number of PTMs are known and their coexistence patterns and associations with genomic regions have been mapped in a large number of different cell types. Conversely, the molecular interplay between chromatin effector proteins and modified chromatin regions as well as their resulting biological output is less well understood on a molecular level. Within the last decade a host of chemical approaches has been developed with the goal to produce synthetic chromatin with a defined arrangement of PTMs. These methods now permit systematic functional studies of individual histone and DNA modifications, and additionally provide a discovery platform to identify further interacting nuclear proteins. Complementary chemical- and synthetic-biology methods have emerged to directly observe and modulate the modification landscape in living cells and to readily probe the effect of altered PTM patterns on biological processes. Herein, we review current methodologies allowing chemical and synthetic biological engineering of distinct chromatin states in vitro and in vivo with the aim of obtaining a molecular understanding of histone and DNA modification function. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Horst Pick
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Sinan Kilic
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Beat Fierz
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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31
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Aguilar CA, Craighead HG. Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics. NATURE NANOTECHNOLOGY 2013; 8:709-18. [PMID: 24091454 PMCID: PMC4072028 DOI: 10.1038/nnano.2013.195] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/28/2013] [Indexed: 05/05/2023]
Abstract
Deoxyribonucleic acid (DNA) is the blueprint on which life is based and transmitted, but the way in which chromatin - a dynamic complex of nucleic acids and proteins - is packaged and behaves in the cellular nucleus has only begun to be investigated. Epigenetic modifications sit 'on top of' the genome and affect how DNA is compacted into chromatin and transcribed into ribonucleic acid (RNA). The packaging and modifications around the genome have been shown to exert significant influence on cellular behaviour and, in turn, human development and disease. However, conventional techniques for studying epigenetic or conformational modifications of chromosomes have inherent limitations and, therefore, new methods based on micro- and nanoscale devices have been sought. Here, we review the development of these devices and explore their use in the study of DNA modifications, chromatin modifications and higher-order chromatin structures.
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Affiliation(s)
- Carlos A. Aguilar
- Massachusetts Institute of Technology - Lincoln Laboratory, 244 Wood St., Lexington, MA 02127
| | - Harold G. Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
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Wang YH, Wei KY, Smolke CD. Synthetic biology: advancing the design of diverse genetic systems. Annu Rev Chem Biomol Eng 2013; 4:69-102. [PMID: 23413816 DOI: 10.1146/annurev-chembioeng-061312-103351] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A major objective of synthetic biology is to make the process of designing genetically encoded biological systems more systematic, predictable, robust, scalable, and efficient. Examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from simple genetic switches to search-and-destroy systems. While significant advances in DNA synthesis capabilities support the construction of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Thus, while synthetic biology offers much promise in developing systems to address challenges faced in the fields of manufacturing, environment and sustainability, and health and medicine, the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems.
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Affiliation(s)
- Yen-Hsiang Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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Abstract
Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell environment and enhance human health. Synthetic biology devices contribute not only to improve our understanding of disease mechanisms, but also provide novel diagnostic tools. Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs. The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already pointed out during a lecture delivered at Kuwait University in 2005. Of two approaches to synthetic biology, top-down and bottom-up, the latter is more relevant to the development of personalized medicines as it provides more flexibility in constructing a partially synthetic cell from basic building blocks for a desired task.
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Affiliation(s)
- K K Jain
- PharmaBiotech, Basel, Switzerland.
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Innovation at the intersection of synthetic and systems biology. Curr Opin Biotechnol 2012; 23:712-7. [DOI: 10.1016/j.copbio.2011.12.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 12/20/2011] [Indexed: 01/06/2023]
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Benenson Y. Biomolecular computing systems: principles, progress and potential. Nat Rev Genet 2012; 13:455-68. [PMID: 22688678 DOI: 10.1038/nrg3197] [Citation(s) in RCA: 219] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing.
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Affiliation(s)
- Yaakov Benenson
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Mattenstrasse 26, 4058 Basel, Switzerland.
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Nigg JT. Future directions in ADHD etiology research. JOURNAL OF CLINICAL CHILD AND ADOLESCENT PSYCHOLOGY 2012; 41:524-33. [PMID: 22642834 DOI: 10.1080/15374416.2012.686870] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Reviews salient emerging themes in the scientific literature related to identifying etiology and pathophysiology of ADHD. While bypassing the need for new treatment research, the review highlights three themes. First, recognition of the epigenetic effects is expected to revitalize the search for and mapping of early environmental influences on the development of ADHD. Second, neurobiological findings will have limited impact if not examined in the context of significant race and cultural variation in ADHD-related developmental processes, and in the context of rapidly changing social and technological contexts of children's development worldwide. Third, further examination of the phenotype and characterization of its dimensional and categorical structure remains a major need. Overall, the coming decades of etiology research on ADHD will be expected to capitalize on new scientific tools. The hope in the field is that new insights into fundamental prevention can emerge.
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Affiliation(s)
- Joel T Nigg
- Department of Psychiatry, Oregon Health & Science University, Portland, OR 97239, USA.
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Ceroni F, Furini S, Stefan A, Hochkoeppler A, Giordano E. A synthetic post-transcriptional controller to explore the modular design of gene circuits. ACS Synth Biol 2012; 1:163-71. [PMID: 23651154 DOI: 10.1021/sb200021s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly from modular parts is an efficient approach for creating new devices in Synthetic Biology. In the "bottom-up" designing strategy, modular parts are characterized in advance, and then mathematical modeling is used to predict the outcome of the final device. A prerequisite for bottom-up design is that the biological parts behave in a modular way when assembled together. We designed a new synthetic device for post-transcriptional regulation of gene expression and tested if the outcome of the device could be described from the features of its components. Modular parts showed unpredictable behavior when assembled in different complex circuits. This prevented a modular description of the device that was possible only under specific conditions. Our findings shed doubts into the feasibility of a pure bottom-up approach in synthetic biology, highlighting the urgency for new strategies for the rational design of synthetic devices.
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Affiliation(s)
- Francesca Ceroni
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy
| | - Simone Furini
- Department of Medical Surgery and Bioengineering, University of Siena, I-53100 Siena, Italy
| | - Alessandra Stefan
- Department of Industrial Chemistry, University of Bologna, Viale Risorgimento 4, I-40136
Bologna, Italy
- CSGI, University of Firenze, Via della Lastruccia 3, I-50019
Sesto Fiorentino, Italy
| | - Alejandro Hochkoeppler
- Department of Industrial Chemistry, University of Bologna, Viale Risorgimento 4, I-40136
Bologna, Italy
- CSGI, University of Firenze, Via della Lastruccia 3, I-50019
Sesto Fiorentino, Italy
| | - Emanuele Giordano
- Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy
- Department of Biochemistry “G. Moruzzi”, University of Bologna, I-40126 Bologna, Italy
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Abstract
In living cells, DNA is packaged along with protein and RNA into chromatin. Chemical modifications to nucleotides and histone proteins are added, removed and recognized by multi-functional molecular complexes. Here I define a new computational model, in which chromatin modifications are information units that can be written onto a one-dimensional string of nucleosomes, analogous to the symbols written onto cells of a Turing machine tape, and chromatin-modifying complexes are modeled as read-write rules that operate on a finite set of adjacent nucleosomes. I illustrate the use of this “chromatin computer” to solve an instance of the Hamiltonian path problem. I prove that chromatin computers are computationally universal – and therefore more powerful than the logic circuits often used to model transcription factor control of gene expression. Features of biological chromatin provide a rich instruction set for efficient computation of nontrivial algorithms in biological time scales. Modeling chromatin as a computer shifts how we think about chromatin function, suggests new approaches to medical intervention, and lays the groundwork for the engineering of a new class of biological computing machines.
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Affiliation(s)
- Barbara Bryant
- Bioinformatics Department, Constellation Pharmaceuticals, Cambridge, Massachusetts, United States of America.
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Abstract
The chromatin organization modifier domain (chromodomain) was first identified as a motif associated with chromatin silencing in Drosophila. There is growing evidence that chromodomains are evolutionary conserved across different eukaryotic species to control diverse aspects of epigenetic regulation. Although originally reported as histone H3 methyllysine readers, the chromodomain functions have now expanded to recognition of other histone and non-histone partners as well as interaction with nucleic acids. Chromodomain binding to a diverse group of targets is mediated by a conserved substructure called the chromobox homology region. This motif can be used to predict methyllysine binding and distinguish chromodomains from related Tudor "Royal" family members. In this review, we discuss and classify various chromodomains according to their context, structure and the mechanism of target recognition.
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Affiliation(s)
- Bartlomiej J Blus
- Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL, USA
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