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Buccheri V, Pasulka J, Malik R, Loubalova Z, Taborska E, Horvat F, Roos Kulmann MI, Jenickova I, Prochazka J, Sedlacek R, Svoboda P. Functional canonical RNAi in mice expressing a truncated Dicer isoform and long dsRNA. EMBO Rep 2024; 25:2896-2913. [PMID: 38769420 PMCID: PMC11239679 DOI: 10.1038/s44319-024-00148-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
Canonical RNA interference (RNAi) is sequence-specific mRNA degradation guided by small interfering RNAs (siRNAs) made by RNase III Dicer from long double-stranded RNA (dsRNA). RNAi roles include gene regulation, antiviral immunity or defense against transposable elements. In mammals, RNAi is constrained by Dicer's adaptation to produce another small RNA class-microRNAs. However, a truncated Dicer isoform (ΔHEL1) supporting RNAi exists in mouse oocytes. A homozygous mutation to express only the truncated ΔHEL1 variant causes dysregulation of microRNAs and perinatal lethality in mice. Here, we report the phenotype and canonical RNAi activity in DicerΔHEL1/wt mice, which are viable, show minimal miRNome changes, but their endogenous siRNA levels are an order of magnitude higher. We show that siRNA production in vivo is limited by available dsRNA, but not by Protein kinase R, a dsRNA sensor of innate immunity. dsRNA expression from a transgene yields sufficient siRNA levels to induce efficient RNAi in heart and muscle. DicerΔHEL1/wt mice with enhanced canonical RNAi offer a platform for examining potential and limits of mammalian RNAi in vivo.
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Grants
- 20-03950X Czech Science Foundation
- 647403 EC | European Research Council (ERC)
- LO1419 Ministry of Education, Youth, and Sports of the Czech Republic
- LM2018126 Ministry of Education, Youth, and Sports of the Czech Republic
- LM2023036 Ministry of Education, Youth, and Sports of the Czech Republic
- LM2023050 Ministry of Education, Youth, and Sports of the Czech Republic
- 90254 Ministry of Education, Youth, and Sports of the Czech Republic
- 90255 Ministry of Education, Youth, and Sports of the Czech Republic
- PhD fellowship Charles University
- RVO 68378050 Czech Academy of Sciences
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Affiliation(s)
- Valeria Buccheri
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
| | - Josef Pasulka
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
| | - Zuzana Loubalova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eliska Taborska
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
| | - Filip Horvat
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Marcos Iuri Roos Kulmann
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic
| | - Irena Jenickova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, 4, Czech Republic.
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2
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Nejepinska J, Malik R, Wagner S, Svoboda P. Reporters transiently transfected into mammalian cells are highly sensitive to translational repression induced by dsRNA expression. PLoS One 2014; 9:e87517. [PMID: 24475301 PMCID: PMC3903663 DOI: 10.1371/journal.pone.0087517] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/23/2013] [Indexed: 11/18/2022] Open
Abstract
In mammals, double-stranded RNA (dsRNA) can mediate sequence-specific RNA interference, activate sequence-independent interferon response, or undergo RNA editing by adenosine deaminases. We showed that long hairpin dsRNA expression had negligible effects on mammalian somatic cells--expressed dsRNA was slightly edited, poorly processed into siRNAs, and it did not activate the interferon response. At the same time, we noticed reduced reporter expression in transient co-transfections, which was presumably induced by expressed dsRNA. Since transient co-transfections are frequently used for studying gene function, we systematically explored the role of expressed dsRNA in this silencing phenomenon. We demonstrate that dsRNA expressed from transiently transfected plasmids strongly inhibits the expression of co-transfected reporter plasmids but not the expression of endogenous genes or reporters stably integrated in the genome. The inhibition is concentration-dependent, it is found in different cell types, and it is independent of transfection method and dsRNA sequence. The inhibition occurs at the level of translation and involves protein kinase R, which binds the expressed dsRNA. Thus, dsRNA expression represents a hidden danger in transient transfection experiments and must be taken into account during interpretation of experimental results.
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Affiliation(s)
- Jana Nejepinska
- Institute of Molecular Genetics of the ASCR, v.v.i., Prague, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics of the ASCR, v.v.i., Prague, Czech Republic
| | - Susan Wagner
- Institute of Microbiology of the ASCR, v.v.i., Prague, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics of the ASCR, v.v.i., Prague, Czech Republic
- * E-mail:
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3
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Deep sequencing reveals complex spurious transcription from transiently transfected plasmids. PLoS One 2012; 7:e43283. [PMID: 22916237 PMCID: PMC3420890 DOI: 10.1371/journal.pone.0043283] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 07/23/2012] [Indexed: 01/03/2023] Open
Abstract
Transient plasmid transfection is a common approach in studies in cultured mammalian cells. To examine behavior of transfected plasmids, we analyzed their transcriptional landscape by deep sequencing. We have found that the entire plasmid sequence is transcribed at different levels. Spurious transcription may have undesirable effects as some plasmids, when co-transfected, inhibited expression of luciferase reporters in a dose-dependent manner. In one case, we attributed this effect to a Kan/Neo resistance cassette, which generated a unique population of edited sense and antisense small RNAs. The unexpected complexity of expression from transiently transfected plasmids underscores the importance of appropriate experimental controls.
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Cheung W, Kotzamanis G, Abdulrazzak H, Goussard S, Kaname T, Kotsinas A, Gorgoulis VG, Grillot-Courvalin C, Huxley C. Bacterial delivery of large intact genomic-DNA-containing BACs into mammalian cells. Bioeng Bugs 2012; 3:86-92. [PMID: 22095052 DOI: 10.4161/bbug.18621] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Efficient delivery of large intact vectors into mammalian cells remains problematical. Here we evaluate delivery by bacterial invasion of two large BACs of more than 150 kb in size into various cells. First, we determined the effect of several drugs on bacterial delivery of a small plasmid into different cell lines. Most drugs tested resulted in a marginal increase of the overall efficiency of delivery in only some cell lines, except the lysosomotropic drug chloroquine, which was found to increase the efficiency of delivery by 6-fold in B16F10 cells. Bacterial invasion was found to be significantly advantageous compared with lipofection in delivering large intact BACs into mouse cells, resulting in 100% of clones containing intact DNA. Furthermore, evaluation of expression of the human hypoxanthine phosphoribosyltransferase (HPRT) gene from its genomic locus, which was present in one of the BACs, showed that single copy integrations of the HPRT-containing BAC had occurred in mouse B16F10 cells and that expression of HPRT from each human copy was 0.33 times as much as from each endogenous mouse copy. These data provide new evidence that bacterial delivery is a convenient and efficient method to transfer large intact therapeutic genes into mammalian cells.
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Affiliation(s)
- Wing Cheung
- Division of Natural Sciences, Imperial College London, London, UK
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5
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Back to BAC: the use of infectious clone technologies for viral mutagenesis. Viruses 2012; 4:211-35. [PMID: 22470833 PMCID: PMC3315213 DOI: 10.3390/v4020211] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/26/2012] [Accepted: 01/30/2012] [Indexed: 12/18/2022] Open
Abstract
Bacterial artificial chromosome (BAC) vectors were first developed to facilitate the propagation and manipulation of large DNA fragments in molecular biology studies for uses such as genome sequencing projects and genetic disease models. To facilitate these studies, methodologies have been developed to introduce specific mutations that can be directly applied to the mutagenesis of infectious clones (icBAC) using BAC technologies. This has resulted in rapid identification of gene function and expression at unprecedented rates. Here we review the major developments in BAC mutagenesis in vitro. This review summarises the technologies used to construct and introduce mutations into herpesvirus icBAC. It also explores developing technologies likely to provide the next leap in understanding these important viruses.
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6
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Nejepinska J, Malik R, Filkowski J, Flemr M, Filipowicz W, Svoboda P. dsRNA expression in the mouse elicits RNAi in oocytes and low adenosine deamination in somatic cells. Nucleic Acids Res 2011; 40:399-413. [PMID: 21908396 PMCID: PMC3245926 DOI: 10.1093/nar/gkr702] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Double-stranded RNA (dsRNA) can enter different pathways in mammalian cells, including sequence-specific RNA interference (RNAi), sequence-independent interferon (IFN) response and editing by adenosine deaminases. To study the routing of dsRNA to these pathways in vivo, we used transgenic mice ubiquitously expressing from a strong promoter, an mRNA with a long hairpin in its 3′-UTR. The expressed dsRNA neither caused any developmental defects nor activated the IFN response, which was inducible only at high expression levels in cultured cells. The dsRNA was poorly processed into siRNAs in somatic cells, whereas, robust RNAi effects were found in oocytes, suggesting that somatic cells lack some factor(s) facilitating siRNA biogenesis. Expressed dsRNA did not cause transcriptional silencing in trans. Analysis of RNA editing revealed that a small fraction of long dsRNA is edited. RNA editing neither prevented the cytoplasmic localization nor processing into siRNAs. Thus, a long dsRNA structure is well tolerated in mammalian cells and is mainly causing a robust RNAi response in oocytes.
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Affiliation(s)
- Jana Nejepinska
- Institute of Molecular Genetics AS CR, Videnska 1083, 14220 Prague 4, Czech Republic
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7
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Pérez-Luz S, Díaz-Nido J. Prospects for the use of artificial chromosomes and minichromosome-like episomes in gene therapy. J Biomed Biotechnol 2010; 2010:642804. [PMID: 20862363 PMCID: PMC2938438 DOI: 10.1155/2010/642804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 06/02/2010] [Accepted: 07/05/2010] [Indexed: 01/19/2023] Open
Abstract
Artificial chromosomes and minichromosome-like episomes are large DNA molecules capable of containing whole genomic loci, and be maintained as nonintegrating, replicating molecules in proliferating human somatic cells. Authentic human artificial chromosomes are very difficult to engineer because of the difficulties associated with centromere structure, so they are not widely used for gene-therapy applications. However, OriP/EBNA1-based episomes, which they lack true centromeres, can be maintained stably in dividing cells as they bind to mitotic chromosomes and segregate into daughter cells. These episomes are more easily engineered than true human artificial chromosomes and can carry entire genes along with all their regulatory sequences. Thus, these constructs may facilitate the long-term persistence and physiological regulation of the expression of therapeutic genes, which is crucial for some gene therapy applications. In particular, they are promising vectors for gene therapy in inherited diseases that are caused by recessive mutations, for example haemophilia A and Friedreich's ataxia. Interestingly, the episome carrying the frataxin gene (deficient in Friedreich's ataxia) has been demonstrated to rescue the susceptibility to oxidative stress which is typical of fibroblasts from Friedreich's ataxia patients. This provides evidence of their potential to treat genetic diseases linked to recessive mutations through gene therapy.
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Affiliation(s)
- Sara Pérez-Luz
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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8
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Kaname T, Yanagi K, Chinen Y, Makita Y, Okamoto N, Maehara H, Owan I, Kanaya F, Kubota Y, Oike Y, Yamamoto T, Kurosawa K, Fukushima Y, Bohring A, Opitz JM, Yoshiura KI, Niikawa N, Naritomi K. Mutations in CD96, a member of the immunoglobulin superfamily, cause a form of the C (Opitz trigonocephaly) syndrome. Am J Hum Genet 2007; 81:835-41. [PMID: 17847009 PMCID: PMC2227933 DOI: 10.1086/522014] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 06/14/2007] [Indexed: 11/03/2022] Open
Abstract
The C syndrome is characterized by trigonocephaly and associated anomalies, such as unusual facies, psychomotor retardation, redundant skin, joint and limb abnormalities, and visceral anomalies. In an individual with the C syndrome who harbors a balanced chromosomal translocation, t(3;18)(q13.13;q12.1), we discovered that the TACTILE gene for CD96, a member of the immunoglobulin superfamily, was disrupted at the 3q13.3 breakpoint. In mutation analysis of nine karyotypically normal patients given diagnoses of the C or C-like syndrome, we identified a missense mutation (839C-->T, T280M) in exon 6 of the CD96 gene in one patient with the C-like syndrome. The missense mutation was not found among 420 unaffected Japanese individuals. Cells with mutated CD96 protein (T280M) lost adhesion and growth activities in vitro. These findings indicate that CD96 mutations may cause a form of the C syndrome by interfering with cell adhesion and growth.
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Affiliation(s)
- Tadashi Kaname
- Department of Medical Genetics, University of the Ryukyus Faculty of Medicine, Nishihara, Okinawa, Japan.
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9
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Pérez-Luz S, Abdulrazzak H, Grillot-Courvalin C, Huxley C. Factor VIII mRNA expression from a BAC carrying the intact locus made by homologous recombination. Genomics 2007; 90:610-9. [PMID: 17822869 DOI: 10.1016/j.ygeno.2007.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 05/22/2007] [Accepted: 07/05/2007] [Indexed: 11/29/2022]
Abstract
Hemophilia A is caused by mutations in the gene encoding factor VIII (F8) and is an important target for gene therapy. The F8 gene contains 26 exons spread over approximately 186 kb and no work using the intact genomic locus has been carried out. We have constructed a 250-kb BAC carrying all 26 exons, the introns, and more than 40 kb of upstream and 20 kb of downstream DNA. This F8 BAC was further retrofitted with either the oriP/EBNA-1 elements from Epstein-Barr virus, which allow episomal maintenance in mammalian cells, or alphoid DNA, which allows human artificial chromosome formation in some human cell lines. Lipofection of the oriP/EBNA-1-containing version into mouse Hepa1-6 cells resulted in expression of F8 mRNA spanning the F8 gene. The >300-kb BAC carrying alphoid DNA was successfully delivered to 293A and HT1080 cells using bacterial delivery, resulting in greater than endogenous levels of F8 mRNA expression.
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10
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Kuroda T, Martuza RL, Todo T, Rabkin SD. Flip-Flop HSV-BAC: bacterial artificial chromosome based system for rapid generation of recombinant herpes simplex virus vectors using two independent site-specific recombinases. BMC Biotechnol 2006; 6:40. [PMID: 16995942 PMCID: PMC1609115 DOI: 10.1186/1472-6750-6-40] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 09/22/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oncolytic herpes simplex virus (HSV) vectors that specifically replicate in and kill tumor cells sparing normal cells are a promising cancer therapy. Traditionally, recombinant HSV vectors have been generated through homologous recombination between the HSV genome and a recombination plasmid, which usually requires laborious screening or selection and can take several months. Recent advances in bacterial artificial chromosome (BAC) technology have enabled cloning of the whole HSV genome as a BAC plasmid and subsequent manipulation in E. coli. Thus, we sought a method to generate recombinant oncolytic HSV vectors more easily and quickly using BAC technology. RESULTS We have developed an HSV-BAC system, termed the Flip-Flop HSV-BAC system, for the rapid generation of oncolytic HSV vectors. This system has the following features: (i) two site-specific recombinases, Cre and FLPe, are used sequentially to integrate desired sequences and to excise the BAC sequences, respectively; and (ii) the size of the HSV-BAC-insert genome exceeds the packaging limit of HSV so only correctly recombined virus grows efficiently. We applied this to the construction of an HSV-BAC plasmid that can be used for the generation of transcriptionally-targeted HSV vectors. BAC sequences were recombined into the UL39 gene of HSV ICP4-deletion mutant d120 to generate M24-BAC virus, from which HSV-BAC plasmid pM24-BAC was isolated. An ICP4 expression cassette driven by an exogenous promoter was re-introduced to pM24-BAC by Cre-mediated recombination and nearly pure preparations of recombinant virus were obtained typically in two weeks. Insertion of the ICP4 coding sequence alone did not restore viral replication and was only minimally better than an ICP4-null construct, whereas insertion of a CMVIE promoter-ICP4 transgene (bM24-CMV) efficiently drove viral replication. The levels of bM24-CMV replication in tumor cells varied considerably compared to hrR3 (UL39 mutant). CONCLUSION Our Flip-Flop HSV-BAC system enables rapid generation of HSV vectors carrying transgene inserts. By introducing a tumor-specific-promoter-driven ICP4 cassette into pM24-BAC using this system, one should be able to generate transcriptionally-targeted oncolytic HSV vectors. We believe this system will greatly facilitate the screening of a plethora of clinically useful tumor-specific promoters in the context of oncolytic HSV vectors.
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Affiliation(s)
- Toshihiko Kuroda
- Molecular Neurosurgery Laboratory, Department of Neurosurgery, Massachusetts General Hospital/Harvard Medical School, 185 Cambridge St., CPZN-3800, Boston, MA 02114, USA
| | - Robert L Martuza
- Molecular Neurosurgery Laboratory, Department of Neurosurgery, Massachusetts General Hospital/Harvard Medical School, 185 Cambridge St., CPZN-3800, Boston, MA 02114, USA
| | - Tomoki Todo
- Molecular Neurosurgery Laboratory, Department of Neurosurgery, Massachusetts General Hospital/Harvard Medical School, 185 Cambridge St., CPZN-3800, Boston, MA 02114, USA
- Present address: Department of Neurosurgery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113–8655, Japan
| | - Samuel D Rabkin
- Molecular Neurosurgery Laboratory, Department of Neurosurgery, Massachusetts General Hospital/Harvard Medical School, 185 Cambridge St., CPZN-3800, Boston, MA 02114, USA
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Tsuji AB, Sugyo A, Sudo H, Sagara M, Ishikawa A, Ohtsuki M, Kimura T, Ogiu T, Miyagishi M, Taira K, Imai T, Harada YN. Defective repair of radiation-induced DNA damage is complemented by a CHORI-230-65K18 BAC clone on rat chromosome 4. Genomics 2005; 87:236-42. [PMID: 16309880 DOI: 10.1016/j.ygeno.2005.09.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Revised: 08/19/2005] [Accepted: 09/29/2005] [Indexed: 11/20/2022]
Abstract
The Long Evans cinnamon (LEC) rat is highly susceptible to X-irradiation due to defective DNA repair and is thus a model for hepatocellular carcinogenesis. We constructed a bacterial artificial chromosome (BAC) contig of rat chromosome 4 completely covering the region associated with radiation susceptibility. We used transient and stable transfections to demonstrate that defective DNA repair in LEC cells is fully complemented by a 200-kb BAC, CHORI-230-65K18. Further analysis showed that the region associated with radiation susceptibility is located in a 128,543-bp region of 65K18 that includes the known gene Rpn1. However, neither knockdown nor overexpression of Rpn1 indicated that this gene is associated with radiation susceptibility. We also mapped three ESTs (TC523872, TC533727, and CB607546) in the 128,543-bp region, suggesting that 65K18 contains an unknown gene associated with X-ray susceptibility in the LEC rat.
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Affiliation(s)
- Atsushi B Tsuji
- RadGenomics Project, Frontier Research Center, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
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12
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Kotzamanis G, Cheung W, Abdulrazzak H, Perez-Luz S, Howe S, Cooke H, Huxley C. Construction of human artificial chromosome vectors by recombineering. Gene 2005; 351:29-38. [PMID: 15837432 DOI: 10.1016/j.gene.2005.01.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Revised: 01/09/2005] [Accepted: 01/24/2005] [Indexed: 11/15/2022]
Abstract
Human artificial chromosomes (HACs) can be formed de novo by transfection of large fragments of cloned alphoid DNA into human HT1080 cells in tissue culture. In order to generate HACs carrying a gene of interest, one can either co-transfect the alphoid DNA and the gene of interest, or one can clone both into a single vector prior to transfection. Here we describe linking approximately 70 kb of alphoid DNA onto a 156-kb BAC carrying the human HPRT gene using Red homologous recombination in the EL350 Escherichia coli host [Lee et al., Genomics 73 (2001) 56-65]. A selectable marker and EGFP marker were then added by loxP/Cre recombination using the arabinose inducible cre gene in the EL350 bacteria. The final construct generates minichromosomes in HT1080 cells and the HPRT gene is expressed. The retrofitting vector can be used to add the approximately 70 kb of alphoid DNA to any BAC carrying a gene of interest to generate a HAC vector. The method can also be used to link any unrelated BAC or PAC insert onto another BAC clone. The EL350 bacteria are an excellent host for building up complex vectors by a combination of homologous and loxP/Cre recombination.
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MESH Headings
- Cell Line, Tumor
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Artificial, Human/genetics
- DNA, Recombinant/genetics
- DNA, Satellite/genetics
- Escherichia coli/genetics
- Genetic Vectors/genetics
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Humans
- Hypoxanthine Phosphoribosyltransferase/genetics
- In Situ Hybridization, Fluorescence
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Recombination, Genetic
- Reverse Transcriptase Polymerase Chain Reaction
- Transfection
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Affiliation(s)
- George Kotzamanis
- Division of Biomedical Sciences, Imperial College London, South Kensington, UK
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13
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Basu J, Stromberg G, Compitello G, Willard HF, Van Bokkelen G. Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays. Nucleic Acids Res 2005; 33:587-96. [PMID: 15673719 PMCID: PMC548352 DOI: 10.1093/nar/gki207] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Efficient construction of BAC-based human artificial chromosomes (HACs) requires optimization of each key functional unit as well as development of techniques for the rapid and reliable manipulation of high-molecular weight BAC vectors. Here, we have created synthetic chromosome 17-derived alpha-satellite arrays, based on the 16-monomer repeat length typical of natural D17Z1 arrays, in which the consensus CENP-B box elements are either completely absent (0/16 monomers) or increased in density (16/16 monomers) compared to D17Z1 alpha-satellite (5/16 monomers). Using these vectors, we show that the presence of CENP-B box elements is a requirement for efficient de novo centromere formation and that increasing the density of CENP-B box elements may enhance the efficiency of de novo centromere formation. Furthermore, we have developed a novel, high-throughput methodology that permits the rapid conversion of any genomic BAC target into a HAC vector by transposon-mediated modification with synthetic alpha-satellite arrays and other key functional units. Taken together, these approaches offer the potential to significantly advance the utility of BAC-based HACs for functional annotation of the genome and for applications in gene transfer.
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Affiliation(s)
- Joydeep Basu
- Institute for Genome Sciences and Policy, Duke University CIEMAS Room 2379, 101 Science Drive, Durham, NC 27708, USA.
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14
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Chatterjee PK, Shakes LA, Srivastava DK, Garland DM, Harewood KR, Moore KJ, Coren JS. Mutually exclusive recombination of wild-type and mutant loxP sites in vivo facilitates transposon-mediated deletions from both ends of genomic DNA in PACs. Nucleic Acids Res 2004; 32:5668-76. [PMID: 15494454 PMCID: PMC524307 DOI: 10.1093/nar/gkh900] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Recombination of wild-type and mutant loxP sites mediated by wild-type Cre protein was analyzed in vivo using a sensitive phage P1 transduction assay. Contrary to some earlier reports, recombination between loxP sites was found to be highly specific: a loxP site recombined in vivo only with another of identical sequence, with no crossover recombination either between a wild-type and mutant site; or between two different mutant sites tested. Mutant loxP sites of identical sequence recombined as efficiently as wild-type. The highly specific and efficient recombination of mutant loxP sites in vivo helped in developing a procedure to progressively truncate DNA from either end of large genomic inserts in P1-derived artificial chromosomes (PACs) using transposons that carry either a wild-type or mutant loxP sequence. PAC libraries of human DNA were constructed with inserts flanked by a wild-type and one of the two mutant loxP sites, and deletions from both ends generated in clones using newly constructed wild-type and mutant loxP transposons. Analysis of the results provides new insight into the very large co-integrates formed during P1 transduction of plasmids with loxP sites: a model with tri- and possibly multimeric co-integrates comprising the PAC plasmid, phage DNA, and transposon plasmid(s) as intermediates in the cell appears best to fit the data. The ability to truncate a large piece of DNA from both ends is likely to facilitate functionally mapping gene boundaries more efficiently, and make available precisely trimmed genes in their chromosomal contexts for therapeutic applications.
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Affiliation(s)
- Pradeep K Chatterjee
- Julius L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA.
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Illenye S, Heintz NH. Functional analysis of bacterial artificial chromosomes in mammalian cells: mouse Cdc6 is associated with the mitotic spindle apparatus. Genomics 2004; 83:66-75. [PMID: 14667810 DOI: 10.1016/s0888-7543(03)00205-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Bacterial artificial chromosomes (BACs) provide a well-characterized resource for studying the functional organization of genes and other large chromosomal domains. To facilitate functional studies in cell cultures, we have developed a simple approach for generating stable cell lines with variable copy numbers of any BAC. Here we describe hamster cell lines with BAC transgenes that express mouse Cdc6 at levels that correlate with BAC copy number; show that mouse Cdc6 is regulated normally during the cell cycle, binds chromatin, and is degraded during apoptosis; and report a novel fraction of Cdc6 that associates with the spindle apparatus during mitosis. With RNA interference to assess genetic complementation by BAC alleles, this system will facilitate functional studies on large chromosomal domains at variable copy number in mammalian cell models.
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Affiliation(s)
- Sharon Illenye
- Department of Pathology and Vermont Cancer Center, University of Vermont College of Medicine, Burlington 05405, USA
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Brake RL, Chatterjee PK, Kees UR, Watt PM. The functional mapping of long-range transcription control elements of the HOX11 proto-oncogene. Biochem Biophys Res Commun 2004; 313:327-35. [PMID: 14684164 DOI: 10.1016/j.bbrc.2003.11.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Mapping of transcriptional control elements normally depends on the generation of a series of deletion mutants. The consequences of particular deletions are then functionally assessed by their ability to alter gene expression. The information derived from such investigations provides a general regulatory profile of the gene of interest, as well as generating a focus for future experiments. Due to the limitations of conventional DNA cloning methods, it has previously not been possible to use such an approach to rapidly assess the role of long-range regulatory elements that frequently lie further than 20 kb away from the coding region. In order to identify regulatory elements of the proto-oncogene HOX11 that may be mutated in a subset of childhood T-cell acute lymphoblastic leukaemia specimens, we generated nested deletions from a P1 artificial chromosome (PAC). This clone contained 95 kilobases (kb) of the HOX11 locus at 10q24; including 63 kb of 5' regulatory DNA. The deletion series was produced by the use of a recombination based cloning system and clones were subsequently transfected into mammalian cells. We have identified several long-range regulatory elements that mediate transcriptional control of HOX11. This approach is simple, rapid, and inexpensive. Furthermore, it generates multiple deletion clones in a single experiment. This novel approach opens up a new avenue for investigating long-range transcription control. Additionally, by allowing analysis of these elements in the natural context of large integrants the approach does not require the use of artificial extrachromosomal elements. This methodology can be applied to any gene cloned into a PAC or BAC vector and could also be useful in identifying appropriately sized deletion mutants for functional testing in transgenic models.
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Affiliation(s)
- Rachael L Brake
- Division of Children's Leukaemia and Cancer Research, Telethon Institute for Child Health Research and Centre for Child Health Research, The University of Western Australia, West Perth, WA 6872, Australia.
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Magin-Lachmann C, Kotzamanis G, D'Aiuto L, Wagner E, Huxley C. Retrofitting BACs with G418 resistance, luciferase, and oriP and EBNA-1 - new vectors for in vitro and in vivo delivery. BMC Biotechnol 2003; 3:2. [PMID: 12609052 PMCID: PMC150596 DOI: 10.1186/1472-6750-3-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2002] [Accepted: 02/03/2003] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Bacterial artificial chromosomes (BACs) have been used extensively for sequencing the human and mouse genomes and are thus readily available for most genes. The large size of BACs means that they can generally carry intact genes with all the long range controlling elements that drive full levels of tissue-specific expression. For gene expression studies and gene therapy applications it is useful to be able to retrofit the BACs with selectable genes such as G418 resistance, reporter genes such as luciferase, and oriP/EBNA-1 from Epstein Barr virus which allows long term episomal maintenance in mammalian cells. RESULTS We describe a series of retrofitting plasmids and a protocol for in vivo loxP/Cre recombination. The vector pRetroNeo carries a G418 resistance cassette, pRetroNeoLuc carries G418 resistance and a luciferase expression cassette, pRetroNeoLucOE carries G418 resistance, luciferase and an oriP/EBNA-1 cassette and pRetroNeoOE carries G418 resistance and oriP/EBNA-1. These vectors can be efficiently retrofitted onto BACs without rearrangement of the BAC clone. The luciferase cassette is expressed efficiently from the retrofitting plasmids and from retrofitted BACs after transient transfection of B16F10 cells in tissue culture and after electroporation into muscles of BALB/c mice in vivo. We also show that a BAC carrying GFP, oriP and EBNA-1 can be transfected into B16F10 cells with Lipofectamine 2000 and can be rescued intact after 5 weeks. CONCLUSION The pRetro vectors allow efficient retrofitting of BACs with G418 resistance, luciferase and/or oriP/EBNA-1 using in vivo expression of Cre. The luciferase reporter gene is expressed after transient transfection of retrofitted BACs into cells in tissue culture and after electroporation into mouse muscle in vivo. OriP/EBNA-1 allows stable maintenance of a 150-kb BAC without rearrangement for at least 5 weeks.
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Affiliation(s)
- Christine Magin-Lachmann
- Boehringer Ingelheim Austria GmbH, A-1121 Vienna, Austria, current address: BAXTER BioScience, A-1220 Vienna, Austria
| | - George Kotzamanis
- MAC group, Clinical Sciences Centre, Imperial College Faculty of Medicine, Hammersmith Campus, Du Cane Road, London W12 ONN, UK
| | - Leonardo D'Aiuto
- MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Ernst Wagner
- Pharmaceutical Biology-Biotechnology, Ludwig-Maximilians-Universität München, Butenandstrasse 5-13, D-81377 Munich, Germany
| | - Clare Huxley
- MAC group, Clinical Sciences Centre, Imperial College Faculty of Medicine, Hammersmith Campus, Du Cane Road, London W12 ONN, UK
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