1
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Zimak J, Wagoner ZW, Nelson N, Waechtler B, Schlosser H, Kopecky M, Wu J, Zhao W. Epigenetic silencing directs expression heterogeneity of stably integrated multi-transcript unit genetic circuits. Sci Rep 2021; 11:2424. [PMID: 33510302 PMCID: PMC7844226 DOI: 10.1038/s41598-021-81975-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022] Open
Abstract
We report that epigenetic silencing causes the loss of function of multi-transcript unit constructs that are integrated using CRISPR-Cas9. Using a modular two color reporter system flanked by selection markers, we demonstrate that expression heterogeneity does not correlate with sequence alteration but instead correlates with chromosomal accessibility. We partially reverse this epigenetic silencing via small-molecule inhibitors of methylation and histone deacetylation. We then correlate each heterogeneously-expressing phenotype with its expected epigenetic state by employing ATAC-seq. The stability of each expression phenotype is reinforced by selective pressure, which indicates that ongoing epigenetic remodeling can occur for over one month after integration. Collectively, our data suggests that epigenetic silencing limits the utility of multi-transcript unit constructs that are integrated via double-strand repair pathways. Our research implies that mammalian synthetic biologists should consider localized epigenetic outcomes when designing complex genetic circuits.
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Affiliation(s)
- Jan Zimak
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Zachary W Wagoner
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Nellie Nelson
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Brooke Waechtler
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Hana Schlosser
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Morgan Kopecky
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jie Wu
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA. .,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA. .,Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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2
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Moisan S, Le Nabec A, Quillévéré A, Le Maréchal C, Férec C. Characterization of GJB2 cis-regulatory elements in the DFNB1 locus. Hum Genet 2019; 138:1275-1286. [PMID: 31586237 DOI: 10.1007/s00439-019-02068-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/29/2019] [Indexed: 11/28/2022]
Abstract
Although most disease-causing variants are within coding region of genes, it is now well established that cis-acting regulatory sequences, depending on 3D-chromatin organization, are required for temporal and spatial control of gene expression. Disruptions of such regulatory elements and/or chromatin conformation are likely to play a critical role in human genetic disease. Hence, recurrent monoallelic cases, who present the most common hereditary type of nonsyndromic hearing loss (i.e., DFNB1), carry only one identified pathogenic allele. This strongly suggests the presence of uncharacterized distal cis-acting elements in the missing allele. Here within, we study the spatial organization of a large DFNB1 locus encompassing the gap junction protein beta 2 (GJB2) gene, the most frequently mutated gene in this inherited hearing loss phenotype, with the chromosome conformation capture carbon copy technology (5C). By combining this approach with functional activity reporter assays and mapping of CCCTC-binding factor (CTCF) along the DFNB1 locus, we identify a novel set of cooperating GJB2 cis-acting elements and suggest a DFNB1 three-dimensional looping regulation model.
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Affiliation(s)
- Stéphanie Moisan
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU de Brest, Bretagne, Brest, France. .,Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France.
| | - Anaïs Le Nabec
- Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France
| | | | - Cédric Le Maréchal
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU de Brest, Bretagne, Brest, France.,Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU de Brest, Bretagne, Brest, France. .,Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France.
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3
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Abstract
Vast repertoires of unique antigen receptors are created in developing lymphocytes. The antigen receptor loci contain many variable (V), diversity (D), and joining (J) gene segments that are arrayed across very large genomic expanses and are joined to form variable-region exons. This process creates the potential for an organism to respond to large numbers of different pathogens. Here, we consider the underlying molecular mechanisms that favor some V genes for recombination prior to selection of the final antigen receptor repertoire. We discuss chromatin structures that form in antigen receptor loci to permit spatial proximity among the V, D, and J gene segments and how these relate to the generation of antigen receptor diversity.
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Affiliation(s)
- Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, 60612-7344, USA
| | - Ann J Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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4
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Singh K, Jha NK, Thakur A. Spatiotemporal chromatin dynamics - A telltale of circadian epigenetic gene regulation. Life Sci 2019; 221:377-391. [PMID: 30721705 DOI: 10.1016/j.lfs.2019.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/27/2019] [Accepted: 02/01/2019] [Indexed: 01/08/2023]
Abstract
Over the course of evolution, nature has forced organisms under selection pressure to hardwire an internal time keeping device that defines 24 h of a daily cycle of physiological and behavioral rhythms, known as circadian rhythms. At the cellular level, the cycle is governed by significant fractions of transcriptomes, which are under the control of transcriptional and translational feedback loop of clock genes. Intriguingly, this feedback loop is regulated at multiple stratums such as at the transcriptional and translational levels, which direct a cell towards producing a robust rhythm by sustaining the repeated stoichiometry of protein products. Moreover, with the advent of state of the art paradigms, epigenetic regulation of circadian rhythms has been becoming more evident at present time. Light-induced recurring fluctuations in chromatin acetylation concurrent with the binding of RNA Pol II and integration of miRNAs monitor the chromatin modifiers or clock genes expression to drive temporal rhythmicity. Furthermore, CLOCK protein intrinsic histone acetyl transferase activity, the interaction of CLOCK-BMAL-1 with HAT enzymes, and the involvement of many histone deacetylases also maintain the rhythmic protein profile. Additionally, the critical role of the rhythmic methylation pattern of clock genes in battery of cancer and metabolic disorders also defines its importance. Therefore, in this review, we focused on accumulating all the present data available on epigenetics and circadian rhythms. Interestingly, we also gathered evidence from the available literature pinpointing towards the dynamic nature of chromatin architecture governed by long and short-range regulatory elements DNA contacts arising daily, that was thought to be steady otherwise.
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Affiliation(s)
- Kunal Singh
- Department of Biotechnology, Noida Institute of Engineering & Technology (NIET), Greater Noida, India.
| | - Niraj Kumar Jha
- Department of Biotechnology, Noida Institute of Engineering & Technology (NIET), Greater Noida, India
| | - Abhimanyu Thakur
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, India
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5
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Mansilla-Soto J, Riviere I, Boulad F, Sadelain M. Cell and Gene Therapy for the Beta-Thalassemias: Advances and Prospects. Hum Gene Ther 2016; 27:295-304. [PMID: 27021486 DOI: 10.1089/hum.2016.037] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The beta-thalassemias are inherited anemias caused by mutations that severely reduce or abolish expression of the beta-globin gene. Like sickle cell disease, a related beta-globin gene disorder, they are ideal candidates for performing a genetic correction in patient hematopoietic stem cells (HSCs). The most advanced approach utilizes complex lentiviral vectors encoding the human β-globin gene, as first reported by May et al. in 2000. Considerable progress toward the clinical implementation of this approach has been made in the past five years, based on effective CD34+ cell mobilization and improved lentiviral vector manufacturing. Four trials have been initiated in the United States and Europe. Of 16 evaluable subjects, 6 have achieved transfusion independence. One of them developed a durable clonal expansion, which regressed after several years without transformation. Although globin lentiviral vectors have so far proven to be safe, this occurrence suggests that powerful insulators with robust enhancer-blocking activity will further enhance this approach. The combined discovery of Bcl11a-mediated γ-globin gene silencing and advances in gene editing are the foundations for another gene therapy approach, which aims to reactivate fetal hemoglobin (HbF) production. Its clinical translation will hinge on the safety and efficiency of gene targeting in true HSCs and the induction of sufficient levels of HbF to achieve transfusion independence. Altogether, the progress achieved over the past 15 years bodes well for finding a genetic cure for severe globin disorders in the next decade.
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Affiliation(s)
- Jorge Mansilla-Soto
- 1 Center for Cell Engineering, Memorial Sloan Kettering Cancer Center , New York, New York
| | - Isabelle Riviere
- 1 Center for Cell Engineering, Memorial Sloan Kettering Cancer Center , New York, New York
| | - Farid Boulad
- 1 Center for Cell Engineering, Memorial Sloan Kettering Cancer Center , New York, New York.,2 Department of Pediatrics, Memorial Sloan Kettering Cancer Center , New York, New York
| | - Michel Sadelain
- 1 Center for Cell Engineering, Memorial Sloan Kettering Cancer Center , New York, New York
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6
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Abstract
Genome function, replication, integrity, and propagation rely on the dynamic structural organization of chromosomes during the cell cycle. Genome folding in interphase provides regulatory segmentation for appropriate transcriptional control, facilitates ordered genome replication, and contributes to genome integrity by limiting illegitimate recombination. Here, we review recent high-resolution chromosome conformation capture and functional studies that have informed models of the spatial and regulatory compartmentalization of mammalian genomes, and discuss mechanistic models for how CTCF and cohesin control the functional architecture of mammalian chromosomes.
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Affiliation(s)
- Matthias Merkenschlager
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom;
| | - Elphège P Nora
- Gladstone Institute of Cardiovascular Disease, San Francisco, California 94158;
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7
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Vasquez PA, Hult C, Adalsteinsson D, Lawrimore J, Forest MG, Bloom K. Entropy gives rise to topologically associating domains. Nucleic Acids Res 2016; 44:5540-9. [PMID: 27257057 PMCID: PMC4937343 DOI: 10.1093/nar/gkw510] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 05/06/2016] [Accepted: 05/25/2016] [Indexed: 12/15/2022] Open
Abstract
We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape in the interphase nucleus. By investigating the genome as a dynamical system, we show that domains of high chromosomal interactions can arise solely from the polymeric nature of the chromosome arms due to entropic interactions and nuclear confinement. In this view, the role of bio-chemical related processes is to modulate and extend the duration of the interacting domains.
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Affiliation(s)
- Paula A Vasquez
- Department of Mathematics, University of South Carolina, Columbia, SC 29808, USA
| | - Caitlin Hult
- Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David Adalsteinsson
- Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Josh Lawrimore
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mark G Forest
- Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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8
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Ghirlando R, Felsenfeld G. Chromatin structure outside and inside the nucleus. Biopolymers 2016; 99:225-32. [PMID: 23348669 DOI: 10.1002/bip.22157] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/07/2012] [Indexed: 11/09/2022]
Abstract
The structure of the 30-nm chromatin fiber has provided, over the years, an important reference in chromatin studies. Originally derived from electron microscopic studies of soluble chromatin fibers released by restriction digestion, the gross structural features of such fragments have been supported by biophysical methods such as low angle X-ray and neutron scattering, sedimentation, light scattering, and electric dichroism. Electron microscopy and sedimentation velocity measurements demonstrated that reconstituted chromatin fibers, prepared from repeating arrays of high affinity nucleosome positioning sequences, retain the same overall features as observed for native chromatin fibers. It had been suggested that the 30 nm fiber might be the form assumed in vivo by transcriptionally silent chromatin, but individual gene or genome-wide studies of chromatin released from nuclei do not reveal any such simple correlation. Furthermore, even though the 30 nm fiber has been thought to represent an intermediate in the hierarchical folding of DNA into chromosomes, most analyses of chromatin folding within the nucleus do not detect any regular extended compact structures. However, there are important exceptions in chicken erythroid cell nuclei as well as in transcribed regions that form extended loops. Localized domains within the nucleus, either at the surface of chromosome domains or constrained as a specialized kind of constitutive heterochromatin by specific DNA binding proteins, may adopt 30 nm fiber-like structures.
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Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0540
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9
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Yang R, Kerschner JL, Gosalia N, Neems D, Gorsic LK, Safi A, Crawford GE, Kosak ST, Leir SH, Harris A. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Nucleic Acids Res 2016; 44:3082-94. [PMID: 26673704 PMCID: PMC4838340 DOI: 10.1093/nar/gkv1358] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/21/2015] [Accepted: 11/24/2015] [Indexed: 12/18/2022] Open
Abstract
Higher order chromatin structure establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms.CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing of cis-regulatory elements and siRNA-mediated depletion of architectural proteins to determine the relative contribution of structural elements and enhancers to the higher order structure and expression of the CFTR locus. We found the boundaries of the CFTRTAD are conserved among diverse cell types and are dependent on CTCF and cohesin complex. Removal of an upstream CTCF-binding insulator alters the interaction profile, but has little effect on CFTR expression. Within the TAD, intronic enhancers recruit cell-type selective transcription factors and deletion of a pivotal enhancer element dramatically decreases CFTR expression, but has minor effect on its 3D structure.
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Affiliation(s)
- Rui Yang
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jenny L Kerschner
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nehal Gosalia
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Daniel Neems
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lidija K Gorsic
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alexias Safi
- Division of Medical Genetics, Department of Pediatrics and Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27708, USA
| | - Gregory E Crawford
- Division of Medical Genetics, Department of Pediatrics and Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27708, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shih-Hsing Leir
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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10
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Fritz A, Barutcu AR, Martin-Buley L, vanWijnen AJ, Zaidi SK, Imbalzano AN, Lian JB, Stein JL, Stein GS. Chromosomes at Work: Organization of Chromosome Territories in the Interphase Nucleus. J Cell Biochem 2016; 117:9-19. [PMID: 26192137 PMCID: PMC4715719 DOI: 10.1002/jcb.25280] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 07/17/2015] [Indexed: 12/26/2022]
Abstract
The organization of interphase chromosomes in chromosome territories (CTs) was first proposed more than one hundred years ago. The introduction of increasingly sophisticated microscopic and molecular techniques, now provide complementary strategies for studying CTs in greater depth than ever before. Here we provide an overview of these strategies and how they are being used to elucidate CT interactions and the role of these dynamically regulated, nuclear-structure building blocks in directly supporting nuclear function in a physiologically responsive manner.
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Affiliation(s)
- Andrew Fritz
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - A. Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Lori Martin-Buley
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - André J. vanWijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Sayyed K. Zaidi
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jane B. Lian
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L. Stein
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Gary S. Stein
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
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11
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Maksimenko O, Gasanov NB, Georgiev P. Regulatory Elements in Vectors for Efficient Generation of Cell Lines Producing Target Proteins. Acta Naturae 2015; 7:15-26. [PMID: 26483956 PMCID: PMC4610161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To date, there has been an increasing number of drugs produced in mammalian cell cultures. In order to enhance the expression level and stability of target recombinant proteins in cell cultures, various regulatory elements with poorly studied mechanisms of action are used. In this review, we summarize and discuss the potential mechanisms of action of such regulatory elements.
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Affiliation(s)
- O. Maksimenko
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, 119334, Moscow, Russia
| | - N. B. Gasanov
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, 119334, Moscow, Russia
| | - P. Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str. 34/5, 119334, Moscow, Russia
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12
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Harraghy N, Calabrese D, Fisch I, Girod PA, LeFourn V, Regamey A, Mermod N. Epigenetic regulatory elements: Recent advances in understanding their mode of action and use for recombinant protein production in mammalian cells. Biotechnol J 2015; 10:967-78. [DOI: 10.1002/biot.201400649] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/20/2015] [Accepted: 05/20/2015] [Indexed: 12/18/2022]
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13
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Liu M, Maurano MT, Wang H, Qi H, Song CZ, Navas PA, Emery DW, Stamatoyannopoulos JA, Stamatoyannopoulos G. Genomic discovery of potent chromatin insulators for human gene therapy. Nat Biotechnol 2015; 33:198-203. [PMID: 25580597 DOI: 10.1038/nbt.3062] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 10/09/2014] [Indexed: 12/29/2022]
Abstract
Insertional mutagenesis and genotoxicity, which usually manifest as hematopoietic malignancy, represent major barriers to realizing the promise of gene therapy. Although insulator sequences that block transcriptional enhancers could mitigate or eliminate these risks, so far no human insulators with high functional potency have been identified. Here we describe a genomic approach for the identification of compact sequence elements that function as insulators. These elements are highly occupied by the insulator protein CTCF, are DNase I hypersensitive and represent only a small minority of the CTCF recognition sequences in the human genome. We show that the elements identified acted as potent enhancer blockers and substantially decreased the risk of tumor formation in a cancer-prone animal model. The elements are small, can be efficiently accommodated by viral vectors and have no detrimental effects on viral titers. The insulators we describe here are expected to increase the safety of gene therapy for genetic diseases.
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Affiliation(s)
- Mingdong Liu
- Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Matthew T Maurano
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Hao Wang
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Heyuan Qi
- 1] Division of Medical Genetics, University of Washington, Seattle, Washington, USA. [2] Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chao-Zhong Song
- 1] Division of Medical Genetics, University of Washington, Seattle, Washington, USA. [2] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Patrick A Navas
- Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - David W Emery
- 1] Division of Medical Genetics, University of Washington, Seattle, Washington, USA. [2] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - John A Stamatoyannopoulos
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington, USA. [2] Department of Medicine, University of Washington, Seattle, Washington, USA
| | - George Stamatoyannopoulos
- 1] Division of Medical Genetics, University of Washington, Seattle, Washington, USA. [2] Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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14
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Fritz AJ, Stojkovic B, Ding H, Xu J, Bhattacharya S, Berezney R. Cell type specific alterations in interchromosomal networks across the cell cycle. PLoS Comput Biol 2014; 10:e1003857. [PMID: 25275626 PMCID: PMC4183423 DOI: 10.1371/journal.pcbi.1003857] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/16/2014] [Indexed: 11/18/2022] Open
Abstract
The interchromosomal organization of a subset of human chromosomes (#1, 4, 11, 12, 16, 17, and 18) was examined in G1 and S phase of human WI38 lung fibroblast and MCF10A breast epithelial cells. Radial positioning of the chromosome territories (CTs) was independent of gene density, but size dependent. While no changes in radial positioning during the cell cycle were detected, there were stage-specific differences between cell types. Each CT was in close proximity (interaction) with a similar number of other CT except the gene rich CT17 which had significantly more interactions. Furthermore, CT17 was a member of the highest pairwise CT combinations with multiple interactions. Major differences were detected in the pairwise interaction profiles of MCF10A versus WI38 including cell cycle alterations from G1 to S. These alterations in interaction profiles were subdivided into five types: overall increase, overall decrease, switching from 1 to ≥2 interactions, vice versa, or no change. A global data mining program termed the chromatic median determined the most probable overall association network for the entire subset of CT. This probabilistic interchromosomal network was nearly completely different between the two cell lines. It was also strikingly altered across the cell cycle in MCF10A, but only slightly in WI38. We conclude that CT undergo multiple and preferred interactions with other CT in the nucleus and form preferred -albeit probabilistic- interchromosomal networks. This network of interactions is altered across the cell cycle and between cell types. It is intriguing to consider the relationship of these alterations to the corresponding changes in the gene expression program across the cell cycle and in different cell types.
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Affiliation(s)
- Andrew J. Fritz
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Branislav Stojkovic
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Hu Ding
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Jinhui Xu
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Sambit Bhattacharya
- Department of Computer Sciences, Fayetteville State University, Fayetteville, North Carolina, United States of America
| | - Ronald Berezney
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York, United States of America
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15
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Girardot M, Feil R, Llères D. Epigenetic deregulation of genomic imprinting in humans: causal mechanisms and clinical implications. Epigenomics 2013; 5:715-28. [DOI: 10.2217/epi.13.66] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian genes controlled by genomic imprinting play important roles in development and diverse postnatal processes. A growing number of congenital disorders have been linked to genomic imprinting. Each of these is caused by perturbed gene expression at one principal imprinted domain. Some imprinting disorders, including the Prader–Willi and Angelman syndromes, are caused almost exclusively by genetic mutations. In several others, including the Beckwith–Wiedemann and Silver–Russell growth syndromes, and transient neonatal diabetes mellitus, imprinted expression is perturbed mostly by epigenetic alterations at ‘imprinting control regions’ and at other specific regulatory sequences. In a minority of these patients, DNA methylation is altered at multiple imprinted loci, suggesting that common trans-acting factors are affected. Here, we review the epimutations involved in congenital imprinting disorders and the associated clinical features. Trans-acting factors known to be causally involved are discussed and other trans-acting factors that are potentially implicated are also presented.
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Affiliation(s)
- Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
| | - David Llères
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
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16
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Aguilar-Arnal L, Hakim O, Patel VR, Baldi P, Hager GL, Sassone-Corsi P. Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nat Struct Mol Biol 2013; 20:1206-13. [PMID: 24056944 PMCID: PMC3885543 DOI: 10.1038/nsmb.2667] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/08/2013] [Indexed: 01/10/2023]
Abstract
Dynamic transitions in the epigenome have been associated with regulated patterns of nuclear organization. The accumulating evidence that chromatin remodeling is implicated in circadian function prompted us to explore whether the clock may control nuclear architecture. We applied the chromosome conformation capture on chip technology in mouse embryonic fibroblasts (MEFs) to demonstrate the presence of circadian long-range interactions using the clock-controlled Dbp gene as bait. The circadian genomic interactions with Dbp were highly specific and were absent in MEFs whose clock was disrupted by ablation of the Bmal1 gene (also called Arntl). We establish that the Dbp circadian interactome contains a wide variety of genes and clock-related DNA elements. These findings reveal a previously unappreciated circadian and clock-dependent shaping of the nuclear landscape.
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Affiliation(s)
- Lorena Aguilar-Arnal
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California Irvine, Irvine, California, U.S.A
| | - Ofir Hakim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, Maryland, U.S.A
| | - Vishal R. Patel
- Institute for Genomics and Bioinformatics, Department of Computer Science, University of California Irvine, Irvine, California, U.S.A
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, Department of Computer Science, University of California Irvine, Irvine, California, U.S.A
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, Maryland, U.S.A
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California Irvine, Irvine, California, U.S.A
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17
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Merkenschlager M, Odom DT. CTCF and cohesin: linking gene regulatory elements with their targets. Cell 2013; 152:1285-97. [PMID: 23498937 DOI: 10.1016/j.cell.2013.02.029] [Citation(s) in RCA: 265] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 12/11/2022]
Abstract
Current epigenomics approaches have facilitated the genome-wide identification of regulatory elements based on chromatin features and transcriptional regulator binding and have begun to map long-range interactions between regulatory elements and their targets. Here, we focus on the emerging roles of CTCF and the cohesin in coordinating long-range interactions between regulatory elements. We discuss how species-specific transposable elements may influence such interactions by remodeling the CTCF binding repertoire and suggest that cohesin's association with enhancers, promoters, and sites defined by CTCF binding has the potential to form developmentally regulated networks of long-range interactions that reflect and promote cell-type-specific transcriptional programs.
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Affiliation(s)
- Matthias Merkenschlager
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK.
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18
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Maksimenko OG, Deykin A, Khodarovich YM, Georgiev PG. Use of transgenic animals in biotechnology: prospects and problems. Acta Naturae 2013; 5:33-46. [PMID: 23556129 PMCID: PMC3612824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
During the past two decades, there have been numerous attempts at using animals in order to produce recombinant human proteins and monoclonal antibodies. However, it is only recently that the first two therapeutic agents isolated from the milk of transgenic animals, C1 inhibitor (Ruconest) and antithrombin (ATryn), appeared on the market. This inspires hope that a considerable number of new recombinant proteins created using such technology could become available for practical use in the near future. In this review, the methods applied to produce transgenic animals are described and the advantages and drawbacks related to their use for producing recombinant human proteins and monoclonal antibodies are discussed.
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Affiliation(s)
- O. G. Maksimenko
- Institute of Gene Biology of the Russian Academy of Sciences, Vavilov St., 34/5, Moscow, Russia, 119334
| | - A.V. Deykin
- Institute of Gene Biology of the Russian Academy of Sciences, Vavilov St., 34/5, Moscow, Russia, 119334
| | - Yu. M. Khodarovich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklucho-Maklai St., 16/10, Moscow, Russia, 117997
| | - P. G. Georgiev
- Institute of Gene Biology of the Russian Academy of Sciences, Vavilov St., 34/5, Moscow, Russia, 119334
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19
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Abstract
Retroviral vector-mediated gene transfer into hematopoietic stem cells provides a potentially curative therapy for severe β-thalassemia. Lentiviral vectors based on human immunodeficiency virus have been developed for this purpose and have been shown to be effective in curing thalassemia in mouse models. One participant in an ongoing clinical trial has achieved transfusion independence after gene transfer into bone marrow stem cells owing, in part, to a genetically modified, dominant clone. Ongoing efforts are focused on improving the efficiency of lentiviral vector-mediated gene transfer into stem cells so that the curative potential of gene transfer can be consistently achieved.
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20
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Alipour E, Marko JF. Self-organization of domain structures by DNA-loop-extruding enzymes. Nucleic Acids Res 2012; 40:11202-12. [PMID: 23074191 PMCID: PMC3526278 DOI: 10.1093/nar/gks925] [Citation(s) in RCA: 321] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The long chromosomal DNAs of cells are organized into loop domains much larger in size than individual DNA-binding enzymes, presenting the question of how formation of such structures is controlled. We present a model for generation of defined chromosomal loops, based on molecular machines consisting of two coupled and oppositely directed motile elements which extrude loops from the double helix along which they translocate, while excluding one another sterically. If these machines do not dissociate from DNA (infinite processivity), a disordered, exponential steady-state distribution of small loops is obtained. However, if dissociation and rebinding of the machines occurs at a finite rate (finite processivity), the steady state qualitatively changes to a highly ordered ‘stacked’ configuration with suppressed fluctuations, organizing a single large, stable loop domain anchored by several machines. The size of the resulting domain can be simply regulated by boundary elements, which halt the progress of the extrusion machines. Possible realizations of these types of molecular machines are discussed, with a major focus on structural maintenance of chromosome complexes and also with discussion of type I restriction enzymes. This mechanism could explain the geometrically uniform folding of eukaryote mitotic chromosomes, through extrusion of pre-programmed loops and concomitant chromosome compaction.
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Affiliation(s)
- Elnaz Alipour
- Center for Cell Analysis and Modeling, University of Connecticut Health Sciences Center, Farmington, CT 06030, USA.
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21
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Abstract
Temporal and spatial organization of the nucleus is critical for the control of transcription, mRNA processing and the assembly of ribosomes. This includes the occupancy of specific territories by mammalian chromosomes, the presence of subnuclear compartments such as the nucleolus and Cajal bodies and the division of chromatin between active and inactive states. These latter are commonly associated with the location of DNA within euchromatin and heterochromatin respectively; critically these distinctions arise through modifications to chromatin-associated proteins, including histones, as well as the preferential localization of heterochromatin at the nuclear periphery. Most research on nuclear organization has focused on metazoa and fungi; however, recent technical advances have made more divergent eukaryotes accessible to study, with some surprising results. For example, the organization of heterochromatin is mediated in metazoan nuclei in large part by lamins, the prototypical intermediate filament proteins. Despite the presence of heterochromatin, detected both biochemically and by EM in most eukaryotic organisms, until this year lamins were thought to be restricted to metazoan taxa, and the proteins comprising the lamina in other lineages were unknown. Recent work indicates the presence of lamin orthologs in amoeba, while trypanosomatids possess a large coiled-coil protein, NUP-1, that performs functions analogous to lamins. These data indicate that the presence of a nuclear lamina is substantially more widespread than previously thought, with major implications for the evolution of eukaryotic gene expression mechanisms. We discuss these and other recent findings on the organization of nuclei in diverse organisms, and the implications of these findings for the evolutionary origin of eukaryotes.
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Affiliation(s)
- Mark C Field
- Department of Pathology; University of Cambridge, Cambridge, UK.
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22
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CTCF occupation of the herpes simplex virus 1 genome is disrupted at early times postreactivation in a transcription-dependent manner. J Virol 2012; 86:12741-59. [PMID: 22973047 DOI: 10.1128/jvi.01655-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In herpes simplex virus 1 (HSV-1), binding clusters enriched in CTCF during latency have been previously identified. We hypothesized that CTCF binding to CTCF clusters in HSV-1 would be disrupted in a reactivation event. To investigate, CTCF occupation of three CTCF binding clusters in HSV-1 was analyzed following sodium butyrate (NaB)- and explant-induced reactivation in the mouse. Our data show that the CTCF domains positioned within the HSV-1 genome, specifically around the latency-associated transcript (LAT) and ICP0 and ICP4 regions of the genome, lose CTCF occupancy following the application of reactivation stimuli in wild-type virus. We also found that CTCF binding clusters upstream of the ICP0 and ICP4 promoters both function as classical insulators capable of acting as enhancer blockers of the LAT enhancer. Finally, our results suggest that CTCF occupation of domains in HSV-1 may be differentially regulated both during latency and at early times following reactivation by the presence of lytic transcripts and further implicate epigenetic regulation of HSV-1 as a critical component of the latency-reactivation transition.
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23
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Martínez-González I, Moreno R, Petriz J, Gratacós E, Aran JM. Engraftment potential of adipose tissue-derived human mesenchymal stem cells after transplantation in the fetal rabbit. Stem Cells Dev 2012; 21:3270-7. [PMID: 22738094 DOI: 10.1089/scd.2012.0032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Due to their favorable intrinsic features, including engraftment, differentiation, and immunomodulatory potential, adult mesenchymal stem cells (MSCs) have been proposed for therapeutic in utero intervention. Further improvement of such attributes for particular diseases might merely be achieved by ex vivo MSC genetic engineering previous to transplantation. Here, we evaluated for the first time the feasibility, biodistribution, long-term engraftment, and transgenic enhanced green fluorescent protein (EGFP) expression of genetically engineered human adipose tissue-derived MSCs (EGFP(+)-ASCs) after intra-amniotic xenotransplantation at E17 of gestation into our validated pregnant rabbit model. Overall, the procedure was safe (86.4% survival rate; absence of anatomical defects). Stable, low-level engraftment of EGFP(+)-ASCs was confirmed by assessing the presence of the pWT-EGFP lentiviral provirus in the young transplanted rabbit tissues. Accordingly, similar frequencies of provirus-positive animals were found at both 8 weeks (60%) and 16 weeks (66.7%) after in utero intervention. The presence of EGFP(+)-ASCs was more frequent in respiratory epithelia (lung and trachea), according to the route of administration. However, we were unable to detect EGFP expression, neither by real-time polymerase chain reaction nor by immunohistochemistry, in the provirus-positive tissues, suggesting EGFP transgene silencing mediated by epigenetic events. Moreover, we noticed lack of both host cellular immune responses against xenogeneic ASCs and humoral immune responses against transgenic EGFP. Therefore, the fetal microchimerism achieved by the EGFP(+)-ASCs in the young rabbit hosts indicates induction of donor-specific tolerance after fetal rabbit xenotransplantation, which should boost postnatal transplantation for the early treatment/prevention of many devastating congenital disorders.
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Affiliation(s)
- Itziar Martínez-González
- Human Molecular Genetics Group, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Barcelona, Spain
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24
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Favorov A, Mularoni L, Cope LM, Medvedeva Y, Mironov AA, Makeev VJ, Wheelan SJ. Exploring massive, genome scale datasets with the GenometriCorr package. PLoS Comput Biol 2012; 8:e1002529. [PMID: 22693437 PMCID: PMC3364938 DOI: 10.1371/journal.pcbi.1002529] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 04/08/2012] [Indexed: 02/06/2023] Open
Abstract
We have created a statistically grounded tool for determining the correlation of genomewide data with other datasets or known biological features, intended to guide biological exploration of high-dimensional datasets, rather than providing immediate answers. The software enables several biologically motivated approaches to these data and here we describe the rationale and implementation for each approach. Our models and statistics are implemented in an R package that efficiently calculates the spatial correlation between two sets of genomic intervals (data and/or annotated features), for use as a metric of functional interaction. The software handles any type of pointwise or interval data and instead of running analyses with predefined metrics, it computes the significance and direction of several types of spatial association; this is intended to suggest potentially relevant relationships between the datasets. Availability and implementation: The package, GenometriCorr, can be freely downloaded at http://genometricorr.sourceforge.net/. Installation guidelines and examples are available from the sourceforge repository. The package is pending submission to Bioconductor.
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Affiliation(s)
- Alexander Favorov
- Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia
- * E-mail: (AF); (SJW)
| | - Loris Mularoni
- Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Leslie M. Cope
- Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yulia Medvedeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - Andrey A. Mironov
- Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Vsevolod J. Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - Sarah J. Wheelan
- Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (AF); (SJW)
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25
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Ganis JJ, Hsia N, Trompouki E, de Jong JLO, DiBiase A, Lambert JS, Jia Z, Sabo PJ, Weaver M, Sandstrom R, Stamatoyannopoulos JA, Zhou Y, Zon LI. Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR. Dev Biol 2012; 366:185-94. [PMID: 22537494 DOI: 10.1016/j.ydbio.2012.03.021] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 02/20/2012] [Accepted: 03/19/2012] [Indexed: 02/02/2023]
Abstract
Globin gene switching is a complex, highly regulated process allowing expression of distinct globin genes at specific developmental stages. Here, for the first time, we have characterized all of the zebrafish globins based on the completed genomic sequence. Two distinct chromosomal loci, termed major (chromosome 3) and minor (chromosome 12), harbor the globin genes containing α/β pairs in a 5'-3' to 3'-5' orientation. Both these loci share synteny with the mammalian α-globin locus. Zebrafish globin expression was assayed during development and demonstrated two globin switches, similar to human development. A conserved regulatory element, the locus control region (LCR), was revealed by analyzing DNase I hypersensitive sites, H3K4 trimethylation marks and GATA1 binding sites. Surprisingly, the position of these sites with relation to the globin genes is evolutionarily conserved, despite a lack of overall sequence conservation. Motifs within the zebrafish LCR include CACCC, GATA, and NFE2 sites, suggesting functional interactions with known transcription factors but not the same LCR architecture. Functional homology to the mammalian α-LCR MCS-R2 region was confirmed by robust and specific reporter expression in erythrocytes of transgenic zebrafish. Our studies provide a comprehensive characterization of the zebrafish globin loci and clarify the regulation of globin switching.
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Affiliation(s)
- Jared J Ganis
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital and Dana Farber Cancer Institute, and Harvard Stem Cell Institute, Harvard Medical School, 1 Blackfan Cir., Karp 7, Boston, MA 02115, USA.
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26
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Abstract
Transcription of eukaryotic genes is an exceedingly sophisticated and complicated process, orchestrated by layers of control mechanisms involving a myriad of transcription factors and DNA control sequences, with both groups subject to multiple modifications. The availability of various recent genomic approaches has provided previously unforeseen opportunities to examine the cis-regulatory landscape of the entire genome, resulting in the identification of a potentially overwhelming number of enhancers and novel enhancer functions. In this review, we focus on the activities of enhancers in metazoans and discuss how they serve to regulate gene expression during early development.
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Affiliation(s)
- Ken W Y Cho
- Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
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27
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Abstract
The genetic engineering of hematopoietic stem cells is the basis for potentially treating a large array of hereditary and acquired diseases, and stands as the paradigm for stem cell engineering in general. Recent clinical reports support the formidable promise of this approach but also highlight the limitations of the technologies used to date, which have on occasion resulted in clonal expansion, myelodysplasia, or leukemogenesis. New research directions, predicated on improved vector designs, targeted gene delivery or the therapeutic use of pluripotent stem cells, herald the advent of safer and more effective hematopoietic stem cell therapies that may transform medical practice. In this review, we place these recent advances in perspective, emphasizing the solutions emerging from a wave of new technologies and highlighting the challenges that lie ahead.
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28
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Chakraborty SA, Simpson RT, Grigoryev SA. A single heterochromatin boundary element imposes position-independent antisilencing activity in Saccharomyces cerevisiae minichromosomes. PLoS One 2011; 6:e24835. [PMID: 21949764 PMCID: PMC3174977 DOI: 10.1371/journal.pone.0024835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 08/22/2011] [Indexed: 11/19/2022] Open
Abstract
Chromatin boundary elements serve as cis-acting regulatory DNA signals required to protect genes from the effects of the neighboring heterochromatin. In the yeast genome, boundary elements act by establishing barriers for heterochromatin spreading and are sufficient to protect a reporter gene from transcriptional silencing when inserted between the silencer and the reporter gene. Here we dissected functional topography of silencers and boundary elements within circular minichromosomes in Saccharomyces cerevisiae. We found that both HML-E and HML-I silencers can efficiently repress the URA3 reporter on a multi-copy yeast minichromosome and we further showed that two distinct heterochromatin boundary elements STAR and TEF2-UASrpg are able to limit the heterochromatin spreading in circular minichromosomes. In surprising contrast to what had been observed in the yeast genome, we found that in minichromosomes the heterochromatin boundary elements inhibit silencing of the reporter gene even when just one boundary element is positioned at the distal end of the URA3 reporter or upstream of the silencer elements. Thus the STAR and TEF2-UASrpg boundary elements inhibit chromatin silencing through an antisilencing activity independently of their position or orientation in S. cerevisiae minichromosomes rather than by creating a position-specific barrier as seen in the genome. We propose that the circular DNA topology facilitates interactions between the boundary and silencing elements in the minichromosomes.
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Affiliation(s)
- Sangita A. Chakraborty
- Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Milton S. Hershey Medical Center, Hershey, Pennsylvania, United States of America
- * E-mail: (SAC); (SAG)
| | - Robert T. Simpson
- Department of Biochemistry and Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sergei A. Grigoryev
- Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Milton S. Hershey Medical Center, Hershey, Pennsylvania, United States of America
- * E-mail: (SAC); (SAG)
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