1
|
Sekiguchi R, Mehlferber M, Matsumoto K, Wang S. Efficient Gene Knockout in Salivary Gland Epithelial Explant Cultures. J Dent Res 2023; 102:197-206. [PMID: 36366748 PMCID: PMC9893391 DOI: 10.1177/00220345221128201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have developed methods to achieve efficient CRISPR-Cas9-mediated gene knockout in ex vivo mouse embryonic salivary epithelial explants. Salivary epithelial explants provide a valuable model for characterizing cell signaling, differentiation, and epithelial morphogenesis, but research has been limited by a paucity of efficient gene perturbation methods. Here, we demonstrate highly efficient gene perturbation by transient transduction of guide RNA-expressing lentiviruses into Cas9-expressing salivary epithelial buds isolated from Cas9 transgenic mice. We first show that salivary epithelial explants can be cultured in low-concentration, nonsolidified Matrigel suspensions in 96-well plates, which greatly increases sample throughput compared to conventional cultures embedded in solidified Matrigel. We further show that salivary epithelial explants can grow and branch with FGF7 alone, while supplementing with insulin, transferrin, and selenium (ITS) enhances growth and branching. We then describe an efficient workflow to produce experiment-ready, high-titer lentiviruses within 1 wk after molecular cloning. To track transduced cells, we designed the lentiviral vector to coexpress a nuclear fluorescent reporter with the guide RNA. We routinely achieved 80% transduction efficiency when antibiotic selection was used. Importantly, we detected robust loss of targeted protein products when testing 9 guide RNAs for 3 different genes. Moreover, targeting the β1 integrin gene (Itgb1) inhibited branching morphogenesis, which supports the importance of cell-matrix adhesion in driving branching morphogenesis. In summary, we have established a lentivirus-based method that can efficiently perturb genes of interest in salivary epithelial explants, which will greatly facilitate studies of specific gene functions using this system.
Collapse
Affiliation(s)
- R. Sekiguchi
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - M.M. Mehlferber
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
- Present address: Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - K. Matsumoto
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - S. Wang
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
- Present address: 4D Cellular Physiology, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| |
Collapse
|
2
|
Miyata Y, Fuse H, Tokumoto S, Hiki Y, Deviatiiarov R, Yoshida Y, Yamada TG, Cornette R, Gusev O, Shagimardanova E, Funahashi A, Kikawada T. Cas9-mediated genome editing reveals a significant contribution of calcium signaling pathways to anhydrobiosis in Pv11 cells. Sci Rep 2021; 11:19698. [PMID: 34611198 PMCID: PMC8492635 DOI: 10.1038/s41598-021-98905-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/16/2021] [Indexed: 01/01/2023] Open
Abstract
Pv11 is an insect cell line established from the midge Polypedilum vanderplanki, whose larval form exhibits an extreme desiccation tolerance known as anhydrobiosis. Pv11 itself is also capable of anhydrobiosis, which is induced by trehalose treatment. Here we report the successful construction of a genome editing system for Pv11 cells and its application to the identification of signaling pathways involved in anhydrobiosis. Using the Cas9-mediated gene knock-in system, we established Pv11 cells that stably expressed GCaMP3 to monitor intracellular Ca2+ mobilization. Intriguingly, trehalose treatment evoked a transient increase in cytosolic Ca2+ concentration, and further experiments revealed that the calmodulin-calcineurin-NFAT pathway contributes to tolerance of trehalose treatment as well as desiccation tolerance, while the calmodulin-calmodulin kinase-CREB pathway conferred only desiccation tolerance on Pv11 cells. Thus, our results show a critical contribution of the trehalose-induced Ca2+ surge to anhydrobiosis and demonstrate temporally different roles for each signaling pathway.
Collapse
Affiliation(s)
- Yugo Miyata
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hiroto Fuse
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shoko Tokumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yusuke Hiki
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Ruslan Deviatiiarov
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Richard Cornette
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Oleg Gusev
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan
| | - Elena Shagimardanova
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan
| | - Takahiro Kikawada
- Division of Biomaterial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
| |
Collapse
|
3
|
Gao Z, van der Velden YU, Fan M, van der Linden CA, Vink M, Herrera-Carrillo E, Berkhout B. Engineered miniature H1 promoters with dedicated RNA polymerase II or III activity. J Biol Chem 2021; 296:100026. [PMID: 33154168 PMCID: PMC7949045 DOI: 10.1074/jbc.ra120.015386] [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: 07/27/2020] [Revised: 10/19/2020] [Accepted: 11/05/2020] [Indexed: 11/24/2022] Open
Abstract
RNA polymerase III (Pol III) promoters, such as 7SK, U6, and H1, are widely used for the expression of small noncoding RNAs, including short hairpin RNAs for RNAi experiments and guide RNAs for CRISPR-mediated genome editing. We previously reported dual RNA polymerase activity (Pol II/III) for the human H1 promoter and demonstrated that this promiscuous RNA polymerase use can be exploited for the simultaneous expression of both a noncoding RNA and an mRNA. However, this combination is not a desired feature in other experimental and therapeutic settings. To overcome this limitation of the H1 promoter, we engineered a miniature H1/7SK hybrid promoter with minimal Pol II activity, thereby boosting Pol III activity to a level that is higher than that of either parental promoter. In parallel, we also engineered small Pol II-specific H1 promoter variants and explored their use as general Pol II promoters for protein expression. The newly engineered promoter variants form an attractive alternative to the commonly used H1 promoter in terms of not only activity and small promoter size but also concerning safety by exclusive expression of the desired therapeutic transcript (either pol II or pol III but not both).
Collapse
Affiliation(s)
- Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Yme Ubeles van der Velden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Minghui Fan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Cynthia Alyssa van der Linden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Monique Vink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
| |
Collapse
|
4
|
Deng H, Liang W, Fan TP, Zheng X, Cai Y. Modular engineering of Shiraia bambusicola for hypocrellin production through an efficient CRISPR system. Int J Biol Macromol 2020; 165:796-803. [PMID: 33010268 DOI: 10.1016/j.ijbiomac.2020.09.208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 11/18/2022]
Abstract
Shiraia bambusicola exhibits an excellent capability to produce high-value pharmacological drugs, such as hypocrellin. However, less effective molecular tools hamper the processes to discover or exploit these metabolites. To address this issue, the more effective CRISPR/Cas9 system was constructed by optimizing the sgRNA transcription elements and disrupting the endogenous non-homologous end-joining pathway. These tactics prompted the gene-targeting frequency of 100% and simultaneously multiplex genome editing in S. bambusicola. This optimal CRISPR system encouraged us to rewire the entire hypocrellin flux and improve the yield by orchestrating the substrate pool supply, the central hypocrellin pathway, and the antioxidant system. Thus, 8632 mg/L hypocrellin was obtained, resulting in a 12-fold increase than that of the wild-type strain. This engineered S. bambusicola can still endure oxidative stresses from higher target metabolites and sustain an excellent biological activity. This study provides a whole conception to establish the more efficient genome-editing system. Higher conserved transcription elements for sgRNA expressions inspire us to adopt this system for gene modifications of other filamentous fungi. The rational and global biosystems outline will offer guidance to modulate metabolite productivity in other filamentous fungi.
Collapse
Affiliation(s)
- Huaxiang Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Weiyue Liang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shanxi 710069, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
5
|
Kulcsár PI, Tálas A, Tóth E, Nyeste A, Ligeti Z, Welker Z, Welker E. Blackjack mutations improve the on-target activities of increased fidelity variants of SpCas9 with 5'G-extended sgRNAs. Nat Commun 2020; 11:1223. [PMID: 32144253 PMCID: PMC7060260 DOI: 10.1038/s41467-020-15021-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/06/2020] [Indexed: 12/17/2022] Open
Abstract
Increased fidelity mutants of the SpCas9 nuclease constitute the most promising approach to mitigating its off-target effects. However, these variants are effective only in a restricted target space, and many of them are reported to work less efficiently when applied in clinically relevant, pre-assembled, ribonucleoprotein forms. The low tolerance to 5'-extended, 21G-sgRNAs contributes, to a great extent, to their decreased performance. Here, we report the generation of Blackjack SpCas9 variant that shows increased fidelity yet remain effective with 21G-sgRNAs. Introducing Blackjack mutations into previously reported increased fidelity variants make them effective with 21G-sgRNAs and increases their fidelity. Two "Blackjack" nucleases, eSpCas9-plus and SpCas9-HF1-plus are superior variants of eSpCas9 and SpCas9-HF1, respectively, possessing matching on-target activity and fidelity but retaining activity with 21G-sgRNAs. They facilitate the use of existing pooled sgRNA libraries with higher specificity and show similar activities whether delivered as plasmids or as pre-assembled ribonucleoproteins.
Collapse
Affiliation(s)
- Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary.
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720, Szeged, Hungary.
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
- School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720, Szeged, Hungary
- Gene Design Ltd, Szeged, H-6726, Hungary
| | | | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary.
| |
Collapse
|
6
|
Chutrakul C, Panchanawaporn S, Jeennor S, Anantayanon J, Vorapreeda T, Vichai V, Laoteng K. Functional Characterization of Novel U6 RNA Polymerase III Promoters: Their Implication for CRISPR-Cas9-Mediated Gene Editing in Aspergillus oryzae. Curr Microbiol 2019; 76:1443-1451. [PMID: 31541261 DOI: 10.1007/s00284-019-01770-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 09/09/2019] [Indexed: 01/04/2023]
Abstract
U6 RNA polymerase III promoter (PU6), which is a key element in controlling the generation of single-guide RNA (sgRNA) for gene editing through CRISPR-Cas9 system, was investigated in this work. Using bioinformatics approach, two novel U6 ribonucleic acid (U6 RNA) sequences of Aspergillus niger were identified, showing that they had conserved motifs similar to other U6 RNAs. The putative PU6 located at the upstream sequence of A. niger U6 RNA exhibited the consensus motif, CCAATYA, and the TATA box which shared highly conserved characteristics across Aspergilli, whereas the A- and B-boxes were found at the intragenic and downstream of the structural genes, respectively. Using Aspergillus oryzae as a workhorse system, the function of A. niger PU6s for controlling the transcripts of sgRNA was verified, in which the orotidine-5'-phosphate decarboxylase (pyrG) sequence was used as a target for gene disruption through CRISPR-Cas9 system. Quantitative reverse transcription-polymerase chain reaction (RT-qPCR) analysis of the selected pyrG auxotrophic strains showed the expression of sgRNA, indicating that the non-native promoters could efficiently drive sgRNA expression in A. oryzae. These identified promoters are useful genetic tools for precise engineering of metabolic pathways in the industrially important fungus through the empowered CRISPR-Cas9-associated gene-editing system.
Collapse
Affiliation(s)
- Chanikul Chutrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand.
| | - Sarocha Panchanawaporn
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Sukanya Jeennor
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Jutamas Anantayanon
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Tayvich Vorapreeda
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC) At King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, 10150, Thailand
| | - Vanicha Vichai
- Biosensing and Bioprospecting Technology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Kobkul Laoteng
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| |
Collapse
|
7
|
Rattanapornsompong K, Ngamkham J, Chavalit T, Jitrapakdee S. Generation of Human Pyruvate Carboxylase Knockout Cell Lines Using Retrovirus Expressing Short Hairpin RNA and CRISPR-Cas9 as Models to Study Its Metabolic Role in Cancer Research. Methods Mol Biol 2019; 1916:273-288. [PMID: 30535704 DOI: 10.1007/978-1-4939-8994-2_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We report two protocols to generate human pyruvate carboxylase knockdown and knockout cell lines using short hairpin RNA (shRNA) and CRISPR-Cas9 technologies. The first protocol involved cloning of a shRNA cassette targeted to human pyruvate carboxylase (PC) under the control of a U6 promoter in a retrovirus-based vector. The stable knockdown cells were achieved following infection of retroviruses expressing shRNA in target cells followed by selecting these in medium containing puromycin. The second protocol describes a CRISPR Cas9-knockout cell constructed by cloning of single guide RNA (gRNA) targeted to the human pyruvate carboxylase gene placed adjacent to Cas 9 in the pSpCas9(BB)-2A-GFP vector. The knockout cells can be selected by sorting the cells expressing GFP. We also describe protocols for detecting the level of PC mRNA and protein in the knockdown or knockout cells using qPCR and Western blot analyses, respectively. The above protocols allow investigators to create PC deficient cell lines as a tool to study role of this enzyme in cancer research.
Collapse
Affiliation(s)
| | | | - Tanit Chavalit
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
| |
Collapse
|
8
|
Sandrock B, Benecke BJ. Two internal sequence elements modulate transcription from the external human 7S K RNA gene promoter in vivo. Gene Expr 2018; 8:105-14. [PMID: 10551798 PMCID: PMC6157388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Constructs of the external promoter of the human 7S K RNA gene in combination with different reporter elements and varying amounts of 7S K internal sequences were analyzed for efficient transcription by RNA polymerase III (pol III) in vitro and in vivo. In vitro, the 7S K promoter alone (-245 to -1) revealed full activity, compared to the entire wild-type gene. In vivo, however, the activity of the gene-external 7S K promoter, albeit clearly functional by itself, was positively modulated by internal sequence elements. Fusion constructs containing increasing amounts of transcribed 7S K sequences revealed that two elements were responsible for this activation. One element is associated with the initiator region (+1 to +8) of this class III gene. The second sequence comprises the 5' half of a cryptic A-box starting at +10 of the 7S K RNA sequence. In the context of a totally unrelated vector sequence, a GGC element alone was sufficient to functionally replace that cryptic A-box. Thus, it appears that in context of the 7S K RNA gene--and possibly the 7S L and U6 RNA genes as well--structurally divergent A-box-like elements function as internal modulators of these pol III promoters.
Collapse
Affiliation(s)
- B Sandrock
- Department of Biochemistry, Faculty of Chemistry, Ruhr University, Bochum, Germany
| | | |
Collapse
|
9
|
Moir-Meyer G, Cheong PL, Olijnik AA, Brown J, Knight S, King A, Kurita R, Nakamura Y, Gibbons RJ, Higgs DR, Buckle VJ, Babbs C. Robust CRISPR/Cas9 Genome Editing of the HUDEP-2 Erythroid Precursor Line Using Plasmids and Single-Stranded Oligonucleotide Donors. Methods Protoc 2018; 1:E28. [PMID: 31164570 PMCID: PMC6481050 DOI: 10.3390/mps1030028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/13/2018] [Accepted: 07/23/2018] [Indexed: 12/23/2022] Open
Abstract
The study of cellular processes and gene regulation in terminal erythroid development has been greatly facilitated by the generation of an immortalised erythroid cell line derived from Human Umbilical Derived Erythroid Precursors, termed HUDEP-2 cells. The ability to efficiently genome edit HUDEP-2 cells and make clonal lines hugely expands their utility as the insertion of clinically relevant mutations allows study of potentially every genetic disease affecting red blood cell development. Additionally, insertion of sequences encoding short protein tags such as Strep, FLAG and Myc permits study of protein behaviour in the normal and disease state. This approach is useful to augment the analysis of patient cells as large cell numbers are obtainable with the additional benefit that the need for specific antibodies may be circumvented. This approach is likely to lead to insights into disease mechanisms and provide reagents to allow drug discovery. HUDEP-2 cells provide a favourable alternative to the existing immortalised erythroleukemia lines as their karyotype is much less abnormal. These cells also provide sufficient material for a broad range of analyses as it is possible to generate in vitro-differentiated erythroblasts in numbers 4-7 fold higher than starting cell numbers within 9-12 days of culture. Here we describe an efficient, robust and reproducible plasmid-based methodology to introduce short (<20 bp) DNA sequences into the genome of HUDEP-2 cells using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 Cas9 system combined with single-stranded oligodeoxynucleotide (ssODN) donors. This protocol produces genetically modified lines in ~30 days and could also be used to generate knock-out and knock-in mutations.
Collapse
Affiliation(s)
- Gemma Moir-Meyer
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Pak Leng Cheong
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Aude-Anais Olijnik
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Jill Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Samantha Knight
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford OX3 7BN, UK.
| | - Andrew King
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, 1-1-3 Shibadaimon, Minato-ku, Tokyo 105-8521, Japan.
| | - Yukio Nakamura
- RIKEN BioResource Research Center, Koyadai 3-1-1, Tsukuba 305-0074, Japan.
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| |
Collapse
|
10
|
Liu Z, Zhang C, Skamagki M, Khodadadi-Jamayran A, Zhang W, Kong D, Chang CW, Feng J, Han X, Townes TM, Li H, Kim K, Zhao R. Elevated p53 Activities Restrict Differentiation Potential of MicroRNA-Deficient Pluripotent Stem Cells. Stem Cell Reports 2018; 9:1604-1617. [PMID: 29141234 PMCID: PMC5688240 DOI: 10.1016/j.stemcr.2017.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/21/2022] Open
Abstract
Pluripotent stem cells (PSCs) deficient for microRNAs (miRNAs), such as Dgcr8−/− or Dicer−/– embryonic stem cells (ESCs), contain no mature miRNA and cannot differentiate into somatic cells. How miRNA deficiency causes differentiation defects remains poorly understood. Here, we report that miR-302 is sufficient to enable neural differentiation of differentiation-incompetent Dgcr8−/− ESCs. Our data showed that miR-302 directly suppresses the tumor suppressor p53, which is modestly upregulated in Dgcr8−/− ESCs and serves as a barrier restricting neural differentiation. We demonstrated that direct inactivation of p53 by SV40 large T antigen, a short hairpin RNA against Trp53, or genetic ablation of Trp53 in Dgcr8−/− PSCs enables neural differentiation, while activation of p53 by the MDM2 inhibitor nutlin-3a in wild-type ESCs inhibits neural differentiation. Together, we demonstrate that a major function of miRNAs in neural differentiation is suppression of p53 and that modest activation of p53 blocks neural differentiation of miRNA-deficient PSCs. miR-302 enables neural differentiation of differentiation-incompetent Dgcr8−/− ESCs miR-302 directly suppresses p53 expression p53 inhibits neural differentiation of Dgcr8−/− and wild-type PSCs p53 may eliminate genetically defective embryos to save maternal resources
Collapse
Affiliation(s)
- Zhong Liu
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Maria Skamagki
- Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Sloan-Kettering Institute, Cell and Developmental Biology Program, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Alireza Khodadadi-Jamayran
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wei Zhang
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dexin Kong
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Chia-Wei Chang
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jingyang Feng
- Cook County Health and Hospital System, John H. Stroger Hospital, Chicago, IL 60612, USA
| | - Xiaosi Han
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tim M Townes
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Kitai Kim
- Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Sloan-Kettering Institute, Cell and Developmental Biology Program, Weill Medical College of Cornell University, New York, NY 10065, USA.
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| |
Collapse
|
11
|
Kulcsár PI, Tálas A, Huszár K, Ligeti Z, Tóth E, Weinhardt N, Fodor E, Welker E. Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Genome Biol 2017; 18:190. [PMID: 28985763 PMCID: PMC6389135 DOI: 10.1186/s13059-017-1318-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/11/2017] [Indexed: 12/19/2022] Open
Abstract
Background The propensity for off-target activity of Streptococcus pyogenes Cas9 (SpCas9) has been considerably decreased by rationally engineered variants with increased fidelity (eSpCas9; SpCas9-HF1). However, a subset of targets still generate considerable off-target effects. To deal specifically with these targets, we generated new “Highly enhanced Fidelity” nuclease variants (HeFSpCas9s) containing mutations from both eSpCas9 and SpCas9-HF1 and examined these improved nuclease variants side by side to decipher the factors that affect their specificities and to determine the optimal nuclease for applications sensitive to off-target effects. Results These three increased-fidelity nucleases can routinely be used only with perfectly matching 20-nucleotide-long spacers, a matching 5′ G extension being more detrimental to their activities than a mismatching one. HeFSpCas9 exhibit substantially improved specificity for those targets for which eSpCas9 and SpCas9-HF1 have higher off-target propensity. The targets can also be ranked by their cleavability and off-target effects manifested by the increased fidelity nucleases. Furthermore, we show that the mutations in these variants may diminish the cleavage, but not the DNA-binding, of SpCas9s. Conclusions No single nuclease variant shows generally superior fidelity; instead, for highest specificity cleavage, each target needs to be matched with an appropriate high-fidelity nuclease. We provide here a framework for generating new nuclease variants for targets that currently have no matching optimal nuclease, and offer a simple means for identifying the optimal nuclease for targets in the absence of accurate target-ranking prediction tools. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1318-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,University of Szeged, Szeged, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,Gene Design Kft, Szeged, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Gene Design Kft, Szeged, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Nóra Weinhardt
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,University of Szeged, Szeged, Hungary
| | - Elfrieda Fodor
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary. .,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
| |
Collapse
|
12
|
Levin RA, Voolstra CR, Agrawal S, Steinberg PD, Suggett DJ, van Oppen MJH. Engineering Strategies to Decode and Enhance the Genomes of Coral Symbionts. Front Microbiol 2017; 8:1220. [PMID: 28713348 PMCID: PMC5492045 DOI: 10.3389/fmicb.2017.01220] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/16/2017] [Indexed: 11/13/2022] Open
Abstract
Elevated sea surface temperatures from a severe and prolonged El Niño event (2014–2016) fueled by climate change have resulted in mass coral bleaching (loss of dinoflagellate photosymbionts, Symbiodinium spp., from coral tissues) and subsequent coral mortality, devastating reefs worldwide. Genetic variation within and between Symbiodinium species strongly influences the bleaching tolerance of corals, thus recent papers have called for genetic engineering of Symbiodinium to elucidate the genetic basis of bleaching-relevant Symbiodinium traits. However, while Symbiodinium has been intensively studied for over 50 years, genetic transformation of Symbiodinium has seen little success likely due to the large evolutionary divergence between Symbiodinium and other model eukaryotes rendering standard transformation systems incompatible. Here, we integrate the growing wealth of Symbiodinium next-generation sequencing data to design tailored genetic engineering strategies. Specifically, we develop a testable expression construct model that incorporates endogenous Symbiodinium promoters, terminators, and genes of interest, as well as an internal ribosomal entry site from a Symbiodinium virus. Furthermore, we assess the potential for CRISPR/Cas9 genome editing through new analyses of the three currently available Symbiodinium genomes. Finally, we discuss how genetic engineering could be applied to enhance the stress tolerance of Symbiodinium, and in turn, coral reefs.
Collapse
Affiliation(s)
- Rachel A Levin
- Centre for Marine Bio-Innovation, The University of New South Wales, SydneyNSW, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, SydneyNSW, Australia.,Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST),Thuwal, Saudi Arabia
| | - Shobhit Agrawal
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST),Thuwal, Saudi Arabia
| | - Peter D Steinberg
- Centre for Marine Bio-Innovation, The University of New South Wales, SydneyNSW, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, SydneyNSW, Australia.,Sydney Institute of Marine Science, MosmanNSW, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, TownsvilleQLD, Australia.,School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
| |
Collapse
|
13
|
Gao Z, Harwig A, Berkhout B, Herrera-Carrillo E. Mutation of nucleotides around the +1 position of type 3 polymerase III promoters: The effect on transcriptional activity and start site usage. Transcription 2017; 8:275-287. [PMID: 28598252 PMCID: PMC5703244 DOI: 10.1080/21541264.2017.1322170] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/18/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
Type 3 RNA polymerase III (Pol III) promoters are widely used for the expression of small RNAs such as short hairpin RNA and guide RNA in the popular RNAi and CRISPR-Cas gene regulation systems. Although it is generally believed that type 3 Pol III promoters use a defined transcription start site (+1 position), most man-made promoter constructs contain local sequence alterations of which the impact on transcription efficiency and initiation accuracy is not known. For three human type 3 Pol III promoters (7SK, U6, and H1), we demonstrated that the nucleotides around the +1 position affect both the transcriptional efficiency and start site selection. Human 7SK and U6 promoters with A or G at the +1 position efficiently produced small RNAs with a precise +1 start site. The human H1 promoter with +1A or G also efficiently produced small RNAs but from multiple start sites in the -3/-1 window. These results provide new insights for the design of vectors for accurate expression of designed small RNAs for research and therapeutic purposes.
Collapse
Affiliation(s)
- Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
14
|
Romanienko PJ, Giacalone J, Ingenito J, Wang Y, Isaka M, Johnson T, You Y, Mark WH. A Vector with a Single Promoter for In Vitro Transcription and Mammalian Cell Expression of CRISPR gRNAs. PLoS One 2016; 11:e0148362. [PMID: 26849369 PMCID: PMC4744079 DOI: 10.1371/journal.pone.0148362] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/19/2016] [Indexed: 11/19/2022] Open
Abstract
The genomes of more than 50 organisms have now been manipulated due to rapid advancement of gene editing technology. One way to perform gene editing in the mouse using the CRISPR/CAS system, guide RNA (gRNA) and CAS9 mRNA transcribed in vitro are microinjected into fertilized eggs that are then allowed to develop to term. As a rule, gRNAs are tested first in tissue culture cells and the one with the highest locus-specific cleavage activity is chosen for microinjection. For cell transfections, gRNAs are typically expressed using the human U6 promoter (hU6). However, gRNAs for microinjection into zygotes are obtained by in vitro transcription from a T7 bacteriophage promoter in a separate plasmid vector. Here, we describe the design and construction of a combined U6T7 hybrid promoter from which the same gRNA sequence can be expressed. An expression vector containing such a hybrid promoter can now be used to generate gRNA for testing in mammalian cells as well as for microinjection purposes. The gRNAs expressed and transcribed from this vector are found to be functional in cells as well as in mice.
Collapse
Affiliation(s)
- Peter J. Romanienko
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Joseph Giacalone
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Joanne Ingenito
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Yijie Wang
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Mayumi Isaka
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Thomas Johnson
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Yun You
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Willie H. Mark
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| |
Collapse
|
15
|
Schuster M, Schweizer G, Reissmann S, Kahmann R. Genome editing in Ustilago maydis using the CRISPR-Cas system. Fungal Genet Biol 2015; 89:3-9. [PMID: 26365384 DOI: 10.1016/j.fgb.2015.09.001] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/26/2022]
Abstract
This communication describes the establishment of the type II bacterial CRISPR-Cas9 system to efficiently disrupt target genes in the fungal maize pathogen Ustilago maydis. A single step transformation of a self-replicating plasmid constitutively expressing the U. maydis codon-optimized cas9 gene and a suitable sgRNA under control of the U. maydis U6 snRNA promoter was sufficient to induce genome editing. On average 70% of the progeny of a single transformant were disrupted within the respective b gene. Without selection the self-replicating plasmid was lost rapidly allowing transient expression of the CRISPR-Cas9 system to minimize potential long-term negative effects of Cas9. This technology will be an important advance for the simultaneous disruption of functionally redundant genes and gene families to investigate their contribution to virulence of U. maydis.
Collapse
Affiliation(s)
- Mariana Schuster
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Gabriel Schweizer
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Stefanie Reissmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany.
| |
Collapse
|
16
|
Ma H, Wu Y, Dang Y, Choi JG, Zhang J, Wu H. Pol III Promoters to Express Small RNAs: Delineation of Transcription Initiation. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e161. [PMID: 24803291 PMCID: PMC4040628 DOI: 10.1038/mtna.2014.12] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 03/10/2014] [Indexed: 12/17/2022]
Abstract
Pol III promoters such as U6 are commonly used to express small RNAs, including small interfering RNA, short hairpin RNA, and guide RNA, for the clustered regularly interspaced short palindromic repeats genome-editing system. However, whether the small RNAs were precisely expressed as desired has not been studied. Here, using deep sequencing to analyze small RNAs, we show that, for mouse U6 promoter, sequences immediately upstream of the putative initiation site, which is often modified to accommodate the restriction enzyme sites that enable easy cloning of small RNAs, are critical for precise transcription initiation. When the promoter is kept unmodified, transcription starts precisely from the first available A or G within the range of positions −1 to +2. In addition, we show that transcription from another commonly used pol III promoter, H1, starts at multiple sites, which results in variability at the 5′ end of the transcripts. Thus, inaccuracy of 5′ end of small RNA transcripts might be a common problem when using these promoters to express small RNAs based on currently believed concepts. Our study provides general guidelines for minimizing the variability of initiation, thereby enabling more accurate expression of small RNAs.
Collapse
Affiliation(s)
- Hongming Ma
- Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Yonggan Wu
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Ying Dang
- Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Jang-Gi Choi
- Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Junli Zhang
- Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Haoquan Wu
- Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| |
Collapse
|
17
|
Function-based gene identification using enzymatically generated normalized shRNA library and massive parallel sequencing. Proc Natl Acad Sci U S A 2010; 107:7377-82. [PMID: 20368428 DOI: 10.1073/pnas.1003055107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As a general strategy for function-based gene identification, an shRNA library containing approximately 150 shRNAs per gene was enzymatically generated from normalized (reduced-redundance) human cDNA. The library was constructed in an inducible lentiviral vector, enabling propagation of growth-inhibiting shRNAs and controlled activity measurements. RNAi activities were measured for 101 shRNA clones representing 100 human genes and for 201 shRNAs derived from a firefly luciferase gene. Structure-activity analysis of these two datasets yielded a set of structural criteria for shRNA efficacy, increasing the frequencies of active shRNAs up to 5-fold relative to random sampling. The same library was used to select shRNAs that inhibit breast carcinoma cell growth by targeting potential oncogenes. Genes targeted by the selected shRNAs were enriched for 10 pathways, 9 of which have been previously associated with various cancers, cell cycle progression, or apoptosis. One hundred nineteen genes, enriched through this selection and represented by two to six shRNAs each, were identified as potential cancer drug targets. Short interfering RNAs against 19 of 22 tested genes in this group inhibited cell growth, validating the efficiency of this strategy for high-throughput target gene identification.
Collapse
|
18
|
Boonanuntanasarn S, Panyim S, Yoshizaki G. Characterization and organization of the U6 snRNA gene in zebrafish and usage of their promoters to express short hairpin RNA. Mar Genomics 2008; 1:115-21. [PMID: 21798162 DOI: 10.1016/j.margen.2008.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 10/23/2008] [Indexed: 10/21/2022]
Abstract
We have characterized three U6 snRNA genes in zebrafish and randomly designated them as U6-1, U6-2, and U6-3. The U6-1 gene is closely related to the mammal U6 snRNA genes and that the U6-2 and U6-3 genes are more closely related to the Drosophila and Xenopus U6 snRNA genes. The upstream regulatory sequences were located based on their conserved position relative to the transcription start site. Furthermore, we speculate that the "CCAAT box" functions as the distal sequence element in the zebrafish U6 snRNA genes. Genomic BLASTn analysis revealed that at least 555 copies of the U6-1 gene are dispersed throughout the zebrafish genome, whereas the U6-2 and U6-3 genes are each present as a single copy. Three U6 snRNA genes are functionally expressed in various tissues. All three putative promoters were able to transcribe short hairpin RNA (shRNA) in zebrafish cell extracts. Our findings demonstrate that these putative promoters have the potential to be used for vector-based RNA interference (RNAi) in zebrafish. Another U6 snRNA was found from the genomic BLASTn search and designated as U6-4, demonstrating that there are four different types of zebrafish U6 snRNA genes.
Collapse
Affiliation(s)
- Surintorn Boonanuntanasarn
- School of Animal Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Muang, Nakhon Ratchasima, 30000 Thailand
| | | | | |
Collapse
|
19
|
Halbig KM, Lekven AC, Kunkel GR. Zebrafish U6 small nuclear RNA gene promoters contain a SPH element in an unusual location. Gene 2008; 421:89-94. [PMID: 18619527 DOI: 10.1016/j.gene.2008.06.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 06/03/2008] [Accepted: 06/03/2008] [Indexed: 11/29/2022]
Abstract
Promoters for vertebrate small nuclear RNA (snRNA) genes contain a relatively simple array of transcriptional control elements, divided into proximal and distal regions. Most of these genes are transcribed by RNA polymerase II (e.g., U1, U2), whereas the U6 gene is transcribed by RNA polymerase III. Previously identified vertebrate U6 snRNA gene promoters consist of a proximal sequence element (PSE) and TATA element in the proximal region, plus a distal region with octamer (OCT) and SphI postoctamer homology (SPH) elements. We have found that zebrafish U6 snRNA promoters contain the SPH element in a novel proximal position immediately upstream of the TATA element. The zebrafish SPH element is recognized by SPH-binding factor/selenocysteine tRNA gene transcription activating factor/zinc finger protein 143 (SBF/Staf/ZNF143) in vitro. Furthermore, a zebrafish U6 promoter with a defective SPH element is inefficiently transcribed when injected into embryos.
Collapse
Affiliation(s)
- Kari M Halbig
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | | | | |
Collapse
|
20
|
Wise TG, Schafer DJ, Lambeth LS, Tyack SG, Bruce MP, Moore RJ, Doran TJ. Characterization and comparison of chicken U6 promoters for the expression of short hairpin RNAs. Anim Biotechnol 2008; 18:153-62. [PMID: 17612838 DOI: 10.1080/10495390600867515] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
RNA interference (RNAi) is a powerful method of sequence-specific gene knockdown that can be mediated by DNA-based expression of short hairpin RNA (shRNA) molecules. A number of vectors for expression of shRNA have been developed with promoters for a small group of RNA polymerase III (pol III) transcripts of either mouse or human origin. To advance the use of RNAi as a tool for functional genomic research and future development of specific therapeutics in the chicken species, we have developed shRNA expression vectors featuring chicken U6 small nuclear RNA (snRNA) promoters. These sequences were identified based on the presence of promoter element sequence motifs upstream of matching snRNA sequences that are characteristic of these types of pol III promoters. To develop suitable shRNA expression vectors specifically for chicken functional genomic RNAi applications, we compared the efficiency of each of these promoters to express shRNA molecules. Promoter activity was measured in the context of RNAi by targeting and silencing the reporter gene encoding the enhanced green fluorescent protein (EGFP). Plasmids containing one of four identified chicken U6 promoters gave a similar degree of knockdown in DF-1 cells (chicken); although, there was some variability in Vero cells (monkey). Because the chicken promoters were not stronger than the benchmark mouse U6 promoter, we suggest that the promoter sequence and structure is more important in determining efficiency in vitro rather than its species origin.
Collapse
Affiliation(s)
- Terry G Wise
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Australia
| | | | | | | | | | | | | |
Collapse
|
21
|
Iijima O, Fukano H, Takahashi H, Shirai M, Suzuki Y. A purine at +2 rather than +1 adjacent to the human U6 promoter is required to prepare effective short hairpin RNAs. Biochem Biophys Res Commun 2006; 350:809-17. [PMID: 17045573 DOI: 10.1016/j.bbrc.2006.08.187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Accepted: 08/10/2006] [Indexed: 02/04/2023]
Abstract
The human U6 (hU6) promoter is widely used to express short hairpin RNAs (shRNAs) in mammalian cells. To verify the validity of the generalized concept-the hU6 promoter essentially requires a purine (usually guanine) at +1 for transcription, we enzymatically constructed an arbitrary shRNA library with the following features: (1) to have any one of adenine, cytosine, guanine, and thymine at the site; (2) to comprise shRNAs of 25-30 nucleotides in stem length which are transcribed through the promoter. cDNA of the catalytic subunit of cAMP-dependent protein kinase (PKACalpha) was used as material for library construction. We then used luciferase reporter cell lines to screen shRNAs which effectively reduced PKACalpha activity. Consequently, a purine was mostly present at +2, not at +1, of the clones isolated, suggesting that a purine at +2 rather than +1 adjacent to the hU6 promoter provides effective shRNAs for target gene silencing.
Collapse
Affiliation(s)
- Osamu Iijima
- GenoFunction, Inc., 1-25-14 Kannondai, Tsukuba, Ibaraki 305-085, Japan
| | | | | | | | | |
Collapse
|
22
|
Nicholson LJ, Philippe M, Paine AJ, Mann DA, Dolphin CT. RNA interference mediated in human primary cells via recombinant baculoviral vectors. Mol Ther 2005; 11:638-44. [PMID: 15771966 DOI: 10.1016/j.ymthe.2004.12.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Accepted: 12/17/2004] [Indexed: 11/22/2022] Open
Abstract
The success of RNA interference (RNAi) in mammalian cells, mediated by siRNAs or shRNA-generating plasmids, is dependent, to an extent, upon transfection efficiency. This is a particular problem with primary cells, which are often difficult to transfect using cationic lipid vehicles. Effective RNAi in primary cells is thus best achieved with viral vectors, and retro-, adeno-, and lentivirus RNAi systems have been described. However, the use of such human viral vectors is inherently problematic, e.g., Class 2 status and requirement of secondary helper functions. Although insect cells are their natural host, baculoviruses also transduce a range of vertebrate cell lines and primary cells with high efficiency. The inability of baculoviral vectors to replicate in mammalian cells, their Class 1 status, and the simplicity of their construction make baculovirus an attractive alternative gene delivery vector. We have developed a baculoviral-based RNAi system designed to express shRNAs and GFP from U6 and CMV promoters, respectively. Transduction of Saos2, HepG2, Huh7, and primary human hepatic stellate cells with a baculoviral construct expressing shRNAs targeting lamin A/C resulted in effective knockdown of the corresponding mRNA and protein. Development of this baculoviral-based system provides an additional shRNA delivery option for RNAi-based investigations in mammalian cells.
Collapse
Affiliation(s)
- Linda J Nicholson
- Department of Oncology, Guy's, King's and St Thomas' School of Medicine, The Rayne Institute, St Thomas' Hospital, London SE1 7EH, UK
| | | | | | | | | |
Collapse
|
23
|
Bardeleben C, Moore RL, Wayne RK. Isolation and Molecular Evolution of the Selenocysteine tRNA (Cf TRSP) and RNase P RNA (Cf RPPH1) Genes in the Dog Family, Canidae. Mol Biol Evol 2004; 22:347-59. [PMID: 15496554 DOI: 10.1093/molbev/msi022] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In an effort to identify rapidly evolving nuclear sequences useful for phylogenetic analyses of closely related species, we isolated two genes transcribed by RNA polymerase III (pol III), the selenocysteine tRNA gene (TRSP) and an RNase P RNA (RPPH1) gene from the domestic dog (Canis familiaris). We focus on genes transcribed by pol III because their coding regions are small (generally 100-300 base pairs [bp]) and their essential promoter elements are located within a couple of hundred bps upstream of the coding region. Therefore, we predicted that regions flanking the coding region and outside of the promoter elements would be free of constraint and would evolve rapidly. We amplified TRSP from 23 canids and RPPH1 from 12 canids and analyzed the molecular evolution of these genes and their utility as phylogenetic markers for resolving relationships among species in Canidae. We compared the rate of evolution of the gene-flanking regions to other noncoding regions of nuclear DNA (introns) and to the mitochondrial encoded COII gene. Alignment of TRSP from 23 canids revealed that regions directly adjacent to the coding region display high sequence variability. We discuss this pattern in terms of functional mechanisms of transcription. Although the flanking regions evolve no faster than introns, both genes were found to be useful phylogenetic markers, in part, because of the synapomorphic indels found in the flanking regions. Gene trees generated from the TRSP and RPPH1 loci were generally in agreement with the published mtDNA phylogeny and are the first phylogeny of Canidae based on nuclear sequences.
Collapse
Affiliation(s)
- Carolyne Bardeleben
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA.
| | | | | |
Collapse
|
24
|
Tiscornia G, Tergaonkar V, Galimi F, Verma IM. CRE recombinase-inducible RNA interference mediated by lentiviral vectors. Proc Natl Acad Sci U S A 2004; 101:7347-51. [PMID: 15123829 PMCID: PMC409921 DOI: 10.1073/pnas.0402107101] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Recently, several systems designed to trigger RNA interference by using small hairpin RNA driven by polymerase III promoters have been described. Here, we report a lentiviral-mediated small interfering RNA delivery system that can be induced by CRE recombinase. The system consists of a lentiviral vector carrying a mouse U6 promoter that is separated from a small hairpin RNA by a random DNA stuffer sequence flanked by modified loxP sites. The silencing cassette is not expressed until activated by addition of CRE recombinase delivered by a lentiviral vector. We have used this system to show specific down-regulation of GFP and two endogenous genes (the tumor suppressor p53 and the NF-kappaB transcription factor subunit p65) in vitro. Furthermore, down-regulation of both p53 and p65 resulted in the expected effect on downstream genes and cellular phenotype. We foresee multiple applications of this system both in vitro and in vivo to down-regulate specific targets in a tissue-specific and localized manner.
Collapse
Affiliation(s)
- Gustavo Tiscornia
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | | | | |
Collapse
|
25
|
|
26
|
Affiliation(s)
- Douglas S Conklin
- Cancer Genome Center, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd, Woodbury, NY 11797, USA.
| |
Collapse
|
27
|
Hinkley CS, Hirsch HA, Gu L, LaMere B, Henry RW. The small nuclear RNA-activating protein 190 Myb DNA binding domain stimulates TATA box-binding protein-TATA box recognition. J Biol Chem 2003; 278:18649-57. [PMID: 12621023 DOI: 10.1074/jbc.m204247200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human U6 small nuclear RNA (snRNA) gene transcription by RNA polymerase III requires cooperative promoter binding involving the snRNA-activating protein complex (SNAP(c)) and the TATA-box binding protein (TBP). To investigate the role of SNAP(c) for TBP function at U6 promoters, TBP recruitment assays were performed using full-length TBP and a mini-SNAP(c) containing SNAP43, SNAP50, and a truncated SNAP190. Mini-SNAP(c) efficiently recruits TBP to the U6 TATA box, and two SNAP(c) subunits, SNAP43 and SNAP190, directly interact with the TBP DNA binding domain. Truncated SNAP190 containing only the Myb DNA binding domain is sufficient for TBP recruitment to the TATA box. Therefore, the SNAP190 Myb domain functions both to specifically recognize the proximal sequence element present in the core promoters of human snRNA genes and to stimulate TBP recognition of the neighboring TATA box present in human U6 snRNA promoters. The SNAP190 Myb domain also stimulates complex assembly with TBP and Brf2, a subunit of a snRNA-specific TFIIIB complex. Thus, interactions between the DNA binding domains of SNAP190 and TBP at juxtaposed promoter elements define the assembly of a RNA polymerase III-specific preinitiation complex.
Collapse
Affiliation(s)
- Craig S Hinkley
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | | | | | | | | |
Collapse
|
28
|
Domitrovich AM, Kunkel GR. Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies. Nucleic Acids Res 2003; 31:2344-52. [PMID: 12711679 PMCID: PMC154217 DOI: 10.1093/nar/gkg331] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Vertebrate U6 small nuclear RNA (snRNA) gene promoters are among the founding members of those recognized by RNA polymerase III in which all control elements for initiation are located in the 5'-flanking region. Previously, one human U6 gene (U6-1) has been studied extensively. We have identified a total of nine full-length U6 loci in the human genome. Unlike human U1 and U2 snRNA genes, most of the full-length U6 loci are dispersed throughout the genome. Of the nine full-length U6 loci, five are potentially active genes (U6-1, U6-2, U6-7, U6-8 and U6-9) since they are bound by TATA-binding protein and enriched in acetylated histone H4 in cultured human 293 cells. These five all contain OCT, SPH, PSE and TATA elements, although the sequences of these elements are variable. Furthermore, these five genes are transcribed to different extents in vitro or after transient transfection of human 293 cells. Of the nine full-length U6 loci, only U6-7 and U6-8 are closely linked and contain highly conserved 5'-flanking regions. However, due to a modest sequence difference in the proximal sequence elements for U6-7 and U6-8, these genes are transcribed at very different levels in transfected cells.
Collapse
Affiliation(s)
- Angela M Domitrovich
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | | |
Collapse
|
29
|
Abstract
RNAi is evolving into a powerful tool for manipulating gene expression in mammalian cells with potential utility for investigating gene function, for high-throughput, function-based genetic screens and potentially for development as a therapeutic tool.
Collapse
Affiliation(s)
- Patrick J Paddison
- Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | | |
Collapse
|
30
|
Mach CM, Hargrove BW, Kunkel GR. The Small RNA gene activator protein, SphI postoctamer homology-binding factor/selenocysteine tRNA gene transcription activating factor, stimulates transcription of the human interferon regulatory factor-3 gene. J Biol Chem 2002; 277:4853-8. [PMID: 11724783 DOI: 10.1074/jbc.m108308200] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many small nuclear RNA gene promoters are activated by SphI postoctamer homology (SPH)-binding factor/selenocysteine tRNA gene transcription activating factor (SBF/Staf). Whereas this transcription factor was initially identified by its ability to bind to SPH elements in such promoters, it was more recently shown to have the capacity to activate transcription of a synthetic mRNA gene promoter through a distinct activation domain. Here, we show that the human interferon regulatory factor-3 (IRF-3) gene promoter contains a functional SPH element that is bound by SBF/Staf in vitro and in transfected cells.
Collapse
Affiliation(s)
- Claire M Mach
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
| | | | | |
Collapse
|
31
|
Jayan GC, Cordelier P, Patel C, BouHamdan M, Johnson RP, Lisziewicz J, Pomerantz RJ, Strayer DS. SV40-derived vectors provide effective transgene expression and inhibition of HIV-1 using constitutive, conditional,and pol III promoters. Gene Ther 2001; 8:1033-42. [PMID: 11438838 DOI: 10.1038/sj.gt.3301481] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2001] [Accepted: 03/19/2001] [Indexed: 11/09/2022]
Abstract
Vectors based on recombinant SV40 viruses (rSV40) are highly effective in delivering transgene expression driven by constitutive promoters. We tested here whether these vectors could be used with conditional promoters and promoters using RNA polymerase III transcription, with inhibition of HIV-1 by Tat activation response (TAR) decoys as a functional measure of effective transgene delivery and activity. TAR decoys inhibit HIV-1 Tat, a trans-activator of HIV-1 transcription. Tat acts early in the viral replicative cycle and is essential for efficient viral replication. We evaluated rSV40 gene delivery using two different inhibitors of Tat. One was a dual function polyTAR gene encoding 25 sequential TAR elements (TAR(25)), plus an antisense tat, driven either by HIV-1 long terminal repeat (HIV-LTR) as a conditional promoter, or by cytomegalovirus immediate-early promoter (CMV-IEP) as a constitutive promoter. The other inhibitor was a single TAR decoy, driven by the U6 small nuclear RNA promoter (U6-P). These decoys were delivered to unselected cells in two different human T lymphocyte lines and to unstimulated primary human peripheral blood mononuclear cells (pbmc). Gene delivery was confirmed by PCR, and expression by RT-PCR. By in situ hybridization analysis, >95% of cells were transduced. These transgene constructs protected all cell types tested from HIV-1, as measured by syncytia formation and p24 antigen release. Somewhat better inhibition of HIV-1 replication was achieved with HIV-1 long terminal repeat (HIV-1 LTR) as a conditional promoter than with the constitutive CMV-IEP. The U6-P was also very effective, driving a TAR(1) transcript. Cell viability was not detectably affected by TAR decoy expression. Thus, rSV40 vectors effectively deliver HIV-1-inhibitory RNAs using either constitutive or conditional pol II promoters, or using a pol III promoter. The versatility of this gene delivery system may prove to be useful in anti-HIV-1 therapeutics.
Collapse
Affiliation(s)
- G C Jayan
- Department of Pathology, Jefferson Medical College, Philadelphia, PA 19107, USA
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Tang YC, Li Y, Qian GX. Reduction of tumorigenicity of SMMC-27721 hepatoma cells by vascular endothelial growth factor antisense gene therapy. World J Gastroenterol 2001; 7:22-7. [PMID: 11819727 PMCID: PMC4688695 DOI: 10.3748/wjg.v7.i1.22] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To test the hypothesis to block VEGF expression of SMMC-7721 hepatomacells may inhibit tumor growth using the rat hepatoma model.
METHODS: Amplifiy the 200 VEGF cDNA fragment and insert it into human U6 gene cassette in the reverse orientation transcribing small antisense RNA which could specifically interact with VEGF165, and VEGF121 mRNA. Construct the retroviral vector containing this antisense VEGF U6 cassette and package the replication-deficient recombinant retrovirus. SMMC-7721 cells were transduced with these virus and positive clones were selected with G418. PCR and Southern blot analysis were performed to determine if U6 cassette integrated into the genomic DNA of positive clone. Transfected tumor cells were evaluated for RNA expression by ribonuclease protection assays. The VEGF protein in the supernatant of parental tumor cells and genetically modified tumor cells was determined with ELISA. In vitro and in vivo growth properties of antisense VEGF cell clone in nude mice were analyzed.
RESULTS: Restriction enzyme digestion and PCR sequencing verified that the antisense VEGF RNA retroviral vector was successfully constructed. After G418 selection, resistant SMMC-7721 cell clone was picked up. PCR and Southern blot analysis suggested that U6 cassette was integrated into the cell genomic DNA. Stable SMMC-7721 cell clone transduced with U6 antisense RNA cassette could express 200 bp small antisense VEGF RNA and secrete reduced levels of VEGF in culture condition. Production of VEGF by antisense transgenea2expressing cells was 65 ± 10 ng/L per 106 cells, 420 ± 45 ng/L per 106 cells in sense group and 485 ± 30 ng/ L per 106 cells in the negative control group, (P < 0.5). The antisense-VEGF cell clone appeared phenotypically indistinguishable from SMMC-7721 cells and SMMC-7721 cells transfected sense VEGF. The growth rate of the antisense-VEGF cell clone was the same as the control cells. When S.C. was implanted into nude mice, growth of antisense-VEGF cell lines was greatly inhibited compared with control cells.
CONCLUSION: Expression of antisense VEGF RNA in SMMC-7721 cells could decrease the tumorigenicity, and antisense-VEGF gene therapy may be an adjuvant treatment for hepatoma.
Collapse
Affiliation(s)
- Y C Tang
- Department of Biochemistry, Shanghai Second Medical University, Shanghai 200025,China.
| | | | | |
Collapse
|
33
|
McCulloch V, Hardin P, Peng W, Ruppert JM, Lobo-Ruppert SM. Alternatively spliced hBRF variants function at different RNA polymerase III promoters. EMBO J 2000; 19:4134-43. [PMID: 10921893 PMCID: PMC306597 DOI: 10.1093/emboj/19.15.4134] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In yeast, a single form of TFIIIB is required for transcription of all RNA polymerase III (pol III) genes. It consists of three subunits: the TATA box-binding protein (TBP), a TFIIB-related factor, BRF, and B". Human TFIIIB is not as well defined and human pol III promoters differ in their requirements for this activity. A human homolog of yeast BRF was shown to be required for transcription at the gene-internal 5S and VA1 promoters. Whether or not it was also involved in transcription from the gene-external human U6 promoter was unclear. We have isolated cDNAs encoding alternatively spliced forms of human BRF that can complex with TBP. Using immunopurified complexes containing the cloned hBRFs, we show that while hBRF1 functions at the 5S, VA1, 7SL and EBER2 promoters, a different variant, hBRF2, is required at the human U6 promoter. Thus, pol III utilizes different TFIIIB complexes at structurally distinct promoters.
Collapse
Affiliation(s)
- V McCulloch
- Department of Medical Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | | | | | | |
Collapse
|
34
|
Abstract
The task of transcribing nuclear genes is shared between three RNA polymerases in eukaryotes: RNA polymerase (pol) I synthesizes the large rRNA, pol II synthesizes mRNA and pol III synthesizes tRNA and 5S rRNA. Although pol II has received most attention, pol I and pol III are together responsible for the bulk of transcriptional activity. This survey will summarise what is known about the process of transcription by pol I and pol III, how it happens and the proteins involved. Attention will be drawn to the similarities between the three nuclear RNA polymerase systems and also to their differences.
Collapse
Affiliation(s)
- M R Paule
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
| | | |
Collapse
|
35
|
Ohkawa J, Taira K. Control of the functional activity of an antisense RNA by a tetracycline-responsive derivative of the human U6 snRNA promoter. Hum Gene Ther 2000; 11:577-85. [PMID: 10724036 DOI: 10.1089/10430340050015761] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In an effort to develop a regulatable derivative of the promoter of the human gene for U6 snRNA, we generated several constructs composed of the human U6 snRNA promoter and sequences derived from the gene for the tetracycline operator of a prokaryotic tetracycline resistance transposon. One of the constructs had strong transcriptional activity in the presence of tetracycline that was equivalent to 80% of the activity of the wild-type promoter. Furthermore, the transcriptional activity was almost completely repressed in the absence of tetracycline. Transcriptional activity became detectable within 4 hr after the addition of tetracycline to the culture medium. We used this system to control the functional activity of an antisense RNA for a chimeric gene derived from genes for the epidermal growth factor receptor (EGFR) and green fluorescent protein (GFP). A plasmid that expressed the chimeric gene and a plasmid that expressed the antisense RNA under the control of the inducible U6 promoter were used to cotransfect HeLa cells that were producing the tetracycline repressor protein (Tet R). Addition of tetracycline to the culture medium 12 hr after transfection resulted in the almost complete disappearance of the fluorescent signal due to the chimeric protein within 24 hr. Our results suggest that this expression system might be a useful tool for controlling the expression of functional RNAs, such as aptamers and antisense RNAs, both in basic research and in gene therapy.
Collapse
Affiliation(s)
- J Ohkawa
- National Institute for Advanced Interdisciplinary Research, Higashi, Tsukuba Science City, Japan
| | | |
Collapse
|
36
|
Jensen RC, Wang Y, Hardin SB, Stumph WE. The proximal sequence element (PSE) plays a major role in establishing the RNA polymerase specificity of Drosophila U-snRNA genes. Nucleic Acids Res 1998; 26:616-22. [PMID: 9421524 PMCID: PMC147272 DOI: 10.1093/nar/26.2.616] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Most small nuclear RNA (snRNA) genes are transcribed by RNA polymerase II, but some (e.g., U6) are transcribed by RNA polymerase III. In vertebrates a TATA box at a fixed distance downstream of the proximal sequence element (PSE) acts as a dominant determinant for recruiting RNA polymerase III to U6 gene promoters. In contrast, vertebrate snRNA genes that contain a PSE but lack a TATA box are transcribed by RNA polymerase II. In plants, transcription of both classes of snRNA genes requires a TATA box in addition to an upstream sequence element (USE), and polymerase specificity is determined by the spacing between these two core promoter elements. In these examples, the PSE (or USE) is interchangeable between the two classes of snRNA genes. Here we report the surprising finding that the Drosophila U1 and U6 PSEs cannot functionally substitute for each other; rather, determination of RNA polymerase specificity is an intrinsic property of the PSE sequence itself. The alteration of two or three base pairs near the 3'-end of the U1 and U6 PSEs was sufficient to switch the RNA polymerase specificity of Drosophila snRNA promoters in vitro. These findings reveal a novel mechanism for achieving RNA polymerase specificity at insect snRNA promoters.
Collapse
Affiliation(s)
- R C Jensen
- Department of Chemistry and Molecular Biology Institute, San Diego State University, San Diego, CA 92182-1030, USA
| | | | | | | |
Collapse
|
37
|
Nakaar V, Günzl A, Ullu E, Tschudi C. Structure of the Trypanosoma brucei U6 snRNA gene promoter. Mol Biochem Parasitol 1997; 88:13-23. [PMID: 9274863 DOI: 10.1016/s0166-6851(97)00078-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Transcription in vivo of small nuclear and cytoplasmic RNA genes of Trypanosoma brucei was previously shown to require the A and B blocks of a divergently transcribed tRNA or tRNA-like gene located approximately 100 nucleotides (nt) upstream. To understand the functioning of these transcription units, we have used the U6 snRNA/tRNA(Thr) genes as a model system. Saturation mutagenesis revealed that for transcription in vivo three elements are essential and sufficient. In addition to the previously described A and B boxes, sequences in the U6 coding region close to the 5' end participate in positioning RNA polymerase III at the start site, and thus constitute a third promoter element. We further showed that the function of the upstream A box, but not the B box, is strictly dependent upon its distance to the U6 gene internal control region. Using our recently developed transcription extract we further demonstrated that in vitro U6 transcription requires only the intragenic sequences and the upstream A box of the tRNA(Thr) gene. This apparent discrepancy between the in vivo and in vitro requirements is highly reminiscent of U6 snRNA gene transcription in the yeast Saccharomyces cerevisiae, and suggests the possibility that similar to the yeast system the B block of the trypanosome U6 snRNA gene promoter might be involved in chromatin organization.
Collapse
Affiliation(s)
- V Nakaar
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520-8022, USA
| | | | | | | |
Collapse
|
38
|
Kawakami K, Masuda K, Nagano K, Ohkuma Y, Roeder RG. Characterization of the core promoter of the Na+/K(+)-ATPase alpha 1 subunit gene. Elements required for transcription by RNA polymerase II and RNA polymerase III in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 237:440-6. [PMID: 8647083 DOI: 10.1111/j.1432-1033.1996.0440k.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We have analyzed the core promoter element of the Na+/K(+)-ATPase alpha 1 subunit gene by means of an in vitro transcription system composed of a HeLa nuclear extract. 5'-deletion and 3'-deletion analyses revealed that this gene is specifically transcribed by RNA polymerase II in a manner that is dependent on the upstream regulatory region of the gene (-102 to -61), and that the 3' boundary of the minimal promoter element does not extend beyond +5. Analysis of linker-substitution mutations and point mutations revealed that the TATA-like sequence (-33 to -26) is required for upstream-sequence-dependent transcription whereas linker-substitution mutations and point mutations near +1 did not abolish transcription. The gene was found to be transcribed by RNA polymerase III when phosphocellulose column fractions were assayed. Deletion analysis mapped the minimal RNA-polymerase-III--specific promoter element from -49 to +17. The phosphocellulose 0.3-M-KCl fraction is absolutely required for transcription by RNA polymerase III, while the 0.85-M-KCl fraction represses aberrant transcription from incorrect initiation sites. Analysis of linker-substitution mutations indicated that the TATA-like sequence is required for RNA-polymerase-III--specific transcription. Although point mutations in the 5' half of the TATA-like sequence did not affect transcription, those in the 3' half shifted the transcription initiation site 3 bp upstream. The results suggest the the Na+/K(+)-ATPase alpha 1 subunit gene promoter contains a TATA-like sequence which can direct transcription by RNA polymerase III in vitro. The mechanism of alternative regulation of RNA polymerase II and RNA polymerase III is discussed.
Collapse
Affiliation(s)
- K Kawakami
- Department of Biology, Jichi Medical School, Tochigi-ken, Japan
| | | | | | | | | |
Collapse
|
39
|
Park JM, Choi IS, Kang SG, Lee JY, Hatfield DL, Lee BJ. Upstream promoter elements are sufficient for selenocysteine tRNA[Ser]Sec gene transcription and to determine the transcription start point. Gene X 1995; 162:13-9. [PMID: 7557401 DOI: 10.1016/0378-1119(95)00340-c] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The TATA box, located upstream at about nt -30, and the proximal sequence element, located at about nt -60, are both essential and sufficient for basal level transcription of the Xenopus laevis (Xl) selenocysteine (Sec) tRNA[Ser]Sec gene as demonstrated by its microinjection into Xl oocytes. Point mutations within either of these regions abolish transcription, while deletion of the internal boxA element or insertion of 13 nt within the internal boxB element does not impair transcription. The latter mutations (within the internal regions) affect processing of the 3'-trailer sequence. Replacement of the tRNA[Ser]Sec coding sequence with an Escherichia coli M1 RNA gene resulted in expression of the E. coli gene governed by the upstream tRNA[Ser]Sec promoter elements. These studies demonstrate unequivocally that the upstream promoter elements are sufficient for the basal level of tRNA[Ser]Sec gene transcription. Primer extension studies with spacer mutants show that the internal elements do not play a role in selecting the transcription start point (tsp), but that selection of the tsp is determined by the region upstream from the gene. Further, studies with spacer mutants show that the distance between the TATA box and the tsp is quite likely the critical factor in selecting the position of tsp.
Collapse
Affiliation(s)
- J M Park
- Laboratory of Molecular Genetics, Seoul National University, South Korea
| | | | | | | | | | | |
Collapse
|
40
|
Goomer RS, Urso O, Kunkel GR. A complex that contains proteins binding to the PSE and TATA sites in a human U6 small nuclear RNA promoter. Gene 1994; 148:269-75. [PMID: 7958954 DOI: 10.1016/0378-1119(94)90698-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The proximal promoter of a human U6 small nuclear RNA (snRNA)-encoding gene contains two separate elements, the proximal sequence element (PSE) and the TATA box. We investigated the interaction of the PSE- and TATA-binding proteins (PBP and TBP) with normal and mutant U6 proximal promoters using an electrophoretic mobility shift assay. We detected a complex containing both PBP and TBP bound to the wild-type U6 promoter. Efficient formation of the triple complex was dependent on the presence of the PSE and the TATA box on the template DNA. Mutant U6 promoters containing an increased spacing between the PSE and TATA box of 5 or 10 bp were impaired in the ability to form a complex that includes TBP. We infer from these results that PBP and TBP interact when their binding sites are properly positioned in a U6 gene promoter.
Collapse
Affiliation(s)
- R S Goomer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station 77843-2128
| | | | | |
Collapse
|
41
|
Functional characterization of elements in a human U6 small nuclear RNA gene distal control region. Mol Cell Biol 1993. [PMID: 8336708 DOI: 10.1128/mcb.13.8.4670] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The promoters of vertebrate U6 small nuclear RNA genes contain a distal control region whose presence results in at least an eightfold level of transcriptional activation in vivo. Previous transfection experiments have demonstrated that most of the distal control region of a human U6 gene resides in a restriction fragment located from -244 to -149 relative to the transcriptional start site. Three octamer-related motifs that bind recombinant Oct-1 transcription factor in vitro exist in this segment of DNA. However, transfection of human 293 cells with various plasmid templates in which these Oct-1 binding sites had been disrupted individually or in combination showed that only the consensus octamer motif located between positions -221 to -214 was functional. Even so, the consensus octamer motif mutant template was expressed at only a moderately reduced level relative to the wild-type promoter. When another octamer-related sequence located nearby, one that did not bind Oct-1 in vitro, was disrupted along with the perfect octamer site, expression was reduced fivefold in transfected cells. A factor that binds this functional, nonconsensus octamer site (NONOCT) was detected in crude cellular extracts. However, the NONOCT sequence was not essential for activation, since its disruption caused only a 40% reduction in U6 gene expression, and mutagenesis to convert the NONOCT sequence to a consensus octamer motif restored wild-type expression. Furthermore, in vitro transcription of a human U6 proximal promoter joined to a single copy of the octamer motif was stimulated by the addition of recombinant Oct-1 protein.
Collapse
|
42
|
Danzeiser DA, Urso O, Kunkel GR. Functional characterization of elements in a human U6 small nuclear RNA gene distal control region. Mol Cell Biol 1993; 13:4670-8. [PMID: 8336708 PMCID: PMC360093 DOI: 10.1128/mcb.13.8.4670-4678.1993] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The promoters of vertebrate U6 small nuclear RNA genes contain a distal control region whose presence results in at least an eightfold level of transcriptional activation in vivo. Previous transfection experiments have demonstrated that most of the distal control region of a human U6 gene resides in a restriction fragment located from -244 to -149 relative to the transcriptional start site. Three octamer-related motifs that bind recombinant Oct-1 transcription factor in vitro exist in this segment of DNA. However, transfection of human 293 cells with various plasmid templates in which these Oct-1 binding sites had been disrupted individually or in combination showed that only the consensus octamer motif located between positions -221 to -214 was functional. Even so, the consensus octamer motif mutant template was expressed at only a moderately reduced level relative to the wild-type promoter. When another octamer-related sequence located nearby, one that did not bind Oct-1 in vitro, was disrupted along with the perfect octamer site, expression was reduced fivefold in transfected cells. A factor that binds this functional, nonconsensus octamer site (NONOCT) was detected in crude cellular extracts. However, the NONOCT sequence was not essential for activation, since its disruption caused only a 40% reduction in U6 gene expression, and mutagenesis to convert the NONOCT sequence to a consensus octamer motif restored wild-type expression. Furthermore, in vitro transcription of a human U6 proximal promoter joined to a single copy of the octamer motif was stimulated by the addition of recombinant Oct-1 protein.
Collapse
Affiliation(s)
- D A Danzeiser
- Department of Biochemistry and Biophysics, Texas A&M University, College Station 77843-2128
| | | | | |
Collapse
|
43
|
Edoh D, Kiss T, Filipowicz W. Activity of U-snRNA genes with modified placement of promoter elements in transfected protoplasts and stably transformed tobacco. Nucleic Acids Res 1993; 21:1533-40. [PMID: 8479903 PMCID: PMC309359 DOI: 10.1093/nar/21.7.1533] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In higher plants the promoter elements of pol II- and pol III-transcribed U-snRNA genes are identical, comprising a -30 TATA box and an upstream sequence element, USE. The USE and TATA are centred approximately four and three helical DNA turns apart in pol II and pol III genes, respectively, and it is this difference in the element spacing that determines the RNA polymerase specificity of the gene. In this study we have analyzed the effect of spacing mutations on activity of Arabidopsis U2 and U6 genes in transfected protoplasts of Nicotiana plumbaginifolia and in stably transformed tobacco. In the pol III-transcribed U6 gene the insertions and deletions of either odd or even numbers of half helical turns completely inactivate transcription in transfected protoplasts, consistent with the high conservation of the element spacing found in all plant U-snRNA genes. Surprisingly, while insertions of 50 base pairs (bp) or more into the spacer of the pol II-specific U2 gene inactivate transcription, a deletion of 5 bp or insertions of as much as 20 bp decrease transcription by only 40 to 70%. This relaxed requirement for the conserved element spacing is only seen in transfected protoplasts since the same mutant U2 genes are not transcribed in stably transformed tobacco when transcription takes place from the chromosome. The results provide some clues about possible factor interactions at the promoters of plant U-snRNA genes and also offer an example of major differences in transcription between transiently and stably transformed cells.
Collapse
Affiliation(s)
- D Edoh
- Friedrich Miescher-Institut, Basel, Switzerland
| | | | | |
Collapse
|
44
|
Sürig D, Bredow S, Benecke BJ. The seemingly identical 7SK and U6 core promoters depend on different transcription factor complexes. Gene Expr 1993; 3:175-85. [PMID: 7505670 PMCID: PMC6081636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/1992] [Accepted: 03/09/1993] [Indexed: 01/25/2023]
Abstract
Fractions obtained from HeLa cell extracts were used to study RNA polymerase III-catalyzed transcription from the human 7SK and mouse U6 RNA promoters in vitro. Although both genes depend on two almost identical core promoter elements (TATA box and PSE), different fractions were required. The 7SK promoter revealed full activity with the phosphocellulose B fraction alone. In contrast, efficient transcription from the U6 promoter depended on the additional presence of the C or D fraction. The analysis of the b1 and b2 subfractions (obtained by DEAE-Sephadex chromatography) revealed that for both promoters the b1 and the phosphocellulose D fraction were mutually interchangeable. However, while both fractions were fully equivalent for the 7SK promoter, the U6 promoter revealed an additional requirement for the C fraction in the presence of the b1 fraction. Since the b1 and the D fractions enclose two different complexes of the TATA-binding protein (TBP), B-TFIID and D-TFIID, our results indicate that functionally these two complexes are responsible for the observed differences in transcription of the 7SK and U6 genes.
Collapse
Affiliation(s)
- D Sürig
- Department of Biochemistry, Faculty of Chemistry, Ruhr University, Bochum, Germany
| | | | | |
Collapse
|