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Laspisa D, Illa-Berenguer E, Bang S, Schmitz RJ, Parrott W, Wallace J. Mining the Utricularia gibba genome for insulator-like elements for genetic engineering. FRONTIERS IN PLANT SCIENCE 2023; 14:1279231. [PMID: 38023853 PMCID: PMC10663240 DOI: 10.3389/fpls.2023.1279231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Introduction Gene expression is often controlled via cis-regulatory elements (CREs) that modulate the production of transcripts. For multi-gene genetic engineering and synthetic biology, precise control of transcription is crucial, both to insulate the transgenes from unwanted native regulation and to prevent readthrough or cross-regulation of transgenes within a multi-gene cassette. To prevent this activity, insulator-like elements, more properly referred to as transcriptional blockers, could be inserted to separate the transgenes so that they are independently regulated. However, only a few validated insulator-like elements are available for plants, and they tend to be larger than ideal. Methods To identify additional potential insulator-like sequences, we conducted a genome-wide analysis of Utricularia gibba (humped bladderwort), one of the smallest known plant genomes, with genes that are naturally close together. The 10 best insulator-like candidates were evaluated in vivo for insulator-like activity. Results We identified a total of 4,656 intergenic regions with expression profiles suggesting insulator-like activity. Comparisons of these regions across 45 other plant species (representing Monocots, Asterids, and Rosids) show low levels of syntenic conservation of these regions. Genome-wide analysis of unmethylated regions (UMRs) indicates ~87% of the targeted regions are unmethylated; however, interpretation of this is complicated because U. gibba has remarkably low levels of methylation across the genome, so that large UMRs frequently extend over multiple genes and intergenic spaces. We also could not identify any conserved motifs among our selected intergenic regions or shared with existing insulator-like elements for plants. Despite this lack of conservation, however, testing of 10 selected intergenic regions for insulator-like activity found two elements on par with a previously published element (EXOB) while being significantly smaller. Discussion Given the small number of insulator-like elements currently available for plants, our results make a significant addition to available tools. The high hit rate (2 out of 10) also implies that more useful sequences are likely present in our selected intergenic regions; additional validation work will be required to identify which will be most useful for plant genetic engineering.
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Affiliation(s)
- Daniel Laspisa
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Eudald Illa-Berenguer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Sohyun Bang
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Wayne Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Science & Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Jason Wallace
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Science & Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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Nguyen NTB, Leung HW, Pang KT, Tay SJ, Walsh I, Choo ABH, Yang Y. Optimizing effector functions of monoclonal antibodies via tailored N-glycan engineering using a dual landing pad CHO targeted integration platform. Sci Rep 2023; 13:15620. [PMID: 37731040 PMCID: PMC10511539 DOI: 10.1038/s41598-023-42925-1] [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: 03/10/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023] Open
Abstract
Monoclonal antibodies (mAbs) eliminate cancer cells via various effector mechanisms including antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC), which are influenced by the N-glycan structures on the Fc region of mAbs. Manipulating these glycan structures on mAbs allows for optimization of therapeutic benefits associated with effector functions. Traditional approaches such as gene deletion or overexpression often lead to only all-or-nothing changes in gene expression and fail to modulate the expression of multiple genes at defined ratios and levels. In this work, we have developed a CHO cell engineering platform enabling modulation of multiple gene expression to tailor the N-glycan profiles of mAbs for enhanced effector functions. Our platform involves a CHO targeted integration platform with two independent landing pads, allowing expression of multiple genes at two pre-determined genomic sites. By combining with internal ribosome entry site (IRES)-based polycistronic vectors, we simultaneously modulated the expression of α-mannosidase II (MANII) and chimeric β-1,4-N-acetylglucosaminyl-transferase III (cGNTIII) genes in CHO cells. This strategy enabled the production of mAbs carrying N-glycans with various levels of bisecting and non-fucosylated structures. Importantly, these engineered mAbs exhibited different degrees of effector cell activation and CDC, facilitating the identification of mAbs with optimal effector functions. This platform was demonstrated as a powerful tool for producing antibody therapeutics with tailored effector functions via precise engineering of N-glycan profiles. It holds promise for advancing the field of metabolic engineering in mammalian cells.
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Affiliation(s)
- Ngan T B Nguyen
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Hau Wan Leung
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Kuin Tian Pang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Shi Jie Tay
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Ian Walsh
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Andre B H Choo
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Yuansheng Yang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore.
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Sugarcane ScDREB2B-1 Confers Drought Stress Tolerance in Transgenic Nicotiana benthamiana by Regulating the ABA Signal, ROS Level and Stress-Related Gene Expression. Int J Mol Sci 2022; 23:ijms23179557. [PMID: 36076957 PMCID: PMC9455921 DOI: 10.3390/ijms23179557] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
The dehydration-responsive element-binding protein (DREB) is a subgroup member of the AP2/ERF family and actively participates in the response of plants to abiotic stress. Although DREB genes have been studied in a variety of plant species, there are few reports of DREB genes in sugarcane (Saccharum spp.). In this study, a novel full-length cDNA sequence of the ScDREB2B-1 gene was cloned from the Saccharum hybrid ROC22, whose encoding protein contained only one AP2-conserved domain and was clustered into the DREB (A-2) subgroup. The diverse promoter elements in the ScDREB2B-1 gene and the accumulated transcripts of its homologous gene (SsAP2/ERF-107) in S. spontaneum under drought stress suggest that the ScDREB2B-1 gene may play a role in drought response. In addition, reverse transcription quantitative PCR analysis showed that the expression level of the ScDREB2B-1 gene was upregulated in the root and leaf of ROC22 under polyethylene glycol, sodium chloride and abscisic acid (ABA) treatments. The yeast two-hybrid experiment demonstrated that ScDREB2B-1 had transcriptional self-activation activity. Compared with wild-type plants, the overexpression of the ScDREB2B-1 gene improved the drought tolerance of the transgenic Nicotiana benthamiana by activating the ABA pathway to enhance the expression of the ABA-responsive gene (NbNCED) and ABA content, regulate the intracellular reactive oxygen species (ROS) level (enhance the transcripts of ROS synthase-related gene NbRbohB and the activities of catalase, peroxidase and superoxide dismutase) and increase the relative water content, proline content and expression level of osmotic stress-related genes (NbERD and NbLEA). Collectively, our data indicate that ScDREB2B-1 is a stress-inducible and ABA-responsive transcription factor gene that responds to drought stress by regulating ABA signaling, ROS levels and stress-related gene expression. This study contributes to a better understanding of the biological function of ScDREB2B-1, which could serve as a foundation for future resistance breeding in sugarcane.
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Ko N, Shim J, Kim HJ, Lee Y, Park JK, Kwak K, Lee JW, Jin DI, Kim H, Choi K. A desirable transgenic strategy using GGTA1 endogenous promoter-mediated knock-in for xenotransplantation model. Sci Rep 2022; 12:9611. [PMID: 35688851 PMCID: PMC9187654 DOI: 10.1038/s41598-022-13536-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/25/2022] [Indexed: 11/09/2022] Open
Abstract
Pig-to-human organ transplantation is a feasible solution to resolve the shortage of organ donors for patients that wait for transplantation. To overcome immunological rejection, which is the main hurdle in pig-to-human xenotransplantation, various engineered transgenic pigs have been developed. Ablation of xeno-reactive antigens, especially the 1,3-Gal epitope (GalT), which causes hyperacute rejection, and insertion of complement regulatory protein genes, such as hCD46, hCD55, and hCD59, and genes to regulate the coagulation pathway or immune cell-mediated rejection may be required for an ideal xenotransplantation model. However, the technique for stable and efficient expression of multi-transgenes has not yet been settled to develop a suitable xenotransplantation model. To develop a stable and efficient transgenic system, we knocked-in internal ribosome entry sites (IRES)-mediated transgenes into the α 1,3-galactosyltransferase (GGTA1) locus so that expression of these transgenes would be controlled by the GGTA1 endogenous promoter. We constructed an IRES-based polycistronic hCD55/hCD39 knock-in vector to target exon4 of the GGTA1 gene. The hCD55/hCD39 knock-in vector and CRISPR/Cas9 to target exon4 of the GGTA1 gene were co-transfected into white yucatan miniature pig fibroblasts. After transfection, hCD39 expressed cells were sorted by FACS. Targeted colonies were verified using targeting PCR and FACS analysis, and used as donors for somatic cell nuclear transfer. Expression of GalT, hCD55, and hCD39 was analyzed by FACS and western blotting. Human complement-mediated cytotoxicity and human antibody binding assays were conducted on peripheral blood mononuclear cells (PBMCs) and red blood cells (RBCs), and deposition of C3 by incubation with human complement serum and platelet aggregation were analyzed in GGTA1 knock-out (GTKO)/CD55/CD39 pig cells. We obtained six targeted colonies with high efficiency of targeting (42.8% of efficiency). Selected colony and transgenic pigs showed abundant expression of targeted genes (hCD55 and hCD39). Knocked-in transgenes were expressed in various cell types under the control of the GGTA1 endogenous promoter in GTKO/CD55/CD39 pig and IRES was sufficient to express downstream expression of the transgene. Human IgG and IgM binding decreased in GTKO/CD55/CD39 pig and GTKO compared to wild-type pig PBMCs and RBCs. The human complement-mediated cytotoxicity of RBCs and PBMCs decreased in GTKO/CD55/CD39 pig compared to cells from GTKO pig. C3 was also deposited less in GTKO/CD55/CD39 pig cells than wild-type pig cells. The platelet aggregation was delayed by hCD39 expression in GTKO/CD55/CD39 pig. In the current study, knock-in into the GGTA1 locus and GGTA1 endogenous promoter-mediated expression of transgenes are an appropriable strategy for effective and stable expression of multi-transgenes. The IRES-based polycistronic transgene vector system also caused sufficient expression of both hCD55 and hCD39. Furthermore, co-transfection of CRISPR/Cas9 and the knock-in vector not only increased the knock-in efficiency but also induced null for GalT by CRISPR/Cas9-mediated double-stranded break of the target site. As shown in human complement-mediated lysis and human antibody binding to GTKO/CD55/CD39 transgenic pig cells, expression of hCD55 and hCD39 with ablation of GalT prevents an effective immunological reaction in vitro. As a consequence, our technique to produce multi-transgenic pigs could improve the development of a suitable xenotransplantation model, and the GTKO/CD55/CD39 pig developed could prolong the survival of pig-to-primate xenotransplant recipients.
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Affiliation(s)
- Nayoung Ko
- Department of Transgenic Animal Research, Optipharm, Inc., Chungcheongbuk-do, Cheongju-si, 28158, Republic of Korea
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Joohyun Shim
- Department of Transgenic Animal Research, Optipharm, Inc., Chungcheongbuk-do, Cheongju-si, 28158, Republic of Korea
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Hyoung-Joo Kim
- Department of Transgenic Animal Research, Optipharm, Inc., Chungcheongbuk-do, Cheongju-si, 28158, Republic of Korea
| | - Yongjin Lee
- Department of Transgenic Animal Research, Optipharm, Inc., Chungcheongbuk-do, Cheongju-si, 28158, Republic of Korea
| | - Jae-Kyung Park
- Department of Transgenic Animal Research, Optipharm, Inc., Chungcheongbuk-do, Cheongju-si, 28158, Republic of Korea
| | - Kyungmin Kwak
- Department of Transgenic Animal Research, Optipharm, Inc., Chungcheongbuk-do, Cheongju-si, 28158, Republic of Korea
| | - Jeong-Woong Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Dajeon, Republic of Korea
| | - Dong-Il Jin
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Hyunil Kim
- Department of Transgenic Animal Research, Optipharm, Inc., Chungcheongbuk-do, Cheongju-si, 28158, Republic of Korea
| | - Kimyung Choi
- Department of Transgenic Animal Research, Optipharm, Inc., Chungcheongbuk-do, Cheongju-si, 28158, Republic of Korea.
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Lensch S, Herschl MH, Ludwig CH, Sinha J, Hinks MM, Mukund A, Fujimori T, Bintu L. Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells. eLife 2022; 11:e75115. [PMID: 35678392 PMCID: PMC9183234 DOI: 10.7554/elife.75115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/23/2022] [Indexed: 12/02/2022] Open
Abstract
In mammalian cells genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthetic gene regulation circuits. Here, we systematically dissect this process in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters, and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that silencing by KRAB, associated with histone methylation, spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by PRC2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. Gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment.
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Affiliation(s)
- Sarah Lensch
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Michael H Herschl
- University of California, Berkeley—University of California, San Francisco Graduate Program in BioengineeringBerkeleyUnited States
| | - Connor H Ludwig
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Joydeb Sinha
- Department of Chemical and Systems Biology, Stanford UniversityStanfordUnited States
| | - Michaela M Hinks
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Adi Mukund
- Biophysics Program, Stanford UniversityStanfordUnited States
| | - Taihei Fujimori
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford UniversityStanfordUnited States
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Xu T, Zhang J, Wang T, Wang X. Recombinant antibodies aggregation and overcoming strategies in CHO cells. Appl Microbiol Biotechnol 2022; 106:3913-3922. [PMID: 35608667 DOI: 10.1007/s00253-022-11977-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Mammalian cell lines are frequently used as the preferred host cells for producing recombinant therapeutic proteins (RTPs) having post-translational modified modifications similar to those observed in proteins produced by human cells. Nowadays, most RTPs approved for marketing are produced in Chinese hamster ovary (CHO) cells. Recombinant therapeutic antibodies (RTAs) are among the most important and promising RTPs for biomedical applications. A major limitation associated with the use of RTAs is their aggregation, which can be caused by a variety of factors; this results in a reduction of quality. RTA aggregations are especially concerning as they can trigger human immune responses in humans and may be fatal. Therefore, the mechanisms underlying RTA aggregation and measures for avoiding aggregation are interesting topics in RTAs research. In this review, we discuss recent progress in the field of RTAs aggregation, with a focus on factors that cause aggregation during RTA production and the development of strategies for overcoming RTA aggregation. KEY POINTS: • The recombinant antibody aggregation in mammalian cell systems is reviewed. • Intracellular environment and extracellular parameters influence recombinant antibody aggregation. • Reducing the aggregations can improve the quality of recombinant antibodies.
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Affiliation(s)
- Tingting Xu
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China.,The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, 453002, Henan, China
| | - Jihong Zhang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China.,School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Tianyun Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China. .,School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
| | - Xiaoyin Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China. .,School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
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Wang J, Khan SU, Cao P, Chen X, Wang F, Zou D, Li H, Zhao H, Xu K, Jiao D, Yang C, Zhu F, Zhang Y, Su Y, Cheng W, Jia B, Qing Y, Jamal MA, Zhao HY, Wei HJ. Construction of PIK3C3 Transgenic Pig and Its Pathogenesis of Liver Damage. Life (Basel) 2022; 12:630. [PMID: 35629298 PMCID: PMC9146193 DOI: 10.3390/life12050630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/26/2022] [Accepted: 04/08/2022] [Indexed: 11/20/2022] Open
Abstract
As a member of the PIKs family, PIK3C3 participates in autophagy and plays a central role in liver function. Several studies demonstrated that the complete suppression of PIK3C3 in mammals can cause hepatomegaly and hepatosteatosis. However, the function of PIK3C3 overexpression on the liver and other organs is still unknown. In this study, we successfully generated PIK3C3 transgenic pigs through somatic cell nuclear transfer (SCNT) by designing a specific vector for the overexpression of PIK3C3. Plasmid identification was performed through enzyme digestion and transfected into the fetal fibroblasts derived from Diannan miniature pigs. After 2 weeks of culturing, six positive colonies obtained from a total of 14 cell colonies were identified through PCR. One positive cell line was selected as the donor cell line for SCNT for the construction of PIK3C3transgenic pigs. Thirty single blastocysts were collected and identified as PIK3C3 transgenic-positive blastocysts. Two surrogates became pregnant after transferring the reconstructed embryos into four surrogates. Fetal fibroblasts of PIK3C3-positive fetuses identified through PCR were used as donor cells for SCNT to generate PIK3C3 transgenic pigs. To further explore the function of PIK3C3 overexpression, genotyping and phenotyping of the fetuses and piglets obtained were performed by PCR, immunohistochemical, HE, and apoptosis staining. The results showed that inflammatory infiltration and vacuolar formation in hepatocytes and apoptotic cells, and the mRNA expression of NF-κB, TGF-β1, TLR4, TNF-α, and IL-6 significantly increased in the livers of PIK3C3 transgenic pigs when compared with wild-type (WT) pigs. Immunofluorescence staining showed that LC3B and LAMP-1-positive cells increased in the livers of PIK3C3 transgenic pigs. In the EBSS-induced autophagy of the porcine fibroblast cells (PFCs), the accumulated LC3II protein was cleared faster in PIK3C3 transgenic (PFCs) thanWT (PFCs). In conclusion, PIK3C3 overexpression promoted autophagy in the liver and associated molecular mechanisms related to the activation of ULK1, AMBR1, DRAM1, and MTOR, causing liver damage in pigs. Therefore, the construction of PIK3C3 transgenic pigs may provide a new experimental animal resource for liver diseases.
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Affiliation(s)
- Jing Wang
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Sami Ullah Khan
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Pan Cao
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Xi Chen
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Fengchong Wang
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Di Zou
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Honghui Li
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Heng Zhao
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Kaixiang Xu
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Deling Jiao
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Chang Yang
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Feiyan Zhu
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Yaxuan Zhang
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Yanhua Su
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Wenmin Cheng
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Baoyu Jia
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Yubo Qing
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Muhammad Ameen Jamal
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hong-Ye Zhao
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Hong-Jiang Wei
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Kunming 650201, China; (J.W.); (S.U.K.); (P.C.); (X.C.); (F.W.); (D.Z.); (H.L.); (H.Z.); (K.X.); (D.J.); (C.Y.); (F.Z.); (Y.Z.); (Y.S.); (W.C.); (B.J.); (Y.Q.); (M.A.J.)
- Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
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8
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Chauhan V, Bahrudeen MNM, Palma CSD, Baptista ISC, Almeida BLB, Dash S, Kandavalli V, Ribeiro AS. Analytical kinetic model of native tandem promoters in E. coli. PLoS Comput Biol 2022; 18:e1009824. [PMID: 35100257 PMCID: PMC8830795 DOI: 10.1371/journal.pcbi.1009824] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 02/10/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Closely spaced promoters in tandem formation are abundant in bacteria. We investigated the evolutionary conservation, biological functions, and the RNA and single-cell protein expression of genes regulated by tandem promoters in E. coli. We also studied the sequence (distance between transcription start sites ‘dTSS’, pause sequences, and distances from oriC) and potential influence of the input transcription factors of these promoters. From this, we propose an analytical model of gene expression based on measured expression dynamics, where RNAP-promoter occupancy times and dTSS are the key regulators of transcription interference due to TSS occlusion by RNAP at one of the promoters (when dTSS ≤ 35 bp) and RNAP occupancy of the downstream promoter (when dTSS > 35 bp). Occlusion and downstream promoter occupancy are modeled as linear functions of occupancy time, while the influence of dTSS is implemented by a continuous step function, fit to in vivo data on mean single-cell protein numbers of 30 natural genes controlled by tandem promoters. The best-fitting step is at 35 bp, matching the length of DNA occupied by RNAP in the open complex formation. This model accurately predicts the squared coefficient of variation and skewness of the natural single-cell protein numbers as a function of dTSS. Additional predictions suggest that promoters in tandem formation can cover a wide range of transcription dynamics within realistic intervals of parameter values. By accurately capturing the dynamics of these promoters, this model can be helpful to predict the dynamics of new promoters and contribute to the expansion of the repertoire of expression dynamics available to synthetic genetic constructs. Tandem promoters are common in nature, but investigations on their dynamics have so far largely relied on synthetic constructs. Thus, their regulation and potentially unique dynamics remain unexplored. We first performed a comprehensive exploration of the conservation of genes regulated by these promoters in E. coli and the properties of their input transcription factors. We then measured protein and RNA levels expressed by 30 Escherichia coli tandem promoters, to establish an analytical model of the expression dynamics of genes controlled by such promoters. We show that start site occlusion and downstream RNAP occupancy can be realistically captured by a model with RNAP binding affinity, the time length of open complex formation, and the nucleotide distance between transcription start sites. This study contributes to a better understanding of the unique dynamics tandem promoters can bring to the dynamics of gene networks and will assist in their use in synthetic genetic circuits.
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Affiliation(s)
- Vatsala Chauhan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Mohamed N. M. Bahrudeen
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Cristina S. D. Palma
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Ines S. C. Baptista
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Bilena L. B. Almeida
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Suchintak Dash
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Vinodh Kandavalli
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andre S. Ribeiro
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Finland
- * E-mail:
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9
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Tripathi S, Brahmachari S, Onuchic JN, Levine H. DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases. Nucleic Acids Res 2021; 50:1269-1279. [PMID: 34951454 PMCID: PMC8860607 DOI: 10.1093/nar/gkab1252] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or ‘push’ between closely spaced RNAPs. However, recent studies have posited that RNAPs separated by longer distances may cooperate by modifying the DNA segment under transcription. Here, we present a theoretical model incorporating the mechanical coupling between RNAP translocation and the DNA torsional response. Using stochastic simulations, we demonstrate DNA supercoiling-mediated long-range cooperation between co-transcribing RNAPs. We find that inhibiting transcription initiation can slow down the already recruited RNAPs, in agreement with recent experimental observations, and predict that the average transcription elongation rate varies non-monotonically with the rate of transcription initiation. We further show that while RNAPs transcribing neighboring genes oriented in tandem can cooperate, those transcribing genes in divergent or convergent orientations can act antagonistically, and that such behavior holds over a large range of intergenic separations. Our model makes testable predictions, revealing how the mechanical interplay between RNAPs and the DNA they transcribe can govern transcriptional dynamics.
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Affiliation(s)
- Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA.,Center for Theoretical Biological Physics & Department of Physics, Northeastern University, Boston, MA, USA
| | | | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Physics and Astronomy, Department of Chemistry, & Department of Biosciences, Rice University, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics & Department of Physics, Northeastern University, Boston, MA, USA
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10
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Smirnov A, Battulin N. Concatenation of Transgenic DNA: Random or Orchestrated? Genes (Basel) 2021; 12:genes12121969. [PMID: 34946918 PMCID: PMC8701086 DOI: 10.3390/genes12121969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022] Open
Abstract
Generation of transgenic organisms by pronuclear microinjection has become a routine procedure. However, while the process of DNA integration in the genome is well understood, we still do not know much about the recombination between transgene molecules that happens in the first moments after DNA injection. Most of the time, injected molecules are joined together in head-to-tail tandem repeats-the so-called concatemers. In this review, we focused on the possible concatenation mechanisms and how they could be studied with genetic reporters tracking individual copies in concatemers. We also discuss various features of concatemers, including palindromic junctions and repeat-induced gene silencing (RIGS). Finally, we speculate how cooperation of DNA repair pathways creates a multicopy concatenated insert.
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Affiliation(s)
- Alexander Smirnov
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Nariman Battulin
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
- Institute of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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11
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Tak H, Negi S, Ganapathi TR. The 5'-upstream region of WRKY18 transcription factor from banana is a stress-inducible promoter with strong expression in guard cells. PHYSIOLOGIA PLANTARUM 2021; 173:1335-1350. [PMID: 33421142 DOI: 10.1111/ppl.13326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/07/2020] [Accepted: 12/24/2020] [Indexed: 06/12/2023]
Abstract
Increasing crop productivity in an ever-changing environmental scenario is a major challenge for maintaining the food supply worldwide. Generation of crops having broad-spectrum pathogen resistance with the ability to cope with water scarcity is the only solution to feed the expanding world population. Stomatal closure has implications on pathogen colonization and drought tolerance. Recent studies have provided novel insights into networks involved in stomatal closure which is being used in biotechnological applications for improving crop endurance. Despite that genetic engineering of stomata requires guard cell preferred or specific regulatory regions to avoid undesirable side effects. In the present study, we describe the 5'-upstream regulatory region of the WRKY18 transcription factor of banana and functionally analyzed its stress meditated activation and strong guard cell preferred activity. Expression of MusaWRKY18 is augmented in leaves of banana cultivars Karibale Monthan, Rasthali and Grand Nain under multiple stress conditions suggesting its role in stress responses of banana plants. Transgenic tobacco lines harboring PMusaWRKY18 -β-D-glucuronidase (GUS) were regenerated and GUS staining demonstrated substantial GUS expression in guard cells which corroborates with multiple Dof1 binding cis-elements in PMusaWRKY18 . Fluorescent β-galactosidase assay demonstrated the stress-mediated strong induction profiles of PMusaWRKY18 at different time points in transgenic tobacco lines exposed to drought, high-salinity, cold, and applications of abscisic acid, salicylic acid, methyl jasmonate, and ethephon. This study sheds novel insights into guard cell preferred expression of WRKY genes under stress and confirm the utility of PMusaWRKY18 for exploring guard cell functions and guard cell engineering.
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Affiliation(s)
- Himanshu Tak
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Sanjana Negi
- Department of Biotechnology, University of Mumbai, Mumbai, India
| | - Thumballi R Ganapathi
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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12
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Mehta D, Chirmade T, Tungekar AA, Gani K, Bhambure R. Cloning and expression of antibody fragment (Fab) I: Effect of expression construct and induction strategies on light and heavy chain gene expression. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Zhou Q, Jiao L, Li W, Hu Z, Li Y, Zhang H, Yang M, Xu L, Yan Y. A Novel Cre/ lox-Based Genetic Tool for Repeated, Targeted and Markerless Gene Integration in Yarrowia lipolytica. Int J Mol Sci 2021; 22:ijms221910739. [PMID: 34639080 PMCID: PMC8509416 DOI: 10.3390/ijms221910739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/28/2021] [Accepted: 10/02/2021] [Indexed: 01/30/2023] Open
Abstract
The unconventional yeast Yarrowia lipolytica is extensively applied in bioproduction fields owing to its excellent metabolite and protein production ability. Nonetheless, utilization of this promising host is still restricted by the limited availability of precise and effective gene integration tools. In this study, a novel and efficient genetic tool was developed for targeted, repeated, and markerless gene integration based on Cre/lox site-specific recombination system. The developed tool required only a single selection marker and could completely excise the unnecessary sequences. A total of three plasmids were created and seven rounds of marker-free gene integration were examined in Y. lipolytica. All the integration efficiencies remained above 90%, and analysis of the protein production and growth characteristics of the engineered strains confirmed that genome modification via the novel genetic tool was feasible. Further work also confirmed that the genetic tool was effective for the integration of other genes, loci, and strains. Thus, this study significantly promotes the application of the Cre/lox system and presents a powerful tool for genome engineering in Y. lipolytica.
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Affiliation(s)
| | | | | | | | | | | | | | - Li Xu
- Correspondence: (L.X.); (Y.Y.)
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14
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Patel YD, Brown AJ, Zhu J, Rosignoli G, Gibson SJ, Hatton D, James DC. Control of Multigene Expression Stoichiometry in Mammalian Cells Using Synthetic Promoters. ACS Synth Biol 2021; 10:1155-1165. [PMID: 33939428 PMCID: PMC8296667 DOI: 10.1021/acssynbio.0c00643] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 01/22/2023]
Abstract
To successfully engineer mammalian cells for a desired purpose, multiple recombinant genes are required to be coexpressed at a specific and optimal ratio. In this study, we hypothesized that synthetic promoters varying in transcriptional activity could be used to create single multigene expression vectors coexpressing recombinant genes at a predictable relative stoichiometry. A library of 27 multigene constructs was created comprising three discrete fluorescent reporter gene transcriptional units in fixed series, each under the control of either a relatively low, medium, or high transcriptional strength synthetic promoter in every possible combination. Expression of each reporter gene was determined by absolute quantitation qRT-PCR in CHO cells. The synthetic promoters did generally function as designed within a multigene vector context; however, significant divergences from predicted promoter-mediated transcriptional activity were observed. First, expression of all three genes within a multigene vector was repressed at varying levels relative to coexpression of identical reporter genes on separate single gene vectors at equivalent gene copies. Second, gene positional effects were evident across all constructs where expression of the reporter genes in positions 2 and 3 was generally reduced relative to position 1. Finally, after accounting for general repression, synthetic promoter transcriptional activity within a local multigene vector format deviated from that expected. Taken together, our data reveal that mammalian synthetic promoters can be employed in vectors to mediate expression of multiple genes at predictable relative stoichiometries. However, empirical validation of functional performance is a necessary prerequisite, as vector and promoter design features can significantly impact performance.
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Affiliation(s)
- Yash D. Patel
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, U.K.
| | - Adam J. Brown
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, U.K.
| | - Jie Zhu
- Cell
Culture and Fermentation Sciences, BioPharmaceuticals Development,
R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Guglielmo Rosignoli
- Dynamic
Omics, Antibody Discovery & Protein Engineering, R&D, AstraZeneca, Cambridge, CB21 6GH, U.K.
| | - Suzanne J. Gibson
- Cell
Culture and Fermentation Sciences, BioPharmaceuticals Development,
R&D, AstraZeneca, Cambridge, CB21 6GH, U.K.
| | - Diane Hatton
- Cell
Culture and Fermentation Sciences, BioPharmaceuticals Development,
R&D, AstraZeneca, Cambridge, CB21 6GH, U.K.
| | - David C. James
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, U.K.
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15
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Bhaskara V, Leal MT, Seigner J, Friedrich T, Kreidl E, Gadermaier E, Tesarz M, Rogalli A, Stangl L, Wallwitz J, Hammel K, Rothbauer M, Moll H, Ertl P, Hahn R, Himmler G, Bauer A, Casanova E. Efficient production of recombinant secretory IgA against Clostridium difficile toxins in CHO-K1 cells. J Biotechnol 2021; 331:1-13. [PMID: 33689865 DOI: 10.1016/j.jbiotec.2021.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/25/2021] [Accepted: 02/22/2021] [Indexed: 12/29/2022]
Abstract
Despite the essential role secretory IgAs play in the defense against pathogenic invasion and the proposed value of recombinant secretory IgAs as novel therapeutics, currently there are no IgA-based therapies in clinics. Secretory IgAs are complex molecules and the major bottleneck limiting their therapeutic potential is a reliable recombinant production system. In this report, we addressed this issue and established a fast and robust production method for secretory IgAs in CHO-K1 cells using BAC-based expression vectors. As a proof of principle, we produced IgAs against Clostridium difficile toxins TcdA and TcdB. Recombinant secretory IgAs produced using our expression system showed comparable titers to IgGs, widely used as therapeutic biologicals. Importantly, secretory IgAs produced using our method were functional and could efficiently neutralize Clostridium difficile toxins TcdA and TcdB. These results show that recombinant secretory IgAs can be efficiently produced, thus opening the possibility to use them as therapeutic agents in clinics.
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Affiliation(s)
- Venugopal Bhaskara
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria.
| | - Maria Trinidad Leal
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | - Jacqueline Seigner
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | - Theresa Friedrich
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | | | | | | | | | - Laura Stangl
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | | | - Katharina Hammel
- Department for Biotechnology, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
| | - Mario Rothbauer
- Institute of Applied Synthetic Chemistry and Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, 1060 Vienna, Austria
| | - Herwig Moll
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | - Peter Ertl
- Institute of Applied Synthetic Chemistry and Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, 1060 Vienna, Austria
| | - Rainer Hahn
- Department for Biotechnology, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
| | | | - Anton Bauer
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria; The Antibody Lab GmbH, 1210 Vienna, Austria.
| | - Emilio Casanova
- Department of Physiology, Center of Physiology and Pharmacology and Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria.
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16
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Doshi J, Willis K, Madurga A, Stelzer C, Benenson Y. Multiple Alternative Promoters and Alternative Splicing Enable Universal Transcription-Based Logic Computation in Mammalian Cells. Cell Rep 2020; 33:108437. [PMID: 33264624 DOI: 10.1016/j.celrep.2020.108437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 09/04/2020] [Accepted: 11/05/2020] [Indexed: 10/22/2022] Open
Abstract
Multi-input logic gene circuits can enable sophisticated control of cell function, yet large-scale synthetic circuitry in mammalian cells has relied on post-transcriptional regulation or recombinase-triggered state transitions. Large-scale transcriptional logic, on the other hand, has been challenging to implement. Inspired by a naturally found regulatory strategy of using multiple alternative promoters, followed by alternative splicing, we developed a scalable and compact platform for transcriptional OR logic using inputs to those promoters. The platform is extended to implement disjunctive normal form (DNF) computations capable of implementing arbitrary logic rules. Specifically, AND logic is implemented at individual promoters using synergistic transcriptional inputs, and NOT logic via microRNA inputs targeting unique exon sequences driven by those promoters. Together, these regulatory programs result in DNF-like logic control of output gene expression. The approach offers flexibility for building complex logic programs in mammalian cells.
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Affiliation(s)
- Jiten Doshi
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Katie Willis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Angela Madurga
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Christoph Stelzer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Yaakov Benenson
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland.
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17
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Sergeeva D, Lee GM, Nielsen LK, Grav LM. Multicopy Targeted Integration for Accelerated Development of High-Producing Chinese Hamster Ovary Cells. ACS Synth Biol 2020; 9:2546-2561. [PMID: 32835482 DOI: 10.1021/acssynbio.0c00322] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ever-growing biopharmaceutical industry relies on the production of recombinant therapeutic proteins in Chinese hamster ovary (CHO) cells. The traditional timelines of CHO cell line development can be significantly shortened by the use of targeted gene integration (TI). However, broad use of TI has been limited due to the low specific productivity (qP) of TI-generated clones. Here, we show a 10-fold increase in the qP of therapeutic glycoproteins in CHO cells through the development and optimization of a multicopy TI method. We used a recombinase-mediated cassette exchange (RMCE) platform to investigate the effect of gene copy number, 5' and 3' gene regulatory elements, and landing pad features on qP. We evaluated the limitations of multicopy expression from a single genomic site as well as multiple genomic sites and found that a transcriptional bottleneck can appear with an increase in gene dosage. We created a dual-RMCE system for simultaneous multicopy TI in two genomic sites and generated isogenic high-producing clones with qP of 12-14 pg/cell/day and product titer close to 1 g/L in fed-batch. Our study provides an extensive characterization of the multicopy TI method and elucidates the relationship between gene copy number and protein expression in mammalian cells. Moreover, it demonstrates that TI-generated CHO cells are capable of producing therapeutic proteins at levels that can support their industrial manufacture.
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Affiliation(s)
- Daria Sergeeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Lars Keld Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane 4072, Australia
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
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18
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Kelleher ES, Barbash DA, Blumenstiel JP. Taming the Turmoil Within: New Insights on the Containment of Transposable Elements. Trends Genet 2020; 36:474-489. [PMID: 32473745 DOI: 10.1016/j.tig.2020.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) are mobile genetic parasites that can exponentially increase their genomic abundance through self-propagation. Classic theoretical papers highlighted the importance of two potentially escalating forces that oppose TE spread: regulated transposition and purifying selection. Here, we review new insights into mechanisms of TE regulation and purifying selection, which reveal the remarkable foresight of these theoretical models. We further highlight emergent connections between transcriptional control enacted by small RNAs and the contribution of TE insertions to structural mutation and host-gene regulation. Finally, we call for increased comparative analysis of TE dynamics and fitness effects, as well as host control mechanisms, to reveal how interconnected forces shape the differential prevalence and distribution of TEs across the tree of life.
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19
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Carver J, Ng D, Zhou M, Ko P, Zhan D, Yim M, Shaw D, Snedecor B, Laird MW, Lang S, Shen A, Hu Z. Maximizing antibody production in a targeted integration host by optimization of subunit gene dosage and position. Biotechnol Prog 2020; 36:e2967. [DOI: 10.1002/btpr.2967] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 01/10/2020] [Accepted: 01/17/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Joe Carver
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - Domingos Ng
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - Michelle Zhou
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - Peggy Ko
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - Dejin Zhan
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - Mandy Yim
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - David Shaw
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - Brad Snedecor
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - Michael W. Laird
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - Steven Lang
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - Amy Shen
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
| | - Zhilan Hu
- Department of Cell CultureGenentech, Inc. South San Francisco California USA
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20
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Betts SD, Basu S, Bolar J, Booth R, Chang S, Cigan AM, Farrell J, Gao H, Harkins K, Kinney A, Lenderts B, Li Z, Liu L, McEnany M, Mutti J, Peterson D, Sander JD, Scelonge C, Sopko X, Stucker D, Wu E, Chilcoat ND. Uniform Expression and Relatively Small Position Effects Characterize Sister Transformants in Maize and Soybean. FRONTIERS IN PLANT SCIENCE 2019; 10:1209. [PMID: 31708936 PMCID: PMC6821721 DOI: 10.3389/fpls.2019.01209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/03/2019] [Indexed: 05/20/2023]
Abstract
Development of transgenic cell lines or organisms for industrial, agricultural, or medicinal applications involves inserting DNA into the target genome in a way that achieves efficacious transgene expression without a deleterious impact on fitness. The genomic insertion site is widely recognized as an important determinant of success. However, the effect of chromosomal location on transgene expression and fitness has not been systematically investigated in plants. Here we evaluate the importance of transgene insertion site in maize and soybean using both random and site-specific transgene integration. We have compared the relative contribution of genomic location on transgene expression levels with other factors, including cis-regulatory elements, neighboring transgenes, genetic background, and zygosity. As expected, cis-regulatory elements and the presence/absence of nearby transgene neighbors can impact transgene expression. Surprisingly, we determined not only that genomic location had the least impact on transgene expression compared to the other factors that were investigated but that the majority of insertion sites recovered supported transgene expression levels that were statistically not distinguishable. All 68 genomic sites evaluated were capable of supporting high-level transgene expression, which was also consistent across generations. Furthermore, multilocation field evaluation detected no to little decrease in agronomic performance as a result of transgene insertion at the vast majority of sites we evaluated with a single construct in five maize hybrid backgrounds.
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Affiliation(s)
| | | | - Joy Bolar
- Corteva Agriscience, Johnston, IA, United States
| | - Russ Booth
- Corteva Agriscience, Johnston, IA, United States
| | - Shujun Chang
- Benson Hill Biosystems, Inc. St. Louis, MO, United States
| | | | | | - Huirong Gao
- Corteva Agriscience, Johnston, IA, United States
| | | | | | | | | | - Lu Liu
- Corteva Agriscience, Johnston, IA, United States
| | | | | | | | | | - Chris Scelonge
- KWS Gateway Research Center, LLC, St. Louis, MO, United States
| | - Xiaoyi Sopko
- Corteva Agriscience, Johnston, IA, United States
| | - Dave Stucker
- Corteva Agriscience, Johnston, IA, United States
| | - Emily Wu
- Corteva Agriscience, Johnston, IA, United States
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21
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Ju X, Li D, Liu S. Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria. Nat Microbiol 2019; 4:1907-1918. [PMID: 31308523 PMCID: PMC6814526 DOI: 10.1038/s41564-019-0500-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/29/2019] [Indexed: 12/18/2022]
Abstract
The ability to determine full-length nucleotide composition of individual RNA molecules is essential for understanding the architecture and function of a transcriptome. However, experimental approaches capable of capturing the sequences of both 5' and 3' termini of the same transcript remain scarce. In the present study, simultaneous 5' and 3' end sequencing (SEnd-seq)-a high-throughput and unbiased method that simultaneously maps transcription start and termination sites with single-nucleotide resolution-is presented. Using this method, a comprehensive view of the Escherichia coli transcriptome was obtained, which displays an unexpected level of complexity. SEnd-seq notably expands the catalogue of transcription start sites and termination sites, defines unique transcription units and detects prevalent antisense RNA. Strikingly, the results of the present study unveil widespread overlapping bidirectional terminators located between opposing gene pairs. Furthermore, it has been shown that convergent transcription is a major contributor to highly efficient bidirectional termination both in vitro and in vivo. This finding highlights an underappreciated role of RNA polymerase conflicts in shaping transcript boundaries and suggests an evolutionary strategy for modulating transcriptional output by arranging gene orientation.
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Affiliation(s)
- Xiangwu Ju
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Dayi Li
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.,The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.
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22
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Li X, Hao F, Hu X, Wang H, Dai B, Wang X, Liang H, Cang M, Liu D. Generation of Tβ4 knock-in Cashmere goat using CRISPR/Cas9. Int J Biol Sci 2019; 15:1743-1754. [PMID: 31360116 PMCID: PMC6643211 DOI: 10.7150/ijbs.34820] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022] Open
Abstract
The cashmere goat breed is known to provide excellent quality cashmere. Here, we attempted to breed high-yielding cashmere goats by specifically inserting the Tβ4 gene into the goat CCR5 locus and provided an animal model for future research. We successfully obtained Tβ4 knock-in goat without any screening and fluorescent markers using CRISPR/Cas9 technology. A series of experiments were performed to examine physical conditions and characteristics of the Tβ4 knock-in goat. The goat exhibited an increase in cashmere yield by 74.5% without affecting the fineness and quality. Additionally, RNA-seq analysis indicated that Tβ4 may promote hair growth by affecting processes such as vasoconstriction, angiogenesis, and vascular permeability around secondary hair follicles. Together, our study can significantly improve the breeding of cashmere goat and thereby increase economic efficiency.
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Affiliation(s)
- Xiaocong Li
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010000, China
| | - Fei Hao
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010000, China
| | - Xiao Hu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010000, China
| | - Hui Wang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010000, China
| | - Bai Dai
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010000, China
| | - Xiao Wang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010000, China
| | - Hao Liang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010000, China
| | - Ming Cang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010000, China
| | - Dongjun Liu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010000, China
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23
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Ong EC, Smidt P, McGrew JT. Limiting the metabolic burden of recombinant protein expression during selection yields pools with higher expression levels. Biotechnol Prog 2019; 35:e2839. [PMID: 31090257 DOI: 10.1002/btpr.2839] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/02/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
In order to avoid the metabolic burden of protein expression during cell growth, and to avoid potential toxicity of recombinant proteins, microbial expression systems typically utilize regulated expression vectors. In contrast, constitutive expression vectors have usually been utilized for isolation of protein expressing mammalian cell lines. In mammalian systems, inducible expression vectors are typically utilized for only those proteins that are toxic when overexpressed. We developed a tetracycline regulated expression system in CHO cells, and show that cell pools selected in the uninduced state recover faster than those selected in the induced state even though the proteins showed no apparent toxicity or expression instability. Furthermore, cell pools selected in the uninduced state had higher expression levels when protein expression was turned on only in production cultures compared to pools that were selected and maintained in the induced state through production. We show a titer improvement of greater than twofold for an Fc-fusion protein and greater than 50% improvement for a recombinant antibody. The improvement is primarily due to an increase in specific productivity. Recombinant protein mRNA levels correlate strongly with protein expression levels and are highest in those cultures selected in the uninduced state and only induced during production. These data are consistent with a model where CHO cell lines with constitutive expression select for subclones with lower expression levels.
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Affiliation(s)
- E-Ching Ong
- Process Design, Just Biotherapeutics, Seattle, Washington
| | - Pauline Smidt
- Process Design, Just Biotherapeutics, Seattle, Washington
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24
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Liu F, Liu J, Yuan Z, Qing Y, Li H, Xu K, Zhu W, Zhao H, Jia B, Pan W, Guo J, Zhang X, Cheng W, Wang W, Zhao HY, Wei HJ. Generation of GTKO Diannan Miniature Pig Expressing Human Complementary Regulator Proteins hCD55 and hCD59 via T2A Peptide-Based Bicistronic Vectors and SCNT. Mol Biotechnol 2019; 60:550-562. [PMID: 29916131 DOI: 10.1007/s12033-018-0091-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Pig-to-human organ transplantation has drawn attention in recent years due to the potential use of pigs as an alternative source of human donor organs. While GGTA1 knockout (GTKO) can protect xenografts from hyperacute rejection, complement-dependent cytotoxicity might still contribute to this type of rejection. To prolong the xenograft survival, we utilized a T2A-mediated pCMV-hCD55-T2A-hCD59-Neo vector and transfected the plasmid into GTKO Diannan miniature pig fetal fibroblasts. After G418 selection combined with single-cell cloning culture, four colonies were obtained, and three of these were successfully transfected with the hCD55 and hCD59. One of the three colonies was selected as donor cells for somatic cell nuclear transfer (SCNT). Then, the reconstructed embryos were transferred into eight recipient gilts, resulting in four pregnancies. Three of the pregnant gilts delivered, yielding six piglets. Only one piglet carried hCD55 and hCD59 genetic modification. The expression levels of the GGTA1, hCD55, and hCD59 in the tissues and fibroblasts of the piglet were determined by q-PCR, fluorescence microscopy, immunohistochemical staining, and western blotting analyses. The results showed the absence of GGTA1 and the coexpression of the hCD55 and hCD59. However, the mRNA expression levels of hCD55 and hCD59 in the GTKO/hCD55/hCD59 pig fibroblasts were lower than that in human 293T cells, which may be caused by low copy number and/or CMV promoter methylation. Furthermore, we performed human complement-mediated cytolysis assays using human serum solutions from 0 to 60%. The result showed that the fibroblasts of this triple-gene modified piglet had greater survival rates than that of wild-type and GTKO controls. Taken together, these results indicate that T2A-mediated polycistronic vector system combined with SCNT can effectively generate multiplex genetically modified pigs, additional hCD55 and hCD59 expression on top of a GTKO genetic background markedly enhance the protective effect towards human serum-mediated cytolysis than those of GTKO alone. Thus, we suggest that GTKO/hCD55/hCD59 triple-gene-modified Diannan miniature pig will be a more eligible donor for xenotransplantation.
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Affiliation(s)
- Fengjuan Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jinji Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Zaimei Yuan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Yubo Qing
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Honghui Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Kaixiang Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Wanyun Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Heng Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Baoyu Jia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Weirong Pan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jianxiong Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuezeng Zhang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Wenmin Cheng
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Wei Wang
- Hunan Xeno Life Science Co., Ltd, Changsha, 410600, China.
- Institute for Cell Transplantation and Gene Therapy, The Third Xiangya Hospital Central-South University, Changsha, 410013, China.
| | - Hong-Ye Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.
| | - Hong-Jiang Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China.
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25
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Transcription termination sequences support the expression of transgene product secreted with milk. Transgenic Res 2019; 28:401-410. [PMID: 30919251 DOI: 10.1007/s11248-019-00122-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 03/12/2019] [Indexed: 01/04/2023]
Abstract
Expression of the reporter gene in transgenic animals depends on the surrounding chromatin environment. Recent genome-wide studies have shown that, in mammals, the entire genome is transcribed. Transcription through a transgene often has a negative effect on the expression of a reporter gene. Here, we compared the ability of well-studied chicken chromatin insulator HS4 and bidirectional transcription terminators from the human genome to support high-level expression of the firefly luciferase gene (Fluc) under control of the previously characterized goat β-casein gene promoter. The insertion of HS4 or either of the two transcription terminators upstream of the promoter resulted in tenfold enhancement of Fluc expression in the mammary glands of transgenic mice. These results suggest that transcriptional terminators, similar to the HS4 insulator, can be used to improve the reporter gene expression in transgenic animals.
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26
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Xie X, Chen C, Liang Q, Wu X, Wang X, Wu W, Ding Q. Characterization of two large duplications of
F9
associated with mild and severe haemophilia B, respectively. Haemophilia 2019; 25:475-483. [PMID: 30866119 DOI: 10.1111/hae.13704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/06/2018] [Accepted: 01/23/2019] [Indexed: 02/01/2023]
Affiliation(s)
- Xiaoling Xie
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Qian Liang
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
| | - Wenman Wu
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
- Faculty of Medical Laboratory Science, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
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27
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Boldogkői Z, Tombácz D, Balázs Z. Interactions between the transcription and replication machineries regulate the RNA and DNA synthesis in the herpesviruses. Virus Genes 2019; 55:274-279. [PMID: 30767118 PMCID: PMC6536478 DOI: 10.1007/s11262-019-01643-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/24/2019] [Indexed: 12/04/2022]
Abstract
The temporal coordination of viral gene expression is imperative for the regulation of the herpesvirus replication cycle. While the main factors of this transcriptional coordination are known, the subtler control mechanisms of gene expression remain elusive. Recent long read sequencing-based approached have revealed an intricate meshwork of overlaps between the herpesvirus transcripts and the overlap of the replication origins with noncoding RNAs. It has been shown that the transcriptional apparatuses can physically interfere with one another while transcribing overlapping regions. We hypothesize that transcriptional interference regulates the global gene expression across the herpesvirus genome. Additionally, an overall decrease in transcriptional activity in individual viral genes has been observed following the onset of DNA replication. An overlap of the replication origins with specific transcripts has also been described in several herpesviruses. The genome-wide interactions between the transcriptional apparatuses and between the replication and transcriptional machineries suggest the existence of novel layers of genetic regulation.
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Affiliation(s)
- Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary.
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
| | - Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., Szeged, 6720, Hungary
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28
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Guan LZ, Zhao S, Shu G, Jiang QY, Cai GY, Wu ZF, Xi QY, Zhang YL. β-Glucanase specific expression in the intestine of transgenic pigs. Transgenic Res 2019; 28:237-246. [PMID: 30697646 DOI: 10.1007/s11248-019-00112-x] [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: 09/15/2018] [Accepted: 01/22/2019] [Indexed: 11/25/2022]
Abstract
Producing heterologous enzymes in the animal digestive tract to improve feed utilization rate is a new research strategy by transgenic technology. In this study, transgenic pigs specifically expressing β-glucanase gene in the intestine were successfully produced by somatic cell nuclear transfer technology in order to improve digestibility of dietary β-glucan and absorption of nutrients. The β-glucanase activity in the intestinal juice of 4 transgenic pigs was found to be 8.59 ± 2.49 U/mL. The feeding trial results showed that the crude protein digestion of 4 transgenic pigs was significantly increased compared with that of the non-transgenic pigs. In order to investigate the inheritance of the transgene, 7 G1 transgenic pigs were successfully obtained. The β-glucanase activity in the intestinal juice of 7 G1 transgenic pigs was found to be 2.35 ± 0.72 U/mL. The feeding trial results showed the crude protein digestion and crude fat digestion were significantly higher in 7 G1 transgenic pigs than in non-transgenic pigs. Taken together, our study demonstrated that the foreign β-glucanase expressing in the intestine of the transgenic pigs could reduce the anti-nutritional effect of β-glucans in feed. In addition, β-glucanase gene could be inherited to the offsprings and maintain its physiological function. It is a promising approach to improve feed utilization by producing transgenic animals.
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Affiliation(s)
- Li-Zeng Guan
- College of Agriculture and Forestry Science, Linyi University, Shuangling Road, Linyi City, China
| | - Shuai Zhao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, SCAU-Alltech Research Joint Alliance, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Gang Shu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, SCAU-Alltech Research Joint Alliance, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Qing-Yan Jiang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, SCAU-Alltech Research Joint Alliance, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Geng-Yuan Cai
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, SCAU-Alltech Research Joint Alliance, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Zhen-Fang Wu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, SCAU-Alltech Research Joint Alliance, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Qian-Yun Xi
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, SCAU-Alltech Research Joint Alliance, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China.
| | - Yong-Liang Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, SCAU-Alltech Research Joint Alliance, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China.
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29
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Lee JS, Park JH, Ha TK, Samoudi M, Lewis NE, Palsson BO, Kildegaard HF, Lee GM. Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing. ACS Synth Biol 2018; 7:2867-2878. [PMID: 30388888 DOI: 10.1021/acssynbio.8b00290] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Generation of recombinant Chinese hamster ovary (rCHO) cell lines is critical for the production of therapeutic proteins. However, the high degree of phenotypic heterogeneity among generated clones, referred to as clonal variation, makes the rCHO cell line development process inefficient and unpredictable. Here, we investigated the major genomic causes of clonal variation. We found the following: (1) consistent with previous studies, a strong variation in rCHO clones in response to hypothermia (33 vs 37 °C) after random transgene integration; (2) altered DNA sequence of randomly integrated cassettes, which occurred during the integration process, affecting the transgene expression level in response to hypothermia; (3) contrary to random integration, targeted integration of the same expression cassette, without any DNA alteration, into three identified integration sites showed the similar response of transgene expression in response to hypothermia, irrespective of integration site; (4) switching the promoter from CMV to EF1α eliminated the hypothermia response; and (5) deleting the enhancer part of the CMV promoter altered the hypothermia response. Thus, we have revealed the effects of integration methods and cassette design on transgene expression levels, implying that rCHO cell line generation can be standardized through detailed genomic understanding. Further elucidation of such understanding is likely to have a broad impact on diverse fields that use transgene integration, from gene therapy to generation of production cell lines.
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Affiliation(s)
- Jae Seong Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jin Hyoung Park
- Department of Biological Sciences, KAIST, 291 Daehak-ro,
Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Tae Kwang Ha
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mojtaba Samoudi
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, La Jolla, California 92093, United States
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, La Jolla, California 92093, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Bernhard O. Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, KAIST, 291 Daehak-ro,
Yuseong-gu, Daejeon 305-701, Republic of Korea
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30
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Kujoth GC, Sullivan TD, Merkhofer R, Lee TJ, Wang H, Brandhorst T, Wüthrich M, Klein BS. CRISPR/Cas9-Mediated Gene Disruption Reveals the Importance of Zinc Metabolism for Fitness of the Dimorphic Fungal Pathogen Blastomyces dermatitidis. mBio 2018; 9:e00412-18. [PMID: 29615501 PMCID: PMC5885028 DOI: 10.1128/mbio.00412-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/18/2022] Open
Abstract
Blastomyces dermatitidis is a human fungal pathogen of the lung that can lead to disseminated disease in healthy and immunocompromised individuals. Genetic analysis of this fungus is hampered by the relative inefficiency of traditional recombination-based gene-targeting approaches. Here, we demonstrate the feasibility of applying CRISPR/Cas9-mediated gene editing to Blastomyces, including to simultaneously target multiple genes. We created targeting plasmid vectors expressing Cas9 and either one or two single guide RNAs and introduced these plasmids into Blastomyces via Agrobacterium gene transfer. We succeeded in disrupting several fungal genes, including PRA1 and ZRT1, which are involved in scavenging and uptake of zinc from the extracellular environment. Single-gene-targeting efficiencies varied by locus (median, 60% across four loci) but were approximately 100-fold greater than traditional methods of Blastomyces gene disruption. Simultaneous dual-gene targeting proceeded with efficiencies similar to those of single-gene-targeting frequencies for the respective targets. CRISPR/Cas9 disruption of PRA1 or ZRT1 had a variable impact on growth under zinc-limiting conditions, showing reduced growth at early time points in low-passage-number cultures and growth similar to wild-type levels by later passage. Individual impairment of PRA1 or ZRT1 resulted in a reduction of the fungal burden in a mouse model of Blastomyces infection by a factor of ~1 log (range, up to 3 logs), and combined disruption of both genes had no additional impact on the fungal burden. These results underscore the utility of CRISPR/Cas9 for efficient gene disruption in dimorphic fungi and reveal a role for zinc metabolism in Blastomyces fitness in vivo IMPORTANCE Blastomyces is a human fungal pathogen that can cause serious, even fatal, lung infections. Genetic analysis of this fungus is possible but inefficient. We applied a recently developed gene editing technology, CRISPR/Cas9, to dramatically improve the efficiency with which gene disruptions are introduced into Blastomyces We used this system to disrupt genes involved in zinc uptake and found that this reduced the fitness of the fungus upon infection.
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Affiliation(s)
- Gregory C Kujoth
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Thomas D Sullivan
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Richard Merkhofer
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Taek-Jin Lee
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Huafeng Wang
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Tristan Brandhorst
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marcel Wüthrich
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Bruce S Klein
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
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31
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Bhukhai K, de Dreuzy E, Giorgi M, Colomb C, Negre O, Denaro M, Gillet-Legrand B, Cheuzeville J, Paulard A, Trebeden-Negre H, Borwornpinyo S, Sii-Felice K, Maouche L, Down JD, Leboulch P, Payen E. Ex Vivo Selection of Transduced Hematopoietic Stem Cells for Gene Therapy of β-Hemoglobinopathies. Mol Ther 2018; 26:480-495. [PMID: 29221807 PMCID: PMC5835017 DOI: 10.1016/j.ymthe.2017.10.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/11/2017] [Accepted: 10/18/2017] [Indexed: 12/14/2022] Open
Abstract
Although gene transfer to hematopoietic stem cells (HSCs) has shown therapeutic efficacy in recent trials for several individuals with inherited disorders, transduction incompleteness of the HSC population remains a hurdle to yield a cure for all patients with reasonably low integrated vector numbers. In previous attempts at HSC selection, massive loss of transduced HSCs, contamination with non-transduced cells, or lack of applicability to large cell populations has rendered the procedures out of reach for human applications. Here, we fused codon-optimized puromycin N-acetyltransferase to herpes simplex virus thymidine kinase. When expressed from a ubiquitous promoter within a complex lentiviral vector comprising the βAT87Q-globin gene, viral titers and therapeutic gene expression were maintained at effective levels. Complete selection and preservation of transduced HSCs were achieved after brief exposure to puromycin in the presence of MDR1 blocking agents, suggesting the procedure's suitability for human clinical applications while affording the additional safety of conditional suicide.
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Affiliation(s)
- Kanit Bhukhai
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France
| | - Edouard de Dreuzy
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France
| | - Marie Giorgi
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France
| | - Charlotte Colomb
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France
| | - Olivier Negre
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France; bluebird bio, Inc., Cambridge, MA 02141, USA; bluebird bio France, Fontenay aux Roses 92260, France
| | | | - Béatrix Gillet-Legrand
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France; bluebird bio France, Fontenay aux Roses 92260, France
| | - Joëlle Cheuzeville
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France; bluebird bio France, Fontenay aux Roses 92260, France
| | - Anaïs Paulard
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France; bluebird bio France, Fontenay aux Roses 92260, France
| | | | | | - Karine Sii-Felice
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France
| | - Leila Maouche
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France; INSERM, Paris 75013, France
| | - Julian D Down
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phillippe Leboulch
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France; Ramathibodi Hospital, Bangkok 10400, Thailand; Harvard Medical School and Genetics Division, Department of Medicine, Brigham & Women's Hospital, Boston, MA 02115, USA.
| | - Emmanuel Payen
- CEA, Institute of Biology François Jacob, Fontenay aux Roses 92260, France; UMR_007, CEA and University of Paris Saclay, Fontenay aux Roses 92260, France; INSERM, Paris 75013, France.
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32
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Advancing Agrobacterium-Based Crop Transformation and Genome Modification Technology for Agricultural Biotechnology. Curr Top Microbiol Immunol 2018; 418:489-507. [PMID: 29959543 DOI: 10.1007/82_2018_97] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The last decade has seen significant strides in Agrobacterium-mediated plant transformation technology. This has not only expanded the number of crop species that can be transformed by Agrobacterium, but has also made it possible to routinely transform several recalcitrant crop species including cereals (e.g., maize, sorghum, and wheat). However, the technology is limited by the random nature of DNA insertions, genotype dependency, low frequency of quality events, and variation in gene expression arising from genomic insertion sites. A majority of these deficiencies have now been addressed by improving the frequency of quality events, developing genotype-independent transformation capability in maize, developing an Agrobacterium-based site-specific integration technology for precise gene targeting, and adopting Agrobacterium-delivered CRISPR-Cas genes for gene editing. These improved transformation technologies are discussed in detail in this chapter.
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Shepelev MV, Kalinichenko SV, Deykin AV, Korobko IV. Production of Recombinant Proteins in the Milk of Transgenic Animals: Current State and Prospects. Acta Naturae 2018; 10:40-47. [PMID: 30397525 PMCID: PMC6209402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The use of transgenic animals as bioreactors for the synthesis of the recombinant proteins secreted into milk is a current trend in the development of biotechnologies. Advances in genetic engineering, in particular the emergence of targeted genome editing technologies, have provided new opportunities and significantly improved efficiency in the generation of animals that produce recombinant proteins in milk, including economically important animals. Here, we present a retrospective review of technologies for generating transgenic animals, with emphasis on the creation of animals that produce recombinant proteins in milk. The current state and prospects for the development of this area of biotechnology are discussed in relation to the emergence of novel genome editing technologies. Experimental and practical techniques are briefly discussed.
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Affiliation(s)
- M. V. Shepelev
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - S. V. Kalinichenko
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - A. V. Deykin
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
| | - I. V. Korobko
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia
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34
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Lou AG, Cai JS, Zhang XM, Cui CD, Piao YS, Guan LZ. The aflatoxin-detoxifizyme specific expression in the parotid gland of transgenic pigs. Transgenic Res 2017; 26:677-687. [DOI: 10.1007/s11248-017-0036-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 07/19/2017] [Indexed: 11/30/2022]
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35
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Chilcoat D, Liu ZB, Sander J. Use of CRISPR/Cas9 for Crop Improvement in Maize and Soybean. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:27-46. [PMID: 28712499 DOI: 10.1016/bs.pmbts.2017.04.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
CRISPR/Cas enables precise improvement of commercially relevant crop species by transgenic and nontransgenic methodologies. We have used CRISPR/Cas with or without DNA repair template in both corn and soybean for a range of applications including enhancing drought tolerance, improving seed oil composition, and endowing herbicide tolerance. Importantly, by pairing CRISPR/Cas technology with recent advances in plant tissue culture, these changes can be introduced directly into commercially relevant genotypes. This powerful combination of technologies enables advanced breeding techniques for introducing natural genetic variations directly into product relevant lines with improved speed and quality compared with traditional breeding methods. Variation generated through such CRISPR/Cas enabled advanced breeding approaches can be indistinguishable from naturally occurring variation and therefore should be readily accessible for commercialization. The precision, reach, and flexibility afforded by CRISPR/Cas promise an important role for genome editing in future crop improvement efforts.
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36
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Ahmadi M, Mahboudi F, Ahmadi S, Ebadat S, Nematpour F, Akbari Eidgahi MR, Davami F. PhiC31 integrase can improve the efficiency of different construct designs for monoclonal antibody expression in CHO cells. Protein Expr Purif 2017; 134:89-95. [PMID: 28400295 DOI: 10.1016/j.pep.2017.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 04/03/2017] [Accepted: 04/07/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVES Several types of expression vectors have been used for recombinant protein expression in Chinese hamster ovary cells (CHO) which usually result in variable and unstable levels of expression. METHODS AND RESULTS In this study, we have compared the mAb0014 expression level of single ORF/IRES vector and dual ORF vector in the presence and absence of phiC31 integrase targeting system. Both expression vectors contain an elongation factor 1α (EF1α) promoter upstream of LC and harboring an attB site. CHO-S cells were co-transfected with single ORF/IRES or dual ORF vectors along with a phiC31 integrase expression vector which can catalyze recombination between attB site and pseudo-attP sites presented in the mammalian genome. Our results demonstrated that dual ORF vector in the presence of phiC31 integrase expression vectors (+FC31 2P) generated more recombinant antibody in comparison to its negative control (-FC31 2P). Moreover, both of +FC31 2P and -FC31 2P cell pools yield higher recombinant protein in comparison to single ORF/IRES vector (FC31 IRES) cell pools. Stability of expression in phiC31 co-transfected cell pools (+FC31 2P and +FC31 IRES) had no considerable changes. CONCLUSIONS Our results indicated that the dual ORF vector using integrase can support the generation of cell lines with stable transgene expression at an elevated mAb relative to single ORF/IRES vector.
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Affiliation(s)
- Maryam Ahmadi
- Medical Biotechnology Department, Semnan University of Medical Sciences, Semnan, Iran; Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Samira Ahmadi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Saeedeh Ebadat
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Nematpour
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Davami
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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37
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Koroleva ON, Dubrovin EV, Yaminsky IV, Drutsa VL. Effect of DNA bending on transcriptional interference in the systems of closely spaced convergent promoters. Biochim Biophys Acta Gen Subj 2016; 1860:2086-96. [DOI: 10.1016/j.bbagen.2016.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 01/22/2023]
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38
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Ahmadi M, Mahboudi F, Akbari Eidgahi MR, Nasr R, Nematpour F, Ahmadi S, Ebadat S, Aghaeepoor M, Davami F. Evaluating the efficiency of phiC31 integrase-mediated monoclonal antibody expression in CHO cells. Biotechnol Prog 2016; 32:1570-1576. [PMID: 27604579 DOI: 10.1002/btpr.2362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 07/19/2016] [Indexed: 01/02/2023]
Abstract
Traditional methods to generate CHO cell lines rely on random integration(s) of the gene of interest and result in unpredictable and unstable protein expression. In comparison, site-specific recombination methods increase the recombinant protein expression by inserting transgene at a locus with specific expression features. PhiC31 serine integrase, catalyze unidirectional integration that occurs at higher frequency in comparison with the reversible integration carried out by recombinases such as Cre. In this study, using different ratios of phiC31 serine integrase, we evaluated the phiC31 mediated gene integration for expression of a humanized IgG1 antibody (mAb0014) in CHO-S cells. Light chain (LC) and heavy chain (HC) genes were expressed in one operon under EF1α promoter and linked by internal ribosome entry site (IRES) element. The clonal selection was carried out by limiting dilution. Targeted integration approach increased recombinant protein yield and stability in cell pools. The productivity of targeted cell pools was about 4 mg/L and about 40 µg/L in the control cell pool. The number of integrated transgenes was about 19 fold higher than the control cells pools. Our results confirmed that the phiC31 integrase leads to mAb expression in more than 90% of colonies. The productivity of the PhiC31 integrated cell pools was stable for three months in the absence of selection as compared with conventional transfection methods. Hence, utilizing PhiC31 integrase can increase protein titer and decrease the required time for protein expression. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1570-1576, 2016.
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Affiliation(s)
- Maryam Ahmadi
- Medical Biotechnology Dept., Semnan University of Medical Sciences, Semnan, Iran.,Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | | | - Reza Nasr
- Medical Biotechnology Dept., Semnan University of Medical Sciences, Semnan, Iran
| | - Fatemeh Nematpour
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Samira Ahmadi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Saeedeh Ebadat
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mojtaba Aghaeepoor
- Medical Biotechnology Dept., Semnan University of Medical Sciences, Semnan, Iran
| | - Fatemeh Davami
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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39
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Epigenetic modulations rendering cell-to-cell variability and phenotypic metastability. J Genet Genomics 2016; 43:503-11. [DOI: 10.1016/j.jgg.2016.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/12/2016] [Accepted: 05/25/2016] [Indexed: 02/01/2023]
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40
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Hoffmann SA, Kruse SM, Arndt KM. Long-range transcriptional interference in E. coli used to construct a dual positive selection system for genetic switches. Nucleic Acids Res 2016; 44:e95. [PMID: 26932362 PMCID: PMC4889929 DOI: 10.1093/nar/gkw125] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 02/21/2016] [Indexed: 11/29/2022] Open
Abstract
We have investigated transcriptional interference between convergent genes in E. coli and demonstrate substantial interference for inter-promoter distances of as far as 3 kb. Interference can be elicited by both strong σ70 dependent and T7 promoters. In the presented design, a strong promoter driving gene expression of a ‘forward’ gene interferes with the expression of a ‘reverse’ gene by a weak promoter. This arrangement allows inversely correlated gene expression without requiring further regulatory components. Thus, modulation of the activity of the strong promoter alters expression of both the forward and the reverse gene. We used this design to develop a dual selection system for conditional operator site binding, allowing positive selection both for binding and for non-binding to DNA. This study demonstrates the utility of this novel system using the Lac repressor as a model protein for conditional DNA binding, and spectinomycin and chloramphenicol resistance genes as positive selection markers in liquid culture. Randomized LacI libraries were created and subjected to subsequent dual selection, but mispairing IPTG and selection cues in respect to the wild-type LacI response, allowing the isolation of a LacI variant with a reversed IPTG response within three rounds of library generation and dual selection.
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Affiliation(s)
- Stefan A Hoffmann
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Sabrina M Kruse
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Katja M Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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41
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Baser B, van den Heuvel J. Assembling Multi-subunit Complexes Using Mammalian Expression. ADVANCED TECHNOLOGIES FOR PROTEIN COMPLEX PRODUCTION AND CHARACTERIZATION 2016; 896:225-38. [DOI: 10.1007/978-3-319-27216-0_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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42
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Wei KY, Smolke CD. Engineering dynamic cell cycle control with synthetic small molecule-responsive RNA devices. J Biol Eng 2015; 9:21. [PMID: 26594238 PMCID: PMC4654890 DOI: 10.1186/s13036-015-0019-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/27/2015] [Indexed: 01/08/2023] Open
Abstract
Background The cell cycle plays a key role in human health and disease, including development and cancer. The ability to easily and reversibly control the mammalian cell cycle could mean improved cellular reprogramming, better tools for studying cancer, more efficient gene therapy, and improved heterologous protein production for medical or industrial applications. Results We engineered RNA-based control devices to provide specific and modular control of gene expression in response to exogenous inputs in living cells. Specifically, we identified key regulatory nodes that arrest U2-OS cells in the G0/1 or G2/M phases of the cycle. We then optimized the most promising key regulators and showed that, when these optimized regulators are placed under the control of a ribozyme switch, we can inducibly and reversibly arrest up to ~80 % of a cellular population in a chosen phase of the cell cycle. Characterization of the reliability of the final cell cycle controllers revealed that the G0/1 control device functions reproducibly over multiple experiments over several weeks. Conclusions To our knowledge, this is the first time synthetic RNA devices have been used to control the mammalian cell cycle. This RNA platform represents a general class of synthetic biology tools for modular, dynamic, and multi-output control over mammalian cells. Electronic supplementary material The online version of this article (doi:10.1186/s13036-015-0019-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathy Y Wei
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA 94305 USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA 94305 USA
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43
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Kang SY, Kim YG, Lee HW, Lee EG. A single-plasmid vector for transgene amplification using short hairpin RNA targeting the 3'-UTR of amplifiable dhfr. Appl Microbiol Biotechnol 2015; 99:10117-26. [PMID: 26245680 DOI: 10.1007/s00253-015-6856-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/12/2015] [Accepted: 07/15/2015] [Indexed: 12/28/2022]
Abstract
Gene amplification using dihydrofolate reductase gene (dhfr) and methotrexate (MTX) is widely used for recombinant protein production in mammalian cells and is typically conducted in DHFR-deficient Chinese hamster ovary (CHO) cell lines. Generation of DHFR-deficient cells can be achieved by an expression vector incorporating short hairpin RNA (shRNA) that targets the 3'-untranslated region (UTR) of endogenous dhfr. Thus, shRNAs were designed to target the 3'-UTR of endogenous dhfr, and shRNA-2 efficiently down-regulated dhfr expression in CHO-K1 cells. A single gene copy of shRNA-2 also decreased the translational level of DHFR by 80% in Flp-In CHO cells. shRNA-2 was then incorporated into a plasmid vector expressing human erythropoietin (EPO) and an exogenous DHFR to develop EPO-producing cells in the Flp-In system. The specific EPO productivity (q EPO) was enhanced by stepwise increments of MTX concentration, and differences in the amplification rate were observed in Flp-In CHO cells that expressed shRNA-2. In addition, the q EPO increased by more than 2.5-fold in the presence of 500 nM MTX. The mRNA expression level and gene copy numbers of dhfr were correlated with increased productivity in the cells, which is influenced by inhibition of endogenous dhfr. This study reveals that an expression vector including shRNA that targets the 3'-UTR of endogenous dhfr can enhance the transgene amplification rate and productivity by generating DHFR-deficient cells. This approach may be applied for amplifying the foreign gene in wild-type cell lines as a versatile single-plasmid vector.
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Affiliation(s)
- Shin-Young Kang
- Department of Bioprocess Engineering, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Republic of Korea
| | - Yeon-Gu Kim
- Department of Bioprocess Engineering, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Republic of Korea.,Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 363-883, Republic of Korea
| | - Hong Weon Lee
- Department of Bioprocess Engineering, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Republic of Korea.,Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 363-883, Republic of Korea
| | - Eun Gyo Lee
- Department of Bioprocess Engineering, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Republic of Korea. .,Biotechnology Process Engineering Center, KRIBB, 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, 363-883, Republic of Korea.
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44
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Zboray K, Sommeregger W, Bogner E, Gili A, Sterovsky T, Fauland K, Grabner B, Stiedl P, Moll HP, Bauer A, Kunert R, Casanova E. Heterologous protein production using euchromatin-containing expression vectors in mammalian cells. Nucleic Acids Res 2015; 43:e102. [PMID: 25977298 PMCID: PMC4652741 DOI: 10.1093/nar/gkv475] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/29/2015] [Indexed: 01/10/2023] Open
Abstract
Upon stable cell line generation, chromosomal integration site of the vector DNA has a major impact on transgene expression. Here we apply an active gene environment, rather than specified genetic elements, in expression vectors used for random integration. We generated a set of Bacterial Artificial Chromosome (BAC) vectors with different open chromatin regions, promoters and gene regulatory elements and tested their impact on recombinant protein expression in CHO cells. We identified the Rosa26 BAC as the most efficient vector backbone showing a nine-fold increase in both polyclonal and clonal production of the human IgG-Fc. Clonal protein production was directly proportional to integrated vector copy numbers and remained stable during 10 weeks without selection pressure. Finally, we demonstrated the advantages of BAC-based vectors by producing two additional proteins, HIV-1 glycoprotein CN54gp140 and HIV-1 neutralizing PG9 antibody, in bioreactors and shake flasks reaching a production yield of 1 g/l.
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Affiliation(s)
- Katalin Zboray
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, 1090, Austria
| | - Wolfgang Sommeregger
- Vienna Institute of BioTechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190, Austria Polymun Scientific GmbH, Klosterneuburg, 3400, Austria
| | - Edith Bogner
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, 1090, Austria
| | - Andreas Gili
- Polymun Scientific GmbH, Klosterneuburg, 3400, Austria
| | | | | | - Beatrice Grabner
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, 1090, Austria
| | - Patricia Stiedl
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, 1090, Austria
| | - Herwig P Moll
- Institute of Pharmacology, Center of Physiology and Pharmacology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, 1090, Austria
| | | | - Renate Kunert
- Vienna Institute of BioTechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Emilio Casanova
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, 1090, Austria Institute of Pharmacology, Center of Physiology and Pharmacology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, 1090, Austria
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Chromatin-Mediated Reversible Silencing of Sense-Antisense Gene Pairs in Embryonic Stem Cells Is Consolidated upon Differentiation. Mol Cell Biol 2015; 35:2436-47. [PMID: 25963662 DOI: 10.1128/mcb.00029-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 04/17/2015] [Indexed: 11/20/2022] Open
Abstract
Genome-wide gene expression studies have indicated that the eukaryotic genome contains many gene pairs showing overlapping sense and antisense transcription. Regulation of these coding and/or noncoding gene pairs involves intricate regulatory mechanisms. In the present study, we utilized an enhanced green fluorescent protein (EGFP)-tagged reporter plasmid cis linked to a doxycycline-inducible antisense promoter, generating antisense transcription that fully overlaps EGFP, to study the mechanism and dynamics of gene silencing after induction of noncoding antisense transcription in undifferentiated and differentiating mouse embryonic stem cells (ESCs). We found that EGFP silencing is reversible in ESCs but is locked into a stable state upon ESC differentiation. Reversible silencing in ESCs is chromatin dependent and is associated with accumulation of trimethylated lysine 36 on histone H3 (H3K36me3) at the EGFP promoter region. In differentiating ESCs, antisense transcription-induced accumulation of H3K36me3 was associated with an increase in CpG methylation at the EGFP promoter. Repression of the sense promoter was affected by small-molecule inhibitors which interfere with DNA methylation and histone demethylation pathways. Our results indicate a general mechanism for silencing of fully overlapping sense-antisense gene pairs involving antisense transcription-induced accumulation of H3K36me3 at the sense promoter, resulting in reversible silencing of the sense partner, which is stabilized during ESC differentiation by CpG methylation.
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Spencer S, Gugliotta A, Koenitzer J, Hauser H, Wirth D. Stability of single copy transgene expression in CHOK1 cells is affected by histone modifications but not by DNA methylation. J Biotechnol 2015; 195:15-29. [DOI: 10.1016/j.jbiotec.2014.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 12/07/2014] [Accepted: 12/11/2014] [Indexed: 12/22/2022]
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47
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Vector modifications to eliminate transposase expression following piggyBac-mediated transgenesis. Sci Rep 2014; 4:7403. [PMID: 25492703 PMCID: PMC4261183 DOI: 10.1038/srep07403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/19/2014] [Indexed: 12/29/2022] Open
Abstract
Transgene insertion plays an important role in gene therapy and in biological studies. Transposon-based systems that integrate transgenes by transposase-catalyzed “cut-and-paste” mechanism have emerged as an attractive system for transgenesis. Hyperactive piggyBac transposon is particularly promising due to its ability to integrate large transgenes with high efficiency. However, prolonged expression of transposase can become a potential source of genotoxic effects due to uncontrolled transposition of the integrated transgene from one chromosomal locus to another. In this study we propose a vector design to decrease post-transposition expression of transposase and to eliminate the cells that have residual transposase expression. We design a single plasmid construct that combines the transposase and the transpositioning transgene element to share a single polyA sequence for termination. Consequently, the separation of the transposase element from the polyA sequence after transposition leads to its deactivation. We also co-express Herpes Simplex Virus thymidine kinase (HSV-tk) with the transposase. Therefore, cells having residual transposase expression can be eliminated by the administration of ganciclovir. We demonstrate the utility of this combination transposon system by integrating and expressing a model therapeutic gene, human coagulation Factor IX, in HEK293T cells.
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48
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Kong Q, Hai T, Ma J, Huang T, Jiang D, Xie B, Wu M, Wang J, Song Y, Wang Y, He Y, Sun J, Hu K, Guo R, Wang L, Zhou Q, Mu Y, Liu Z. Rosa26 locus supports tissue-specific promoter driving transgene expression specifically in pig. PLoS One 2014; 9:e107945. [PMID: 25232950 PMCID: PMC4169413 DOI: 10.1371/journal.pone.0107945] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/17/2014] [Indexed: 11/19/2022] Open
Abstract
Genetically modified pigs have become a popular model system in fundamental research, agricultural and biomedical applications. However, random integration often result in unstable expression of transgene and unpredictable phenotypes. The Rosa26 locus has been widely used to produce genetic modified animals with high and consistent expressing of transgene in mouse, human and rat, as it can be targeted efficiently and is not subject to gene-silencing effects. Recently, the first case of reporter gene targeting pigs in porcine Rosa26 (pRosa26) locus was reported. In the study, full sequence of pRosa26 locus was further characterized, and the pRosa26 promoter (pR26) was cloned and we evidenced that the new porcine endogenous promoter is suitable for driving transgene expression in a high and stable manner by avoiding DNA methylation. Furthermore, elongation factor 1a promoter (EF1a) -driven GFP reporter and Myostatin promoter (MyoP)-driven Follistatin (Fst) were successfully targeted into the pRosa26 locusby traditional homologous recombination (HR) strategy. EF1a showed high activity and hypomethylation at the locus. And, muscle-specific promoter MyoP was activated strictly in muscle of the pRosa26 targeted pigs, indicating Rosa26 locus supports tissue-specific promoter driving transgene expression in its own manner. The study provided further demonstration on biomedical and agricultural applications of porcine Rosa26 promoter and locus.
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Affiliation(s)
- Qingran Kong
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Tang Hai
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jing Ma
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Tianqing Huang
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Dandan Jiang
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Bingteng Xie
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Meiling Wu
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Jiaqiang Wang
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Yuran Song
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Ying Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yilong He
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Jialu Sun
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Kui Hu
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Runfa Guo
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Liu Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanshuang Mu
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
| | - Zhonghua Liu
- Laboratory of Embryo Biotechnology, College of life science, Northeast Agricultural University, Harbin, China
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Meyer S, Beslon G. Torsion-mediated interaction between adjacent genes. PLoS Comput Biol 2014; 10:e1003785. [PMID: 25188032 PMCID: PMC4154641 DOI: 10.1371/journal.pcbi.1003785] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/26/2014] [Indexed: 11/17/2022] Open
Abstract
DNA torsional stress is generated by virtually all biomolecular processes involving the double helix, in particular transcription where a significant level of stress propagates over several kilobases. If another promoter is located in this range, this stress may strongly modify its opening properties, and hence facilitate or hinder its transcription. This mechanism implies that transcribed genes distant of a few kilobases are not independent, but coupled by torsional stress, an effect for which we propose the first quantitative and systematic model. In contrast to previously proposed mechanisms of transcriptional interference, the suggested coupling is not mediated by the transcription machineries, but results from the universal mechanical features of the double-helix. The model shows that the effect likely affects prokaryotes as well as eukaryotes, but with different consequences owing to their different basal levels of torsion. It also depends crucially on the relative orientation of the genes, enhancing the expression of eukaryotic divergent pairs while reducing that of prokaryotic convergent ones. To test the in vivo influence of the torsional coupling, we analyze the expression of isolated gene pairs in the Drosophila melanogaster genome. Their orientation and distance dependence is fully consistent with the model, suggesting that torsional gene coupling may constitute a widespread mechanism of (co)regulation in eukaryotes.
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Affiliation(s)
- Sam Meyer
- Université de Lyon, INSA Lyon, INRIA, LIRIS, CNRS UMR5205, Lyon, France
| | - Guillaume Beslon
- Université de Lyon, INSA Lyon, INRIA, LIRIS, CNRS UMR5205, Lyon, France
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50
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Lin J, Zhang Q, Zhu LQ, Yu QH, Yang Q. The copy number and integration site analysis of IGF-1 transgenic goat. Int J Mol Med 2014; 34:900-10. [PMID: 25018125 DOI: 10.3892/ijmm.2014.1841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 06/12/2014] [Indexed: 11/05/2022] Open
Abstract
Transgenic animals have been used previously to study gene function, produce important proteins, and generate models for the study of human diseases. As the number of transgenic species increases, reliable detection and molecular characterization of integration sites and copy number are crucial for confirming transgene expression and genetic stability, as well as for safety evaluation and to meet commercial demands. In this study, we generated four transgenic goats by somatic cell nuclear transfer (SCNT). After birth, the cloned goat contained transferred insulin-like growth factor I (IGF-1) gene was initially confirmed using a polymerase chain reaction (PCR)‑based method. The four cloned goats were identified as IGF-1 transgenic goats by southern blotting. The number of copies of the IGF-1 gene in each of the transgenic goats was determined. Additionally, four integration sites of the transgene in the transgenic goats with a modified thermal asymmetric interlaced (TAIL)-PCR method were identified. The four different integration sites were located on chromosomes 2, 11, 16 and 18. The present study identified the copy number and integration sites using quantitative PCR (qPCR) and TAIL-PCR, enabling the bio-safety evaluation of the transgenic goats.
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Affiliation(s)
- Jian Lin
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Qiang Zhang
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Li Q Zhu
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Qing H Yu
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
| | - Qian Yang
- Key Laboratory of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, P.R. China
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