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Teng F, Gang O, Freimuth P. Overexpression of human ACE2 protein in mouse fibroblasts stably transfected with the intact ACE2 gene. Virology 2024; 592:109988. [PMID: 38244322 DOI: 10.1016/j.virol.2024.109988] [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] [Received: 09/01/2023] [Revised: 12/04/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
Infection by SARS-CoV-2 is dependent on binding of the viral spike protein to angiotensin converting enzyme 2 (ACE2), a membrane glycoprotein expressed on epithelial cells in the human upper respiratory tract. Recombinant ACE2 protein has potential application for anti-viral therapy. Here we co-transfected mouse fibroblasts (A9 cells) with a cloned fragment of human genomic DNA containing the intact ACE2 gene and an unlinked neomycin phosphotransferase gene, and then selected stable neomycin-resistant transfectants. Transfectant clones expressed ACE2 protein at levels that were generally proportional to the number of ACE2 gene copies integrated in the cell genome, ranging up to approximately 50 times the level of ACE2 present of Vero-E6 cells. Cells overexpressing ACE2 were hypersensitive to infection by spike-pseudotyped vesicular stomatitis virus (VSV-S), and adsorption of VSV-S to these cells occurred at an accelerated rate compared to Vero-E6 cells. The transfectant cell clones described here therefore have favorable attributes as feedstocks for large-scale production of recombinant human ACE2 protein.
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Affiliation(s)
- Feiyue Teng
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA; Department of Chemical Engineering and Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA
| | - Paul Freimuth
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA.
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2
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Koblan LW, Erdos MR, Wilson C, Cabral WA, Levy JM, Xiong ZM, Tavarez UL, Davison LM, Gete YG, Mao X, Newby GA, Doherty SP, Narisu N, Sheng Q, Krilow C, Lin CY, Gordon LB, Cao K, Collins FS, Brown JD, Liu DR. In vivo base editing rescues Hutchinson-Gilford progeria syndrome in mice. Nature 2021; 589:608-614. [PMID: 33408413 PMCID: PMC7872200 DOI: 10.1038/s41586-020-03086-7] [Citation(s) in RCA: 244] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS or progeria) is typically caused by a dominant-negative C•G-to-T•A mutation (c.1824 C>T; p.G608G) in LMNA, the gene that encodes nuclear lamin A. This mutation causes RNA mis-splicing that produces progerin, a toxic protein that induces rapid ageing and shortens the lifespan of children with progeria to approximately 14 years1-4. Adenine base editors (ABEs) convert targeted A•T base pairs to G•C base pairs with minimal by-products and without requiring double-strand DNA breaks or donor DNA templates5,6. Here we describe the use of an ABE to directly correct the pathogenic HGPS mutation in cultured fibroblasts derived from children with progeria and in a mouse model of HGPS. Lentiviral delivery of the ABE to fibroblasts from children with HGPS resulted in 87-91% correction of the pathogenic allele, mitigation of RNA mis-splicing, reduced levels of progerin and correction of nuclear abnormalities. Unbiased off-target DNA and RNA editing analysis did not detect off-target editing in treated patient-derived fibroblasts. In transgenic mice that are homozygous for the human LMNA c.1824 C>T allele, a single retro-orbital injection of adeno-associated virus 9 (AAV9) encoding the ABE resulted in substantial, durable correction of the pathogenic mutation (around 20-60% across various organs six months after injection), restoration of normal RNA splicing and reduction of progerin protein levels. In vivo base editing rescued the vascular pathology of the mice, preserving vascular smooth muscle cell counts and preventing adventitial fibrosis. A single injection of ABE-expressing AAV9 at postnatal day 14 improved vitality and greatly extended the median lifespan of the mice from 215 to 510 days. These findings demonstrate the potential of in vivo base editing as a possible treatment for HGPS and other genetic diseases by directly correcting their root cause.
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Affiliation(s)
- Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Wilson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Wayne A Cabral
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan M Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Zheng-Mei Xiong
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Urraca L Tavarez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lindsay M Davison
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yantenew G Gete
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Xiaojing Mao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Sean P Doherty
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chad Krilow
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Therapeutic Innovation Center, Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Kronos, Bio Inc., Cambridge, MA, USA
| | - Leslie B Gordon
- Hasbro Children's Hospital, Alpert Medical School of Brown University, Providence, RI, USA
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kan Cao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Jonathan D Brown
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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Heintz N, Gong S. Working with Bacterial Artificial Chromosomes (BACs) and Other High-Capacity Vectors. Cold Spring Harb Protoc 2020; 2020:2020/10/pdb.top097998. [PMID: 33004554 DOI: 10.1101/pdb.top097998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Genetic targeting of specific cell types is fundamentally important for modern molecular-genetic studies. The development of simple methods to engineer high-capacity vectors-in particular, bacterial artificial chromosomes (BACs)-for the preparation of transgenic lines that accurately express a gene of interest has resulted in commonplace usage of transgenic techniques in a wide variety of experimental systems. Here we provide a brief description of each of the four major types of large-capacity vectors, with a focus on the use of BAC vectors.
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Tellier M, Chalmers R. Compensating for over-production inhibition of the Hsmar1 transposon in Escherichia coli using a series of constitutive promoters. Mob DNA 2020; 11:5. [PMID: 31938044 PMCID: PMC6954556 DOI: 10.1186/s13100-020-0200-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/01/2020] [Indexed: 01/03/2023] Open
Abstract
Background Transposable elements (TEs) are a diverse group of self-mobilizing DNA elements. Transposition has been exploited as a powerful tool for molecular biology and genomics. However, transposition is sometimes limited because of auto-regulatory mechanisms that presumably allow them to cohabit within their hosts without causing excessive genomic damage. The papillation assay provides a powerful visual screen for hyperactive transposases. Transposition is revealed by the activation of a promoter-less lacZ gene when the transposon integrates into a non-essential gene on the host chromosome. Transposition events are detected as small blue speckles, or papillae, on the white background of the main Escherichia coli colony. Results We analysed the parameters of the papillation assay including the strength of the transposase transcriptional and translational signals. To overcome certain limitations of inducible promoters, we constructed a set of vectors based on constitutive promoters of different strengths to widen the range of transposase expression. We characterized and validated our expression vectors with Hsmar1, a member of the mariner transposon family. The highest rate of transposition was observed with the weakest promoters. We then took advantage of our approach to investigate how the level of transposition responds to selected point mutations and the effect of joining the transposase monomers into a single-chain dimer. Conclusions We generated a set of vectors to provide a wide range of transposase expression which will be useful for screening libraries of transposase mutants. The use of weak promoters should allow screening for truly hyperactive transposases rather than those that are simply resistant to auto-regulatory mechanisms, such as overproduction inhibition (OPI). We also found that mutations in the Hsmar1 dimer interface provide resistance to OPI in bacteria, which could be valuable for improving bacterial transposon mutagenesis techniques.
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Affiliation(s)
- Michael Tellier
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH UK.,2Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE UK
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH UK
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Buckley KM, Dong P, Cameron RA, Rast JP. Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms. Brief Funct Genomics 2019; 17:362-371. [PMID: 29045542 DOI: 10.1093/bfgp/elx031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome sequences contain all the necessary information-both coding and regulatory sequences-to construct an organism. The developmental process translates this genomic information into a three-dimensional form. One interpretation of this translation process can be described using gene regulatory network (GRN) models, which are maps of interactions among regulatory gene products in time and space. As high throughput investigations reveal increasing complexity within these GRNs, it becomes apparent that efficient methods are required to test the necessity and sufficiency of regulatory interactions. One of the most complete GRNs for early development has been described in the purple sea urchin, Strongylocentrotus purpuratus. This work has been facilitated by two resources: a well-annotated genome sequence and transgenes generated in bacterial artificial chromosome (BAC) constructs. BAC libraries played a central role in assembling the S. purpuratus genome sequence and continue to serve as platforms for generating reporter constructs for use in expression and regulatory analyses. Optically transparent echinoderm larvae are highly amenable to transgenic approaches and are therefore particularly well suited for experiments that rely on BAC-based reporter transgenes. Here, we discuss the experimental utility of BAC constructs in the context of understanding developmental processes in echinoderm embryos and larvae.
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Affiliation(s)
- Katherine M Buckley
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Ping Dong
- California Institute of Technology, California, USA
| | - R Andrew Cameron
- Beckman Institute Center for Computational Regulatory Genomics, California Institute for Technology, California, USA
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6
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Wang L, Koppitch K, Cutting A, Dong P, Kudtarkar P, Zeng J, Cameron RA, Davidson EH. Developmental effector gene regulation: Multiplexed strategies for functional analysis. Dev Biol 2019; 445:68-79. [PMID: 30392838 DOI: 10.1016/j.ydbio.2018.10.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 01/18/2023]
Abstract
The staggering complexity of the genome controls for developmental processes is revealed through massively parallel cis-regulatory analysis using new methods of perturbation and readout. The choice of combinations of these new methods is tailored to the system, question and resources at hand. Our focus is on issues that include the necessity or sufficiency of given cis-regulatory modules, cis-regulatory function in the normal spatial genomic context, and easily accessible high throughput and multiplexed analysis methods. In the sea urchin embryonic model, recombineered BACs offer new opportunities for consecutive modes of cis-regulatory analyses that answer these requirements, as we here demonstrate on a diverse suite of previously unstudied sea urchin effector genes expressed in skeletogenic cells. Positively active cis-regulatory modules were located in single Nanostring experiments per BAC containing the gene of interest, by application of our previously reported "barcode" tag vectors of which> 100 can be analyzed at one time. Computational analysis of DNA sequences that drive expression, based on the known skeletogenic regulatory state, then permitted effective identification of functional target site clusters. Deletion of these sub-regions from the parent BACs revealed module necessity, as simultaneous tests of the same regions in short constructs revealed sufficiency. Predicted functional inputs were then confirmed by site mutations, all generated and tested in multiplex formats. There emerged the simple conclusion that each effector gene utilizes a small subset of inputs from the skeletogenic GRN. These inputs may function to only adjust expression levels or in some cases necessary for expression. Since we know the GRN architecture upstream of the effector genes, we could then conceptually isolate and compare the wiring of the effector gene driver sub-circuits and identify the inputs whose removal abolish expression.
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Affiliation(s)
- Lijun Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Kari Koppitch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Ann Cutting
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Ping Dong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Parul Kudtarkar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Jenny Zeng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - R Andrew Cameron
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
| | - Eric H Davidson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
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7
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Tocchetti A, Donadio S, Sosio M. Large inserts for big data: artificial chromosomes in the genomic era. FEMS Microbiol Lett 2018; 365:4935161. [DOI: 10.1093/femsle/fny064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/13/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
| | - Stefano Donadio
- Naicons Srl, 20139 Milano, Italy
- Ktedogen Srl, Via Ortles 22/4, 20139 Milano, Italy
| | - Margherita Sosio
- Naicons Srl, 20139 Milano, Italy
- Ktedogen Srl, Via Ortles 22/4, 20139 Milano, Italy
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8
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Disease onset in X-linked dystonia-parkinsonism correlates with expansion of a hexameric repeat within an SVA retrotransposon in TAF1. Proc Natl Acad Sci U S A 2017; 114:E11020-E11028. [PMID: 29229810 PMCID: PMC5754783 DOI: 10.1073/pnas.1712526114] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The genetic basis of X-Linked dystonia-parkinsonism (XDP) has been difficult to unravel, in part because all patients inherit the same haplotype of seven sequence variants, none of which has ever been identified in control individuals. This study revealed that one of the haplotype markers, a retrotransposon insertion within an intron of TAF1, has a variable number of hexameric repeats among affected individuals with an increase in repeat number strongly correlated with earlier age at disease onset. These data support a contributing role for this sequence in disease pathogenesis while further suggesting that XDP may be part of a growing list of neurodegenerative disorders associated with unstable repeat expansions. X-linked dystonia-parkinsonism (XDP) is a neurodegenerative disease associated with an antisense insertion of a SINE-VNTR-Alu (SVA)-type retrotransposon within an intron of TAF1. This unique insertion coincides with six additional noncoding sequence changes in TAF1, the gene that encodes TATA-binding protein–associated factor-1, which appear to be inherited together as an identical haplotype in all reported cases. Here we examined the sequence of this SVA in XDP patients (n = 140) and detected polymorphic variation in the length of a hexanucleotide repeat domain, (CCCTCT)n. The number of repeats in these cases ranged from 35 to 52 and showed a highly significant inverse correlation with age at disease onset. Because other SVAs exhibit intrinsic promoter activity that depends in part on the hexameric domain, we assayed the transcriptional regulatory effects of varying hexameric lengths found in the unique XDP SVA retrotransposon using luciferase reporter constructs. When inserted sense or antisense to the luciferase reading frame, the XDP variants repressed or enhanced transcription, respectively, to an extent that appeared to vary with length of the hexamer. Further in silico analysis of this SVA sequence revealed multiple motifs predicted to form G-quadruplexes, with the greatest potential detected for the hexameric repeat domain. These data directly link sequence variation within the XDP-specific SVA sequence to phenotypic variability in clinical disease manifestation and provide insight into potential mechanisms by which this intronic retroelement may induce transcriptional interference in TAF1 expression.
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Teh AHT, Lee SM, Dykes GA. Identification of potential Campylobacter jejuni genes involved in biofilm formation by EZ-Tn5 Transposome mutagenesis. BMC Res Notes 2017; 10:182. [PMID: 28499399 PMCID: PMC5427567 DOI: 10.1186/s13104-017-2504-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/05/2017] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Biofilm formation has been suggested to play a role in the survival of Campylobacter jejuni in the environment and contribute to the high incidence of human campylobacteriosis. Molecular studies of biofilm formation by Campylobacter are sparse. RESULTS We attempted to identify genes that may be involved in biofilm formation in seven C. jejuni strains through construction of mutants using the EZ-Tn5 Transposome system. Only 14 mutants with reduced biofilm formation were obtained, all from one strain of C. jejuni. Three different genes of interest, namely CmeB (synthesis of multidrug efflux system transporter proteins), NusG (transcription termination and anti-termination protein) and a putative transmembrane protein (involved in membrane protein function) were identified. The efficiency of the EZ::TN5 transposon mutagenesis approach was strain dependent and was unable to generate any mutants from most of the strains used. CONCLUSIONS A diverse range of genes may be involved in biofilm formation by C. jejuni. The application of the EZ::TN5 system for construction of mutants in different Campylobacter strains is limited.
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Affiliation(s)
- Amy Huei Teen Teh
- School of Science, Monash University, Jalan Lagoon Selatan, Bandar Sunway, 46150 Selangor Darul Ehsan Malaysia
| | - Sui Mae Lee
- School of Science, Monash University, Jalan Lagoon Selatan, Bandar Sunway, 46150 Selangor Darul Ehsan Malaysia
| | - Gary A. Dykes
- School of Public Health, Curtin University, Bentley, WA 6102 Australia
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10
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Hajdu M, Calle J, Puno A, Haruna A, Arenas-Mena C. Transcriptional and post-transcriptional regulation of histone variantH2A.Zduring sea urchin development. Dev Growth Differ 2016; 58:727-740. [DOI: 10.1111/dgd.12329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/06/2016] [Accepted: 10/27/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Mihai Hajdu
- Department of Biology; College of Staten Island and Graduate Center; The City University of New York (CUNY); Staten Island New York 10314 USA
| | - Jasmine Calle
- Department of Biology; College of Staten Island and Graduate Center; The City University of New York (CUNY); Staten Island New York 10314 USA
| | - Andrea Puno
- Department of Biology; College of Staten Island and Graduate Center; The City University of New York (CUNY); Staten Island New York 10314 USA
| | - Aminat Haruna
- Department of Biology; College of Staten Island and Graduate Center; The City University of New York (CUNY); Staten Island New York 10314 USA
| | - César Arenas-Mena
- Department of Biology; College of Staten Island and Graduate Center; The City University of New York (CUNY); Staten Island New York 10314 USA
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11
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Khateb M, Fourier N, Barnea-Yizhar O, Ram S, Kovalev E, Azriel A, Rand U, Nakayama M, Hauser H, Gepstein L, Levi BZ. The Third Intron of the Interferon Regulatory Factor-8 Is an Initiator of Repressed Chromatin Restricting Its Expression in Non-Immune Cells. PLoS One 2016; 11:e0156812. [PMID: 27257682 PMCID: PMC4892516 DOI: 10.1371/journal.pone.0156812] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/19/2016] [Indexed: 12/03/2022] Open
Abstract
Interferon Regulatory Factor-8 (IRF-8) serves as a key factor in the hierarchical differentiation towards monocyte/dendritic cell lineages. While much insight has been accumulated into the mechanisms essential for its hematopoietic specific expression, the mode of restricting IRF-8 expression in non-hematopoietic cells is still unknown. Here we show that the repression of IRF-8 expression in restrictive cells is mediated by its 3rd intron. Removal of this intron alleviates the repression of Bacterial Artificial Chromosome (BAC) IRF-8 reporter gene in these cells. Fine deletion analysis points to conserved regions within this intron mediating its restricted expression. Further, the intron alone selectively initiates gene silencing only in expression-restrictive cells. Characterization of this intron’s properties points to its role as an initiator of sustainable gene silencing inducing chromatin condensation with suppressive histone modifications. This intronic element cannot silence episomal transgene expression underlining a strict chromatin-dependent silencing mechanism. We validated this chromatin-state specificity of IRF-8 intron upon in-vitro differentiation of induced pluripotent stem cells (iPSCs) into cardiomyocytes. Taken together, the IRF-8 3rd intron is sufficient and necessary to initiate gene silencing in non-hematopoietic cells, highlighting its role as a nucleation core for repressed chromatin during differentiation.
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Affiliation(s)
- Mamduh Khateb
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa, Israel
| | - Nitsan Fourier
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa, Israel
| | - Ofer Barnea-Yizhar
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa, Israel
| | - Sigal Ram
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa, Israel
| | - Ekaterina Kovalev
- Rappaport Faculty of Medicine and Research Institute, Technion—Israel Institute of Technology, Haifa, Israel
| | - Aviva Azriel
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa, Israel
| | - Ulfert Rand
- Department of Gene Regulation and Differentiation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Manabu Nakayama
- Department of Technology Development, Kazusa DNA Research Institute, Kazusa-Kamatari, Kazusa, Japan
| | - Hansjörg Hauser
- Department of Gene Regulation and Differentiation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lior Gepstein
- Rappaport Faculty of Medicine and Research Institute, Technion—Israel Institute of Technology, Haifa, Israel
| | - Ben-Zion Levi
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa, Israel
- * E-mail:
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12
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RecET direct cloning and Redαβ recombineering of biosynthetic gene clusters, large operons or single genes for heterologous expression. Nat Protoc 2016; 11:1175-90. [PMID: 27254463 DOI: 10.1038/nprot.2016.054] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Full-length RecE and RecT from Rac prophage mediate highly efficient linear-linear homologous recombination that can be used to clone large DNA regions directly from genomic DNA into expression vectors, bypassing library construction and screening. Homologous recombination mediated by Redαβ from lambda phage has been widely used for recombinant DNA engineering. Here we present a protocol for direct cloning and engineering of biosynthetic gene clusters, large operons or single genes from genomic DNA using one Escherichia coli host that harbors both RecET and Redαβ systems. The pipeline uses standardized cassettes for horizontal gene transfer options, as well as vectors with different replication origins configured to minimize recombineering background through the use of selectively replicating templates or CcdB counterselection. These optimized reagents and protocols facilitate fast acquisition of transgenes from genomic DNA preparations, which are ready for heterologous expression within 1 week.
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13
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Barakat TS, Gribnau J. Generation of knockout alleles by RFLP based BAC targeting of polymorphic embryonic stem cells. Methods Mol Biol 2015; 1227:143-80. [PMID: 25239745 DOI: 10.1007/978-1-4939-1652-8_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The isolation of germ line competent mouse Embryonic Stem (ES) cells and the ability to modify the genome by homologous recombination has revolutionized life science research. Since its initial discovery, several approaches have been introduced to increase the efficiency of homologous recombination, including the use of isogenic DNA for the generation of targeting constructs, and the use of Bacterial Artificial Chromosomes (BACs). BACs have the advantage of combining long stretches of homologous DNA, thereby increasing targeting efficiencies, with the possibilities delivered by BAC recombineering approaches, which provide the researcher with almost unlimited possibilities to efficiently edit the genome in a controlled fashion. Despite these advantages of BAC targeting approaches, a widespread use has been hampered, mainly because of the difficulties in identifying BAC-targeted knockout alleles by conventional methods like Southern Blotting. Recently, we introduced a novel BAC targeting strategy, in which Restriction Fragment Length Polymorphisms (RFLPs) are targeted in polymorphic mouse ES cells, enabling an efficient and easy PCR-based readout to identify properly targeted alleles. Here we provide a detailed protocol for the generation of targeting constructs, targeting of ES cells, and convenient PCR-based analysis of targeted clones, which enable the user to generate knockout ES cells of almost every gene in the mouse genome within a 2-month period.
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Affiliation(s)
- Tahsin Stefan Barakat
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Room Ee 09-71, PO Box 2040, 3000 CA, Rotterdam, The Netherlands,
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Oßwald C, Zaburannyi N, Burgard C, Hoffmann T, Wenzel SC, Müller R. A highly unusual polyketide synthase directs dawenol polyene biosynthesis in Stigmatella aurantiaca. J Biotechnol 2014; 191:54-63. [DOI: 10.1016/j.jbiotec.2014.07.447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 07/17/2014] [Accepted: 07/25/2014] [Indexed: 01/29/2023]
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15
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Shakes LA, Wolf HM, Norford DC, Grant DJ, Chatterjee PK. Harnessing mobile genetic elements to explore gene regulation. Mob Genet Elements 2014; 4:e29759. [PMID: 25054085 PMCID: PMC4092005 DOI: 10.4161/mge.29759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/20/2014] [Accepted: 06/27/2014] [Indexed: 11/19/2022] Open
Abstract
Sequences that regulate expression of a gene in cis but are located at large distances along the DNA from the gene, as found with most developmentally regulated genes in higher vertebrates, are difficult to identify if those sequences are not conserved across species. Mutating suspected gene-regulatory sequences to alter expression then becomes a hit-or-miss affair. The relaxed specificity of transposon insertions offers an opportunity to develop alternate strategies, to scan in an unbiased manner, pieces of chromosomal DNA cloned in BACs for transcription enhancing elements. This article illustrates how insertions of Tn10 with enhancer-traps into BAC DNA containing the gene, and its germ-line expression in zebrafish, have identified distal regulatory elements functionally. Transposition of Tn10 first introduces the enhancer-trap with a loxP site randomly into BAC DNA. Cre-recombination between the inserted loxP and the loxP endogenous to a BAC-end positions the enhancer-trap to the newly created truncated end of BAC DNA. The procedure generates a library of integration-ready enhancer-trap BACs with progressive truncations from an end in a single experiment. Individual enhancer-trap BACs from the library can be evaluated functionally in zebrafish or mice. Furthermore, the ability to readily alter sequences in a small transposon plasmid containing a regulatory domain of the gene allows re-introduction of altered parts of a BAC back into itself. It serves as a useful strategy to functionally dissect multiple discontinuous regulatory domains of a gene quickly. These methodologies have been successfully used in identifying novel regulatory domains of the Amyloid Precursor Protein (appb) gene in zebrafish, and provided important clues for regulation of the gene in humans.
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Affiliation(s)
- Leighcraft A Shakes
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Hope M Wolf
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Derek C Norford
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Delores J Grant
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
| | - Pradeep K Chatterjee
- Julius L. Chambers Biomedical/ Biotechnology Research Institute and Department of Chemistry; North Carolina Central University; Durham, NC USA
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16
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Zhao L, Ng ET, Koopman P. ApiggyBactransposon- and gateway-enhanced system for efficient BAC transgenesis. Dev Dyn 2014; 243:1086-94. [DOI: 10.1002/dvdy.24153] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 05/20/2014] [Accepted: 06/05/2014] [Indexed: 11/07/2022] Open
Affiliation(s)
- Liang Zhao
- Institute for Molecular Bioscience; The University of Queensland; Brisbane QLD 4072 Australia
| | - Ee Ting Ng
- Institute for Molecular Bioscience; The University of Queensland; Brisbane QLD 4072 Australia
| | - Peter Koopman
- Institute for Molecular Bioscience; The University of Queensland; Brisbane QLD 4072 Australia
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17
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Deussing JM. Targeted mutagenesis tools for modelling psychiatric disorders. Cell Tissue Res 2013; 354:9-25. [PMID: 24078022 DOI: 10.1007/s00441-013-1708-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/16/2013] [Indexed: 12/15/2022]
Abstract
In the 1980s, the basic principles of gene targeting were discovered and forged into sharp tools for efficient and precise engineering of the mouse genome. Since then, genetic mouse models have substantially contributed to our understanding of major neurobiological concepts and are of utmost importance for our comprehension of neuropsychiatric disorders. The "domestication" of site-specific recombinases and the continuous creative technological developments involving the implementation of previously identified biological principles such as transcriptional and posttranslational control now enable conditional mutagenesis with high spatial and temporal resolution. The initiation and successful accomplishment of large-scale efforts to annotate functionally the entire mouse genome and to build strategic resources for the research community have significantly accelerated the rapid proliferation and broad propagation of mouse genetic tools. Addressing neurobiological processes with the assistance of genetic mouse models is a routine procedure in psychiatric research and will be further extended in order to improve our understanding of disease mechanisms. In light of the highly complex nature of psychiatric disorders and the current lack of strong causal genetic variants, a major future challenge is to model of psychiatric disorders more appropriately. Humanized mice, and the recently developed toolbox of site-specific nucleases for more efficient and simplified tailoring of the genome, offer the perspective of significantly improved models. Ultimately, these tools will push the limits of gene targeting beyond the mouse to allow genome engineering in any model organism of interest.
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Affiliation(s)
- Jan M Deussing
- Max Planck Institute of Psychiatry, Molecular Neurogenetics, Kraepelinstrasse 2-10, 80804, Munich, Germany,
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18
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Chatterjee PK, Shakes LA, Wolf HM, Mujalled MA, Zhou C, Hatcher C, Norford DC. Identifying Distal cis-acting Gene-Regulatory Sequences by Expressing BACs Functionalized with loxP-Tn10 Transposons in Zebrafish. RSC Adv 2013; 3:8604-8617. [PMID: 24772295 DOI: 10.1039/c3ra40332g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bacterial Artificial Chromosomes (BACs) are large pieces of DNA from the chromosomes of organisms propagated faithfully in bacteria as large extra-chromosomal plasmids. Expression of genes contained in BACs can be monitored after functionalizing the BAC DNA with reporter genes and other sequences that allow stable maintenance and propagation of the DNA in the new host organism. The DNA in BACs can be altered within its bacterial host in several ways. Here we discuss one such approach, using Tn10 mini-transposons, to introduce exogenous sequences into BACs for a variety of purposes. The largely random insertions of Tn10 transposons carrying lox sites have been used to position mammalian cell-selectable antibiotic resistance genes, enhancer-traps and inverted repeat ends of the vertebrate transposon Tol2 precisely at the ends of the genomic DNA insert in BACs. These modified BACs are suitable for expression in zebrafish or mouse, and have been used to functionally identify important long-range gene regulatory sequences in both species. Enhancer-trapping using BACs should prove uniquely useful in analyzing multiple discontinuous DNA domains that act in concert to regulate expression of a gene, and is not limited by genome accessibility issues of traditional enhancer-trapping methods.
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Affiliation(s)
- Pradeep K Chatterjee
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Leighcraft A Shakes
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Hope M Wolf
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Mohammad A Mujalled
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Constance Zhou
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Charles Hatcher
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Derek C Norford
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
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19
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Itaya M. Tools for Genome Synthesis. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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20
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A Low-Copy-Number Plasmid for Retrieval of Toxic Genes from BACs and Generation of Conditional Targeting Constructs. Mol Biotechnol 2012; 54:504-14. [DOI: 10.1007/s12033-012-9591-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Shi X, Zeng H, Xue Y, Luo M. A pair of new BAC and BIBAC vectors that facilitate BAC/BIBAC library construction and intact large genomic DNA insert exchange. PLANT METHODS 2011; 7:33. [PMID: 21985432 PMCID: PMC3213141 DOI: 10.1186/1746-4811-7-33] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Accepted: 10/11/2011] [Indexed: 05/25/2023]
Abstract
BACKGROUND Large-insert BAC and BIBAC libraries are important tools for structural and functional genomics studies of eukaryotic genomes. To facilitate the construction of BAC and BIBAC libraries and the transfer of complete large BAC inserts into BIBAC vectors, which is desired in positional cloning, we developed a pair of new BAC and BIBAC vectors. RESULTS The new BAC vector pIndigoBAC536-S and the new BIBAC vector BIBAC-S have the following features: 1) both contain two 18-bp non-palindromic I-SceI sites in an inverted orientation at positions that flank an identical DNA fragment containing the lacZ selection marker and the cloning site. Large DNA inserts can be excised from the vectors as single fragments by cutting with I-SceI, allowing the inserts to be easily sized. More importantly, because the two vectors contain different antibiotic resistance genes for transformant selection and produce the same non-complementary 3' protruding ATAA ends by I-SceI that suppress self- and inter-ligations, the exchange of intact large genomic DNA inserts between the BAC and BIBAC vectors is straightforward; 2) both were constructed as high-copy composite vectors. Reliable linearized and dephosphorylated original low-copy pIndigoBAC536-S and BIBAC-S vectors that are ready for library construction can be prepared from the high-copy composite vectors pHZAUBAC1 and pHZAUBIBAC1, respectively, without the need for additional preparation steps or special reagents, thus simplifying the construction of BAC and BIBAC libraries. BIBAC clones constructed with the new BIBAC-S vector are stable in both E. coli and Agrobacterium. The vectors can be accessed through our website http://GResource.hzau.edu.cn. CONCLUSIONS The two new vectors and their respective high-copy composite vectors can largely facilitate the construction and characterization of BAC and BIBAC libraries. The transfer of complete large genomic DNA inserts from one vector to the other is made straightforward.
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Affiliation(s)
- Xue Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyang Zeng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yadong Xue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meizhong Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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22
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Bacterial artificial chromosome libraries of pulse crops: characteristics and applications. J Biomed Biotechnol 2011; 2012:493186. [PMID: 21811383 PMCID: PMC3144660 DOI: 10.1155/2012/493186] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 05/29/2011] [Accepted: 05/30/2011] [Indexed: 12/01/2022] Open
Abstract
Pulse crops are considered minor on a global scale despite their nutritional value for human consumption. Therefore, they are relatively less extensively studied in comparison with the major crops. The need to improve pulse crop production and quality will increase with the increasing global demand for food security and people's awareness of nutritious food. The improvement of pulse crops will require fully utilizing all their genetic resources. Bacterial artificial chromosome (BAC) libraries of pulse crops are essential genomic resources that have the potential to accelerate gene discovery and enhance molecular breeding in these crops. Here, we review the availability, characteristics, applications, and potential applications of the BAC libraries of pulse crops.
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23
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Puspasari N, Rowley SM, Gordon L, Lockhart PJ, Ioannou PA, Delatycki MB, Sarsero JP. Long range regulation of human FXN gene expression. PLoS One 2011; 6:e22001. [PMID: 21760943 PMCID: PMC3132285 DOI: 10.1371/journal.pone.0022001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 06/10/2011] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Friedreich ataxia (FRDA) is the most common form of hereditary ataxia characterized by the presence of a GAA trinucleotide repeat expansion within the first intron of the FXN gene. The expansion inhibits FXN gene expression resulting in an insufficiency of frataxin protein. METHODOLOGY/PRINCIPAL FINDING In this study, computational analyses were performed on the 21.3 kb region upstream of exon 1 of the human FXN gene and orthologs from other species in order to identify conserved non-coding DNA sequences with potential regulatory functions. The conserved non-coding regions identified were individually analyzed in two complementing assay systems, a conventional luciferase reporter system and a novel Bacterial Artificial Chromosome (BAC)-based genomic reporter. The BAC system allows the evaluation of gene expression to be made in the context of its entire genomic locus and preserves the normal location and spacing of many regulatory elements which may be positioned over large distances from the initiation codon of the gene. CONCLUSIONS/SIGNIFICANCE The two approaches were used to identify a region of 17 bp located approximately 4.9 kb upstream of the first exon of the FXN gene that plays an important role in FXN gene expression. Modulation of FXN gene expression was found to be mediated by the action of the Oct-1 transcription factor at this site. A better understanding of cis-acting regulatory elements that control FXN gene expression has the potential to develop new strategies for the upregulation of the FXN gene as a therapy for FRDA.
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Affiliation(s)
- Novita Puspasari
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Cell and Gene Therapy, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Simone M. Rowley
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Lavinia Gordon
- Bioinformatics Unit, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Paul J. Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Panos A. Ioannou
- Cell and Gene Therapy, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Martin B. Delatycki
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia
| | - Joseph P. Sarsero
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Cell and Gene Therapy, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
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Terabayashi Y, Morita K, Park JY, Saito S, Shiina T, Inoko H, Ishiwata I, Fujimori KE, Hirano T. Construction of Japanese BAC library Yamato-2 (JY2): a set of 330K clone resources of damage-minimized DNA taken from a genetically established Japanese individual. Hum Cell 2011; 24:135-45. [PMID: 21611881 DOI: 10.1007/s13577-011-0019-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 04/26/2011] [Indexed: 11/30/2022]
Abstract
A bacterial artificial chromosome (BAC) library referred to as Yamato-2 (JY2), was constructed from a Japanese individual and contained 330,000 clones. Library construction was based on 2 concepts: Japanese pedigree and non-immortalization. Genomic DNA was extracted from white blood cells from umbilical cord blood of a Japanese male individual. Four traits of the sample, (1) amelogenin DNA, (2) short tandem repeat (STR), (3) mitochondrial DNA (mtDNA), and (4) HLA-allele typing, were investigated to verify attribution of the donor. One of the samples with quite good Japanese characteristics was named JY2 and used as a resource for construction of a BAC library. Amelogenin DNA indicated male. STR indicated Mongoloid. MtDNA suggested haplogroup B, which is different from any other diploid whose sequence has been reported. The HLA gene was classified into east-Asian specific haplotype. These results revealed that JY2 was obtained from a Japanese male. We sequenced both ends of 185,012 BAC clones. By using the BLAST search, BAC end sequences (BESs) were mapped on the human reference sequence provided by NCBI. Inserts of individual BAC clones were mapped with both ends properly placed. As a result, 103,647 BAC clones were successfully mapped. The average insert size of BAC calculated from the mapping information was 130 kb. Coverage and redundancy of the reference sequence by successfully mapped BAC clones were 96.4% and 3.9-fold, respectively. This library will be especially suitable as a Japanese standard genome resource. The availability of an accurate library is indispensable for diagnostics or drug-design based on genome information, and JY2 will provide an accurate sequence of the Japanese genome as an important addition to the human genome.
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Affiliation(s)
- Yasunobu Terabayashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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25
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Simón O, Palma L, Beperet I, Muñoz D, López-Ferber M, Caballero P, Williams T. Sequence comparison between three geographically distinct Spodoptera frugiperda multiple nucleopolyhedrovirus isolates: Detecting positively selected genes. J Invertebr Pathol 2011; 107:33-42. [PMID: 21238456 DOI: 10.1016/j.jip.2011.01.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 12/22/2010] [Accepted: 01/10/2011] [Indexed: 11/18/2022]
Abstract
The complete genomic sequence of a Nicaraguan plaque purified Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV) genotype SfMNPV-B was determined and compared to previously sequenced isolates from United States (SfMNPV-3AP2) and Brazil (SfMNPV-19). The genome of SfMNPV-B (132,954bp) was 1623bp and 389bp larger than that of SfMNPV-3AP2 and SfMNPV-19, respectively. Genome size differences were mainly due to a deletion located in the SfMNPV-3AP2 egt region and small deletions and point mutations in SfMNPV-19. Nucleotide sequences were strongly conserved (99.35% identity) and a high degree of predicted amino acid sequence identity was observed. A total of 145 open reading frames (ORFs) were identified in SfMNPV-B, two of them (sf39a and sf110a) had not been previously identified in the SfMNPV-3AP2 and SfMNPV-19 genomes and one (sf57a) was absent in both these genomes. In addition, sf6 was not previously identified in the SfMNPV-19 genome. In contrast, SfMNPV-B and SfMNPV-19 both lacked sf129 that had been reported in SfMNPV-3AP2. In an effort to identify genes potentially involved in virulence or in determining population adaptations, selection pressure analysis was performed. Three ORFs were identified undergoing positive selection: sf49 (pif-3), sf57 (odv-e66b) and sf122 (unknown function). Strong selection for ODV envelope protein genes indicates that the initial infection process in the insect midgut is one critical point at which adaptation acts during the transmission of these viruses in geographically distant populations. The function of ORF sf122 is being examined.
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Affiliation(s)
- Oihane Simón
- Instituto de Agrobiotecnología, CSIC, Universidad Pública de Navarra, Gobierno de Navarra, Campus Arrosadia, 31192 Mutilva Baja, Navarra, Spain
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Genome-wide interrogation of Mammalian stem cell fate determinants by nested chromosome deletions. PLoS Genet 2010; 6:e1001241. [PMID: 21170304 PMCID: PMC3000362 DOI: 10.1371/journal.pgen.1001241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 11/05/2010] [Indexed: 01/26/2023] Open
Abstract
Understanding the function of important DNA elements in mammalian stem cell genomes would be enhanced by the availability of deletion collections in which segmental haploidies are precisely characterized. Using a modified Cre-loxP–based system, we now report the creation and characterization of a collection of ∼1,300 independent embryonic stem cell (ESC) clones enriched for nested chromosomal deletions. Mapping experiments indicate that this collection spans over 25% of the mouse genome with good representative coverage of protein-coding genes, regulatory RNAs, and other non-coding sequences. This collection of clones was screened for in vitro defects in differentiation of ESC into embryoid bodies (EB). Several putative novel haploinsufficient regions, critical for EB development, were identified. Functional characterization of one of these regions, through BAC complementation, identified the ribosomal gene Rps14 as a novel haploinsufficient determinant of embryoid body formation. This new library of chromosomal deletions in ESC (DelES: http://bioinfo.iric.ca/deles) will serve as a unique resource for elucidation of novel protein-coding and non-coding regulators of ESC activity. Stem cells have received considerable public attention in part because of their potential application in regenerative therapies. Stem cells can be operationally defined as cells that have the unique property to self-renew, as well as to generate more differentiated progeny (differentiation). However, much remains to be learned about the genes regulating stem cell differentiation and renewal, their relationship to each other, and the signaling pathways that control their expression and/or activity. In this paper, we present a new resource developed in our laboratory, called DelES, for chromosomal deletion in ES cells. By reinserting deleted DNA fragments in a set of ESC clones harboring nested chromosomal deletions, we identified the Rps14 gene as being haploinsufficient for embryoid body formation. We think that our library of more than 1,300 clones represents a new resource that should allow the identification of genes and other elements that are essential for stem cell activity.
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Steward CA, Humphray S, Plumb B, Jones MC, Quail MA, Rice S, Cox T, Davies R, Bonfield J, Keane TM, Nefedov M, de Jong PJ, Lyons P, Wicker L, Todd J, Hayashizaki Y, Gulban O, Danska J, Harrow J, Hubbard T, Rogers J, Adams DJ. Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes. Genomics 2009; 95:105-10. [PMID: 19909804 PMCID: PMC2824108 DOI: 10.1016/j.ygeno.2009.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 10/23/2009] [Accepted: 10/23/2009] [Indexed: 11/16/2022]
Abstract
Non-obese diabetic (NOD) mice spontaneously develop type 1 diabetes (T1D) due to the progressive loss of insulin-secreting β-cells by an autoimmune driven process. NOD mice represent a valuable tool for studying the genetics of T1D and for evaluating therapeutic interventions. Here we describe the development and characterization by end-sequencing of bacterial artificial chromosome (BAC) libraries derived from NOD/MrkTac (DIL NOD) and NOD/ShiLtJ (CHORI-29), two commonly used NOD substrains. The DIL NOD library is composed of 196,032 BACs and the CHORI-29 library is composed of 110,976 BACs. The average depth of genome coverage of the DIL NOD library, estimated from mapping the BAC end-sequences to the reference mouse genome sequence, was 7.1-fold across the autosomes and 6.6-fold across the X chromosome. Clones from this library have an average insert size of 150 kb and map to over 95.6% of the reference mouse genome assembly (NCBIm37), covering 98.8% of Ensembl mouse genes. By the same metric, the CHORI-29 library has an average depth over the autosomes of 5.0-fold and 2.8-fold coverage of the X chromosome, the reduced X chromosome coverage being due to the use of a male donor for this library. Clones from this library have an average insert size of 205 kb and map to 93.9% of the reference mouse genome assembly, covering 95.7% of Ensembl genes. We have identified and validated 191,841 single nucleotide polymorphisms (SNPs) for DIL NOD and 114,380 SNPs for CHORI-29. In total we generated 229,736,133 bp of sequence for the DIL NOD and 121,963,211 bp for the CHORI-29. These BAC libraries represent a powerful resource for functional studies, such as gene targeting in NOD embryonic stem (ES) cell lines, and for sequencing and mapping experiments.
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von Maltzahn J, Kreuzberg MM, Matern G, Euwens C, Höher T, Wörsdörfer P, Willecke K. C-terminal tagging with eGFP yields new insights into expression of connexin45 but prevents rescue of embryonic lethal connexin45-deficient mice. Eur J Cell Biol 2009; 88:481-94. [DOI: 10.1016/j.ejcb.2009.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 04/09/2009] [Accepted: 04/20/2009] [Indexed: 10/20/2022] Open
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29
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Wang S, Zhao Y, Leiby MA, Zhu J. Studying human telomerase gene transcription by a chromatinized reporter generated by recombinase-mediated targeting of a bacterial artificial chromosome. Nucleic Acids Res 2009; 37:e111. [PMID: 19528078 PMCID: PMC2761251 DOI: 10.1093/nar/gkp511] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The endogenous human telomerase reverse transcriptase (hTERT) gene is repressed in somatic cells. To study the mechanisms of its repression, we developed a strategy of retrovirus-directed Cre recombinase-mediated BAC targeting, or RMBT, to generate single-copy integrations of BAC at pre-engineered chromosomal sites. This technique involved retroviral transduction of acceptor loci, containing an HSV thymidine kinase marker, and subsequent integration of BAC constructs into the acceptor sites, utilizing the loxP and lox511 sites present in the vector backbones. The BAC reporter, with a Renilla luciferase cassette inserted downstream of the hTERT promoter, was retrofitted with a puromycin marker. Through puromycin selection and ganciclovir counter-selection, a targeting efficiency of over 50% was achieved. We demonstrated that the activity and chromatin structures of the hTERT promoter in chromosomally integrated BAC reporter recapitulated its endogenous counterpart of the host cells. Therefore, we have established a genetically amendable platform to study chromatin and epigenetic regulation of the hTERT gene. The highly efficient and versatile RMBT technique has general applicability for studying largely unexplored chromatin-dependent mechanisms of promoter regulation of various genes.
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Affiliation(s)
- Shuwen Wang
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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Savory JG, Pilon N, Grainger S, Sylvestre JR, Béland M, Houle M, Oh K, Lohnes D. Cdx1 and Cdx2 are functionally equivalent in vertebral patterning. Dev Biol 2009; 330:114-22. [DOI: 10.1016/j.ydbio.2009.03.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 03/16/2009] [Accepted: 03/16/2009] [Indexed: 11/27/2022]
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Garigliany MM, Cloquette K, Leroy M, Decreux A, Goris N, De Clercq K, Desmecht D. Modulating mouse innate immunity to RNA viruses by expressing the Bos taurus Mx system. Transgenic Res 2009; 18:719-32. [PMID: 19387858 DOI: 10.1007/s11248-009-9268-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 04/02/2009] [Indexed: 10/20/2022]
Abstract
Mx proteins are interferon-induced members of the dynamin superfamily of large guanosine triphosphatases. These proteins have attracted much attention because some display antiviral activity against pathogenic RNA viruses, such as members of the orthomyxoviridae, bunyaviridae, and rhabdoviridae families. Among the diverse mammalian Mx proteins examined so far, we have recently demonstrated in vitro that the Bos taurus isoform 1 (boMx1) is endowed with exceptional anti-rabies-virus activity. This finding has prompted us to seek an appropriate in vivo model for confirming and evaluating gene therapy strategies. Using a BAC transgene, we have generated transgenic mouse lines expressing the antiviral boMx1 protein and boMx2 proteins under the control of their natural promoter and short- and long-range regulatory elements. Expressed boMx1 and boMx2 are correctly assembled, as deduced from mRNA sequencing and western blotting. Poly-I/C-subordinated expression of boMx1 was detected in various organs by immunohistochemistry, and transgenic lines were readily classified as high- or low-expression lines on the basis of tissue boMx1 concentrations measured by ELISA. Poly-I/C-induced Madin-Darby bovine kidney cells, bovine turbinate cells, and cultured cells from high-expression line of transgenic mice were found to contain about the same concentration of boMx1, suggesting that this protein is produced at near-physiological levels. Furthermore, insertion of the bovine Mx system rendered transgenic mice resistant to vesicular-stomatitis-virus-associated morbidity and mortality, and embryonic fibroblasts derived from high-expression transgenic mice were far less permissive to the virus. These results demonstrate that the Bos taurus Mx system is a powerful anti-VSV agent in vivo and suggest that the transgenic mouse lines generated here constitute a good model for studying in vivo the various antiviral functions-known and yet to be discovered-exerted by bovine Mx proteins, with priority emphasis on the antirabic function of boMx1.
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Affiliation(s)
- M-M Garigliany
- Department of Pathology, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
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Serotonergic transcription of human FEV reveals direct GATA factor interactions and fate of Pet-1-deficient serotonin neuron precursors. J Neurosci 2009; 28:12748-58. [PMID: 19036967 DOI: 10.1523/jneurosci.4349-08.2008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Altered expression of the human FEV (fifth Ewing variant) ETS transcription factor gene impacts the level of CNS serotonin (5-HT) neuron gene expression and maternal nurturing. However, the regulatory mechanisms that determine FEV expression are poorly understood. Here, we investigated the cis-regulatory control of FEV to begin to identify the upstream transcription factors that restrict FEV expression to 5-HT neurons. We find that sequences extending only 275 bp upstream of the FEV 5' untranslated region are sufficient to direct FEV transgene expression to embryonic 5-HT neurons, although sequences farther upstream are required for maintenance in adult 5-HT neurons. Two highly conserved consensus GATA factor binding sites within the 275 bp region interact with GATA factors in vitro. Chromatin immunoprecipitations with embryonic hindbrain demonstrated Gata-2 interactions with the orthologous mouse Pet-1 ETS cis-regulatory region. Mutagenesis of GATA sites revealed that one or the other site is required for serotonergic FEV transgene expression. Unexpectedly, FEV-LacZ transgenes enabled determination of 5-HT neuron precursor fate in the adult Pet-1(-/-) dorsal and median raphe nuclei and thus provided additional insight into FEV/Pet-1 function. Comparable numbers of FEV-LacZ-positive cells were detected in Pet-1(+/-) and Pet-1(-/-) adult dorsal raphe nuclei, indicating that the majority of mutant serotonergic precursors are not fated to apoptosis. However, B7 dorsal raphe cells were aberrantly distributed, suggesting a role for FEV/Pet-1 in their midline organization. Our findings identify a direct transcriptional interaction between Gata-2 and FEV and a unique marker for new insight into FEV/Pet-1 function in 5-HT neuron development.
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Possee RD, Hitchman RB, Richards KS, Mann SG, Siaterli E, Nixon CP, Irving H, Assenberg R, Alderton D, Owens RJ, King LA. Generation of baculovirus vectors for the high-throughput production of proteins in insect cells. Biotechnol Bioeng 2008; 101:1115-22. [PMID: 18781697 DOI: 10.1002/bit.22002] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The baculovirus expression system is one of the most popular methods used for the production of recombinant proteins but has several complex steps which have proved inherently difficult to adapt to a multi-parallel process. We have developed a bacmid vector that does not require any form of selection pressure to separate recombinant virus from non-recombinant parental virus. The method relies on homologous recombination in insect cells between a transfer vector containing a gene to be expressed and a replication-deficient bacmid. The target gene replaces a bacterial replicon at the polyhedrin loci, simultaneously restoring a virus gene essential for replication. Therefore, only recombinant virus can replicate facilitating the rapid production of multiple recombinant viruses on automated platforms in a one-step procedure. Using this vector allowed us to automate the generation of multiple recombinant viruses with a robotic liquid handler and then rapidly screen infected insect cell supernatant for the presence of secreted proteins.
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Affiliation(s)
- Robert D Possee
- National Environmental Research Council, Centre for Hydrology & Ecology, Oxford, UK
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Sasaki M, Idiris A, Tada A, Kumagai H, Giga-Hama Y, Tohda H. The gap-filling sequence on the left arm of chromosome 2 in fission yeast Schizosaccharomyces pombe. Yeast 2008; 25:673-9. [PMID: 18727152 DOI: 10.1002/yea.1613] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We report a gap-filling sequence between SPBPB21E7.09 (in contig c1348) and SPBPB10D8.01 (in contig pB10D8) on the left arm of chromosome 2 in the fission yeast, Schizosaccharomyces pombe. The sequence was determined from a BAC clone overlapping SPBPB21E7.01c (eno102) (in contig c1348) and SPBC1683.07 (mal1) (in contig pB10D8). The gap-filling sequence is 17,881 bp in length and contains five putative open reading frames, which were systematically named as SPBC460.01c, SPBC460.02c, SPBC460.03, SPBC460.04c and SPBC460.05. Their deduced amino acid sequences respectively include protein motifs corresponding to amino acid permease, glutathione S-transferase C-terminal domain, taurine catabolism dioxygenase TauD TfdA family and major facilitator superfamily, whereas their functions are unknown.
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Affiliation(s)
- Mayumi Sasaki
- ASPEX Division, Research Centre, Asahi Glass Co., Ltd., Japan
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Sequence and analysis of a plasmid-encoded mercury resistance operon from Mycobacterium marinum identifies MerH, a new mercuric ion transporter. J Bacteriol 2008; 191:439-44. [PMID: 18931130 PMCID: PMC2612448 DOI: 10.1128/jb.01063-08] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we report the DNA sequence and biological analysis of a mycobacterial mercury resistance operon encoding a novel Hg(2+) transporter. MerH was found to transport mercuric ions in Escherichia coli via a pair of essential cysteine residues but only when coexpressed with the mercuric reductase.
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The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen. BMC Genomics 2008; 9:427. [PMID: 18801193 PMCID: PMC2556355 DOI: 10.1186/1471-2164-9-427] [Citation(s) in RCA: 217] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 09/18/2008] [Indexed: 12/04/2022] Open
Abstract
Background Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium that is the causative agent of furunculosis, a bacterial septicaemia of salmonid fish. While other species of Aeromonas are opportunistic pathogens or are found in commensal or symbiotic relationships with animal hosts, A. salmonicida subsp. salmonicida causes disease in healthy fish. The genome sequence of A. salmonicida was determined to provide a better understanding of the virulence factors used by this pathogen to infect fish. Results The nucleotide sequences of the A. salmonicida subsp. salmonicida A449 chromosome and two large plasmids are characterized. The chromosome is 4,702,402 bp and encodes 4388 genes, while the two large plasmids are 166,749 and 155,098 bp with 178 and 164 genes, respectively. Notable features are a large inversion in the chromosome and, in one of the large plasmids, the presence of a Tn21 composite transposon containing mercury resistance genes and an In2 integron encoding genes for resistance to streptomycin/spectinomycin, quaternary ammonia compounds, sulphonamides and chloramphenicol. A large number of genes encoding potential virulence factors were identified; however, many appear to be pseudogenes since they contain insertion sequences, frameshifts or in-frame stop codons. A total of 170 pseudogenes and 88 insertion sequences (of ten different types) are found in the A. salmonicida genome. Comparison with the A. hydrophila ATCC 7966T genome reveals multiple large inversions in the chromosome as well as an approximately 9% difference in gene content indicating instances of single gene or operon loss or gain. A limited number of the pseudogenes found in A. salmonicida A449 were investigated in other Aeromonas strains and species. While nearly all the pseudogenes tested are present in A. salmonicida subsp. salmonicida strains, only about 25% were found in other A. salmonicida subspecies and none were detected in other Aeromonas species. Conclusion Relative to the A. hydrophila ATCC 7966T genome, the A. salmonicida subsp. salmonicida genome has acquired multiple mobile genetic elements, undergone substantial rearrangement and developed a significant number of pseudogenes. These changes appear to be a consequence of adaptation to a specific host, salmonid fish, and provide insights into the mechanisms used by the bacterium for infection and avoidance of host defence systems.
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Alizadeh A, Fitch KR, Niswender CM, McKnight GS, Barsh GS. Melanocyte-lineage expression of Cre recombinase using Mitf regulatory elements. Pigment Cell Melanoma Res 2008; 21:63-9. [PMID: 18353144 DOI: 10.1111/j.1755-148x.2007.00425.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Manipulation of gene expression in melanocytes is an important tool for studying pigment cell biology. We constructed transgenic mice in which Cre recombinase was placed under the control of regulatory elements from the Microphthalmia-associated transcriptional factor (Mitf) gene using bacterial artificial chromosome (BAC). Bacterial artificial chromosome that contained either 50 or 108 kb DNA 5' to the melanocyte-specific (1M) transcriptional start site gave rise to transgenic lines in which Cre is expressed specifically in cells of the melanocyte lineage, as judged by activation of the Gt(Rosa)26(tm1Sor)(R26R) reporter locus. Activation of R26R is first detectable in melanoblasts of midgestation embryos, and completely marks all melanocyte components of the skin in postnatal animals. To test the utility of the MitfCre transgene, we used a loxP-targeted allele of the protein kinase A alpha catalytic subunit (Prkaca), modified such that Cre-mediated recombination activates PKA signaling. On an agouti background, animals carrying both the MitfCre transgene and the targeted Prkaca allele (CalphaR) exhibited a darker coat color than control littermates, due to a shift from pheomelanin to eumelanin synthesis. Our results confirm that PKA signaling is a key component of pigment type-switching, and provide a new tool for studying pigment cell biology.
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Affiliation(s)
- Azita Alizadeh
- Departments of Genetics and Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
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Osoegawa K, de Jong PJ, Frengen E, Ioannou PA. Construction of bacterial artificial chromosome (BAC/PAC) libraries. ACTA ACUST UNITED AC 2008; Chapter 5:Unit 5.15. [PMID: 18428289 DOI: 10.1002/0471142905.hg0515s21] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This unit describes the construction of BAC and PAC libraries. Two vectors, pCYPAC2 and pPAC4 have been used for preparing PAC libraries, and a new BAC vector pBACe3.6 has been developed for construction of BAC libraries. A support protocol describes preparation of PAC or BAC vector DNA for cloning by digestion with BamHI or EcoRI, simultaneous dephosphorylation with alkaline phosphatase, and subsequent purification through pulsed-field gel electrophoresis (PFGE). For the preparation of high-molecular weight DNA for cloning, support protocols provide procedures for embedding total genomic DNA from lymphocytes or animal tissue cells, respectively, in InCert agarose. Another support protocol details the next steps for the genomic DNA: partial digestion with MboI or with a combination of EcoRI endonuclease and EcoRI methylase, and subsequent size fractionation by preparative PFGE. The final support protocol covers the isolation of BAC and PAC plasmid DNA for analyzing clones.
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Affiliation(s)
- K Osoegawa
- Roswell Park Cancer Institute, Buffalo, New York, USA
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Regulated expression of the human gastrin gene in mice. ACTA ACUST UNITED AC 2008; 151:115-22. [PMID: 18456349 DOI: 10.1016/j.regpep.2008.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Accepted: 03/17/2008] [Indexed: 01/11/2023]
Abstract
Gastrin is secreted from neuroendocrine cells residing in the adult antrum called G cells, but constitutively low levels are also expressed in the duodenum and fetal pancreas. Gastrin normally regulates gastric acid secretion by stimulating the proliferation of enterochromaffin-like cells and the release of histamine. Gastrin and progastrin forms are expressed in a number of pathological conditions and malignancies. However, the DNA regulatory elements in the human versus the mouse gastrin promoters differ suggesting differences in their transcriptional control. Thus, we describe here the expression of the human gastrin gene using a bacterial artificial chromosome (BAC) in the antral and duodenal cells of gastrin null mice. All 5 founder lines expressed the 253 kb human gastrin BAC. hGasBAC transgenic mice were bred onto a gastrin null background so that the levels of human gastrin peptide could be analyzed by immunohistochemistry and radioimmunoassay without detecting endogenous mouse gastrin. We have shown previously that chronically elevated gastrin levels suppress somatostatin. Indeed, infusion of amidated rat gastrin depressed somatostatin levels, stimulated gastric acid secretion and an increase in the numbers of G cells in the antrum and duodenum. In conclusion, human gastrin was expressed in mouse enteroendocrine cells and was regulated by somatostatin. This mouse model provides a unique opportunity to study regulation of the human gastrin promoter in vivo by somatostatin and possibly other extracellular regulators contributing to our understanding of the mechanisms involved in transcriptional control of the human gene.
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Fuhrmann C, Schmidt-Kittler O, Stoecklein NH, Petat-Dutter K, Vay C, Bockler K, Reinhardt R, Ragg T, Klein CA. High-resolution array comparative genomic hybridization of single micrometastatic tumor cells. Nucleic Acids Res 2008; 36:e39. [PMID: 18344524 PMCID: PMC2367728 DOI: 10.1093/nar/gkn101] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Only few selected cancer cells drive tumor progression and are responsible for therapy resistance. Their specific genomic characteristics, however, are largely unknown because high-resolution genome analysis is currently limited to DNA pooled from many cells. Here, we describe a protocol for array comparative genomic hybridization (array CGH), which enables the detection of DNA copy number changes in single cells. Combining a PCR-based whole genome amplification method with arrays of highly purified BAC clones we could accurately determine known chromosomal changes such as trisomy 21 in single leukocytes as well as complex genomic imbalances of single cell line cells. In single T47D cells aberrant regions as small as 1-2 Mb were identified in most cases when compared to non-amplified DNA from 10(6) cells. Most importantly, in single micrometastatic cancer cells isolated from bone marrow of breast cancer patients, we retrieved and confirmed amplifications as small as 4.4 and 5 Mb. Thus, high-resolution genome analysis of single metastatic precursor cells is now possible and may be used for the identification of novel therapy target genes.
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Affiliation(s)
- Christine Fuhrmann
- Division of Oncogenomics, Department of Pathology, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
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Osoegawa K, de Jong PJ, Frengen E, Ioannou PA. Construction of bacterial artificial chromosome (BAC/PAC) libraries. ACTA ACUST UNITED AC 2008; Chapter 5:Unit 5.9. [PMID: 18265253 DOI: 10.1002/0471142727.mb0509s55] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Large-insert genomic libraries are necessary for physical mapping of large chromosomal regions, for isolation of complete genes, and for use as intermediates in DNA sequencing of entire genomes. Construction of BAC and PAC libraries is detailed in the unit, including preparation of PAC or BAC vector DNA for cloning by digestion with BamHI or EcoRI, dephosphorylation with alkaline phosphatase, and purification through pulsed-field gel electrophoresis (PFGE). For the preparation of high-molecular weight DNA for cloning, procedures for embedding total genomic DNA from lymphocytes or animal tissue cells are also provided. Other protocols detail partial digestion of genomic DNA with MboI or with a combination of EcoRI endonuclease and EcoRI methylase (including methods for optimizing the extent of digestion), and subsequent size fractionation by preparative PFGE. Finally, the isolation of BAC and PAC plasmid DNA for analyzing clones is also presented.
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Affiliation(s)
- K Osoegawa
- Children's Hospital Oakland Research Institute, Oakland, California, USA
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Contribution of type IV pili to the virulence of Aeromonas salmonicida subsp. salmonicida in Atlantic salmon (Salmo salar L.). Infect Immun 2008; 76:1445-55. [PMID: 18212071 DOI: 10.1128/iai.01019-07] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aeromonas salmonicida subsp. salmonicida, a bacterial pathogen of Atlantic salmon, has no visible pili, yet its genome contains genes for three type IV pilus systems. One system, Tap, is similar to the Pseudomonas aeruginosa Pil system, and a second, Flp, resembles the Actinobacillus actinomycetemcomitans Flp pilus, while the third has homology to the mannose-sensitive hemagglutinin pilus of Vibrio cholerae. The latter system is likely nonfunctional since eight genes, including the gene encoding the main pilin subunit, are deleted compared with the orthologous V. cholerae locus. The first two systems were characterized to investigate their expression and role in pathogenesis. The pili of A. salmonicida subsp. salmonicida were imaged using atomic force microscopy and Tap- and Flp-overexpressing strains. The Tap pili appeared to be polar, while the Flp pili appeared to be peritrichous. Strains deficient in tap and/or flp were used in live bacterial challenges of Atlantic salmon, which showed that the Tap pilus made a moderate contribution to virulence, while the Flp pilus made little or no contribution. Delivery of the tap mutant by immersion resulted in reduced cumulative morbidity compared with the cumulative morbidity observed with the wild-type strain; however, delivery by intraperitoneal injection resulted in cumulative morbidity similar to that of the wild type. Unlike the pili of other piliated bacterial pathogens, A. salmonicida subsp. salmonicida type IV pili are not absolutely required for virulence in Atlantic salmon. Significant differences in the behavior of the two mutant strains indicated that the two pilus systems are not redundant.
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Brandt W, Khandekar M, Suzuki N, Yamamoto M, Lim KC, Engel JD. Defining the functional boundaries of the Gata2 locus by rescue with a linked bacterial artificial chromosome transgene. J Biol Chem 2008; 283:8976-83. [PMID: 18211891 DOI: 10.1074/jbc.m709364200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription factor GATA-2 is vital for both hematopoietic progenitor cell function and urogenital patterning. Transgenic mapping studies have shown that the hematopoietic and urogenital enhancers are located hundreds of kbp 5' and 3' to the Gata2 structural gene, and both are vital for embryonic development. Because the size of mammalian genes, including all of their associated regulatory elements, can exceed a megabase, transgenic complementation in mice has, in specific instances, proven to be a formidable hurdle. After incorporating the Gata2 structural gene as well as the distant hematopoietic and urogenital enhancers into a single, contiguous piece of DNA by fusing two bacterial artificial chromosomes (BACs) into one, we formally tested the hypothesis that the functional boundaries of this locus are contained within this contiguous genomic span. We show that two independent lines of transgenic mice bearing a multicopy 413-kbp-linked Gata2 BAC transgene (bearing sequences from -187 to +226 kbp of the locus) are able to fully rescue Gata2 null mutant embryonic lethality and that the rescued animals behave and reproduce normally. Surprisingly, the linked BAC confers expression in the ureteric epithelium, whereas sequences within any of the overlapping parental BACs and a yeast artificial chromosome that were originally tested do not, and thus these experiments also define a novel synthetic enhancer activity that has not been previously described. These genetic complementation studies define the required outer limits of the Gata2 locus and formally demonstrate that enhancers lying beyond those boundaries are not necessary for Gata2-regulated viability or fecundity.
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Affiliation(s)
- William Brandt
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200, USA
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Mosaic complementation demonstrates a regulatory role for myosin VIIa in actin dynamics of stereocilia. Mol Cell Biol 2007; 28:1702-12. [PMID: 18160714 PMCID: PMC2258769 DOI: 10.1128/mcb.01282-07] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed a bacterial artificial chromosome transgenesis approach that allowed the expression of myosin VIIa from the mouse X chromosome. We demonstrated the complementation of the Myo7a null mutant phenotype producing a fine mosaic of two types of sensory hair cells within inner ear epithelia of hemizygous transgenic females due to X inactivation. Direct comparisons between neighboring auditory hair cells that were different only with respect to myosin VIIa expression revealed that mutant stereocilia are significantly longer than those of their complemented counterparts. Myosin VIIa-deficient hair cells showed an abnormally persistent tip localization of whirlin, a protein directly linked to elongation of stereocilia, in stereocilia. Furthermore, myosin VIIa localized at the tips of all abnormally short stereocilia of mice deficient for either myosin XVa or whirlin. Our results strongly suggest that myosin VIIa regulates the establishment of a setpoint for stereocilium heights, and this novel role may influence their normal staircase-like arrangement within a bundle.
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Kim YJ, Song ES, Choi SY, Park SC. Engineering lacZ Reporter Gene into an ephA8 Bacterial Artificial Chromosome Using a Highly Efficient Bacterial Recombination System. BMB Rep 2007; 40:656-61. [DOI: 10.5483/bmbrep.2007.40.5.656] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Caught in the evolutionary act: precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins. Dev Biol 2007; 312:584-95. [PMID: 17956756 DOI: 10.1016/j.ydbio.2007.09.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 09/02/2007] [Accepted: 09/06/2007] [Indexed: 02/07/2023]
Abstract
The regulatory control of otxbeta1/2 in the sea urchin Strongylocentrotus purpuratus and the sea star Asterina miniata provides an exceptional opportunity to determine the genomic basis of evolutionary change in gene regulatory network (GRN) architectures. Network perturbation analyses in both taxa show that Otx regulates the transcription factors gatae and krox/blimp1 and both of these transcription factors also feed back and regulate otx. The otx gene also autoregulates. This three way interaction is an example of a GRN kernel. It has been conserved for 500 million years since these two taxa last shared a common ancestor. Amid this high level of conservation we show here one significant regulatory change. Tbrain is required for correct otxbeta1/2 expression in the sea star but not in the sea urchin. In sea urchin, tbrain is not co-expressed with otxbeta1/2 and instead has an essential role in specification of the embryonic skeleton. Tbrain in these echinoderms is thus a perfect example of an orthologous gene co-opted for entirely different developmental processes. We isolate and test the sea star otxbeta1/2 cis-regulatory module and demonstrate functional binding sites for each of the predicted inputs, including Tbrain. We compare it to the logic processing operating in the sea urchin otxbeta1/2 cis-regulatory module and present an evolutionary scenario of the change in Tbrain dependence. Finally, inter-specific gene transfer experiments confirm this scenario and demonstrate evolution occurring at the level of sequence changes to the cis-regulatory module.
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Suetsugu Y, Minami H, Shimomura M, Sasanuma SI, Narukawa J, Mita K, Yamamoto K. End-sequencing and characterization of silkworm (Bombyx mori) bacterial artificial chromosome libraries. BMC Genomics 2007; 8:314. [PMID: 17822570 PMCID: PMC2014780 DOI: 10.1186/1471-2164-8-314] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 09/07/2007] [Indexed: 11/24/2022] Open
Abstract
Background We performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two BAC libraries (an EcoRI- and a BamHI-digested library) and conducted an in silico analysis to characterize the obtained sequence data, to make them a useful resource for genomic research on the silkworm (Bombyx mori). Results More than 94000 BAC end sequences (BESs), comprising more than 55 Mbp and covering about 10.4% of the silkworm genome, were sequenced. Repeat-sequence analysis with known repeat sequences indicated that the long interspersed nuclear elements (LINEs) were abundant in BamHI BESs, whereas DNA-type elements were abundant in EcoRI BESs. Repeat-sequence analysis revealed that the abundance of LINEs might be due to a GC bias of the restriction sites and that the GC content of silkworm LINEs was higher than that of mammalian LINEs. In a BLAST-based sequence analysis of the BESs against two available whole-genome shotgun sequence data sets, more than 70% of the BESs had a BLAST hit with an identity of ≥ 99%. About 14% of EcoRI BESs and about 8% of BamHI BESs were paired-end clones with unique sequences at both ends. Cluster analysis of the BESs clarified the proportion of BESs containing protein-coding regions. Conclusion As a result of this characterization, the identified BESs will be a valuable resource for genomic research on Bombyx mori, for example, as a base for construction of a BAC-based physical map. The use of multiple complementary BAC libraries constructed with different restriction enzymes also makes the BESs a more valuable genomic resource. The GenBank accession numbers of the obtained end sequences are DE283657–DE378560.
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Affiliation(s)
- Yoshitaka Suetsugu
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Hiroshi Minami
- Mitsubishi Space Software Co. Ltd., 1-6-1 Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Michihiko Shimomura
- Mitsubishi Space Software Co. Ltd., 1-6-1 Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Shun-ichi Sasanuma
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Junko Narukawa
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Kazuei Mita
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Kimiko Yamamoto
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
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Bignell GR, Santarius T, Pole JC, Butler AP, Perry J, Pleasance E, Greenman C, Menzies A, Taylor S, Edkins S, Campbell P, Quail M, Plumb B, Matthews L, McLay K, Edwards PA, Rogers J, Wooster R, Futreal PA, Stratton MR. Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res 2007; 17:1296-303. [PMID: 17675364 PMCID: PMC1950898 DOI: 10.1101/gr.6522707] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
For decades, cytogenetic studies have demonstrated that somatically acquired structural rearrangements of the genome are a common feature of most classes of human cancer. However, the characteristics of these rearrangements at sequence-level resolution have thus far been subject to very limited description. One process that is dependent upon somatic genome rearrangement is gene amplification, a mechanism often exploited by cancer cells to increase copy number and hence expression of dominantly acting cancer genes. The mechanisms underlying gene amplification are complex but must involve chromosome breakage and rejoining. We sequenced 133 different genomic rearrangements identified within four cancer amplicons involving the frequently amplified cancer genes MYC, MYCN, and ERBB2. The observed architectures of rearrangement were diverse and highly distinctive, with evidence for sister chromatid breakage-fusion-bridge cycles, formation and reinsertion of double minutes, and the presence of bizarre clusters of small genomic fragments. There were characteristic features of sequences at the breakage-fusion junctions, indicating roles for nonhomologous end joining and homologous recombination-mediated repair mechanisms together with nontemplated DNA synthesis. Evidence was also found for sequence-dependent variation in susceptibility of the genome to somatic rearrangement. The results therefore provide insights into the DNA breakage and repair processes operative in somatic genome rearrangement and illustrate how the evolutionary histories of individual cancers can be reconstructed from large-scale cancer genome sequencing.
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Affiliation(s)
- Graham R. Bignell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas Santarius
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Jessica C.M. Pole
- Department of Pathology, University of Cambridge, Hutchinson/MRC Research Centre, Cambridge, CB2 2XZ, United Kingdom
| | - Adam P. Butler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Janet Perry
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Erin Pleasance
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Chris Greenman
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Andrew Menzies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Sheila Taylor
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Sarah Edkins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Michael Quail
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Bob Plumb
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Lucy Matthews
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Kirsten McLay
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Paul A.W. Edwards
- Department of Pathology, University of Cambridge, Hutchinson/MRC Research Centre, Cambridge, CB2 2XZ, United Kingdom
| | - Jane Rogers
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Richard Wooster
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - P. Andrew Futreal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Corresponding authors.E-mail ; fax +44-(0)1223-494809.E-mail ; fax +44-(0)1223-494809
| | - Michael R. Stratton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Institute of Cancer Research, Sutton, Surrey, SM2 5NG, United Kingdom
- Corresponding authors.E-mail ; fax +44-(0)1223-494809.E-mail ; fax +44-(0)1223-494809
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Farrar K, Donnison IS. Construction and screening of BAC libraries made from Brachypodium genomic DNA. Nat Protoc 2007; 2:1661-74. [PMID: 17641631 DOI: 10.1038/nprot.2007.204] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacterial artificial chromosome (BAC) libraries are the large DNA insert libraries of choice and valuable tools for the map-based cloning of target quantitative trait loci, physical mapping, molecular cytogenetics and comparative genomics. The protocol reported here is a simplified method used to produce and screen BAC libraries from Brachypodium species and other related grasses. Intact nuclei, containing high molecular weight (HMW) DNA, are isolated and embedded in agarose plugs. The HMW DNA is digested using an appropriate restriction enzyme and size-fractionated using pulsed-field gel electrophoresis. The DNA is isolated by dialysis, ligated into pre-prepared vector and electroporated into competent Escherichia coli cells. A PCR-based method for screening the library is also described. The entire protocol takes at least 6 weeks to complete.
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Affiliation(s)
- Kerrie Farrar
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth SY23 4AR, UK
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Mukherjee A, Soyal SM, Wheeler DA, Fernandez-Valdivia R, Nguyen J, DeMayo FJ, Lydon JP. Targeting iCre expression to murine progesterone receptor cell-lineages using bacterial artificial chromosome transgenesis. Genesis 2007; 44:601-10. [PMID: 17149722 DOI: 10.1002/dvg.20257] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Gene-targeting in embryonic stem cells has been the dominant genetic approach when engineering mouse models to query the physiologic importance of the progesterone receptor (PR). Although these models have been instrumental in disclosing the in vivo significance of the progesterone signaling pathway, generation of such mice exacts considerable expenditure of time, effort, and expense. Considering the growing list of new PR mouse models that are urgently required to address the next questions in progestin biology, bacterial artificial chromosome (BAC) recombineering in conjunction with transgenesis was evaluated as an alternative method to accelerate the creation of these models in the future. Using this approach, we describe the generation of three PR-BAC(iCre) transgenic lines in which improved Cre recombinase (iCre) was targeted in-frame, downstream, and under the control of the PR promoter contained within a BAC transgene. Crossing with the ROSA26R revealed that the PR-BAC(iCre) transgenic expresses active iCre only in cell-lineages that express the PR. The specificity of the PR-BAC(iCre) transgene not only underscores the importance of BAC-mediated transgenesis as a quick, easy, and affordable method by which to engineer the next generation of PR mouse models, but also provides a unique opportunity to investigate transcriptional control of PR expression as well as PR structure-function relationships in vivo.
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Affiliation(s)
- Atish Mukherjee
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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