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Nashimoto M. TRUE Gene Silencing. Int J Mol Sci 2022; 23:5387. [PMID: 35628198 PMCID: PMC9141469 DOI: 10.3390/ijms23105387] [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: 04/11/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
TRUE gene silencing is an RNA-mediated gene expression control technology and is termed after tRNase ZL-utilizing efficacious gene silencing. In this review, I overview the potentiality of small guide RNA (sgRNA) for TRUE gene silencing as novel therapeutics. First, I describe the physiology of tRNase ZL and cellular small RNA, and then sgRNA and TRUE gene silencing. An endoribonuclease, tRNase ZL, which can efficiently remove a 3' trailer from pre-tRNA, is thought to play the role in tRNA maturation in the nucleus and mitochondria. There exist various small RNAs including miRNA and fragments from tRNA and rRNA, which can function as sgRNA, in living cells, and human cells appear to be harnessing cytosolic tRNase ZL for gene regulation together with these small RNAs. By utilizing the property of tRNase ZL to recognize and cleave micro-pre-tRNA, a pre-tRNA-like or micro-pre-tRNA-like complex, as well as pre-tRNA, tRNase ZL can be made to cleave any target RNA at any desired site under the direction of an artificial sgRNA that binds a target RNA and forms the pre-tRNA-like or micro-pre-tRNA-like complex. This general RNA cleavage method underlies TRUE gene silencing. Various examples of the application of TRUE gene silencing are reviewed including the application to several human cancer cells in order to induce apoptosis. Lastly, I discuss the potentiality of sgRNA as novel therapeutics for multiple myeloma.
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Affiliation(s)
- Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
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Takahashi M, Seki M, Nashimoto M. A naked antisense oligonucleotide with phosphorothioate linkages is taken up intracellularly more efficiently but functions less effectively. Biochem Biophys Res Commun 2021; 573:140-144. [PMID: 34411896 DOI: 10.1016/j.bbrc.2021.08.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/05/2021] [Accepted: 08/12/2021] [Indexed: 10/20/2022]
Abstract
We have been developing a gene silencing technology by harnessing a tRNA 3' processing endoribonuclease, tRNase ZL, with antisense oligonucleotides. Here, to further improve this technology, we investigated how the length and the modifications of naked oligonucleotides affect the efficiency of their uptake by HeLa, HEK293, and HL60 cells by flow cytometry and fluorescence microscopy. 7-30-nt Alexa-Fluor-568-labeled DNAs with phosphorothioate linkages and 7-30-nt Alexa-Fluor-568-labeled, 2'-O-methylated RNAs without phosphorothioate linkages were examined, and, on the whole, longer oligonucleotides were shown to be intracellularly taken up more efficiently. In addition, a 2'-O-methoxyethylated RNA without phosphorothioate linkages, a 2'-fluoriated RNA without phosphorothioate linkages, a 2'-O-methylated RNA with phosphorothioate linkages, and a 2'-O-methylated RNA with phosphorothioate linkages and LNA modifications of 5'-/3'-terminal nucleotides were examined. The oligonucleotides with phosphorothioate linkages were taken up by the cells more efficiently than those without the linkages. Furthermore, we examined how the phosphorothioate linkages of oligonucleotides affect their antisense effects using 22-nt anti-miR16 oligonucleotides with and without phosphorothioate linkages. The latter oligonucleotide decreased the miR16 level much more intensively than the former, although the latter was intracellularly taken up much less efficiently. These observations may be not generalized and differ depending on features of oligonucleotides and cell types. Taken together these results suggest that the productive uptake efficiency for an antisense oligonucleotide needs to be considered to select its length and modifications.
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Affiliation(s)
- Masayuki Takahashi
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan.
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Nozaki T, Takahashi M, Ishikawa T, Haino A, Seki M, Kikuchi H, Yuan B, Nashimoto M. The heptamer sgRNA targeting the human OCT4 mRNA can upregulate the OCT4 expression. Biochem Biophys Rep 2021; 26:100918. [PMID: 33553691 PMCID: PMC7859166 DOI: 10.1016/j.bbrep.2021.100918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/24/2020] [Accepted: 01/07/2021] [Indexed: 11/17/2022] Open
Abstract
TRUE gene silencing is one of the gene suppression technologies. This technology exploits the enzymatic property of the tRNA 3' processing endoribonuclease tRNase ZL, which is that it can cleave a target RNA under the direction of a small guide RNA (sgRNA). We have been working on the development of therapeutic sgRNAs for hematological malignancies. In the course of an experiment to examine the ability of the heptamer-type sgRNA H15792 targeting the OCT4 mRNA to differentiate human amnion stem cells, we observed unexpectedly that the amnion cells exhibited a morphology resembling initialized cells. Here we investigated the effect of H15792 on human HL60 leukemia cells, and found that H15792 can upregulate the OCT4 expression and the expression of alkaline phosphatase in the cells.
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Affiliation(s)
- Tadasuke Nozaki
- Department of Clinical Molecular Genetics, Faculty of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Horinouchi 1432-1, Hachioji, Tokyo, 192-0392, Japan
| | - Masayuki Takahashi
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata, 956-8603, Japan
| | - Tatsuya Ishikawa
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata, 956-8603, Japan
| | - Arisa Haino
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata, 956-8603, Japan
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata, 956-8603, Japan
| | - Hidetomo Kikuchi
- Department of Clinical Molecular Genetics, Faculty of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Horinouchi 1432-1, Hachioji, Tokyo, 192-0392, Japan
| | - Bo Yuan
- Department of Clinical Molecular Genetics, Faculty of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Horinouchi 1432-1, Hachioji, Tokyo, 192-0392, Japan
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata, 956-8603, Japan
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Ninomiya S, Ishikawa T, Takahashi M, Seki M, Nashimoto M. Potential physiological roles of the 31/32-nucleotide Y4-RNA fragment in human plasma. Noncoding RNA Res 2019; 4:135-140. [PMID: 32072081 PMCID: PMC7012775 DOI: 10.1016/j.ncrna.2019.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 11/29/2022] Open
Abstract
The 31- and 32-nt 5′-fragments of Y4-RNA (Y4RNAfr) exist abundantly in human plasma. The Y4RNAfr can function as 5′-half-tRNA-type sgRNA for tRNase ZL, although we do not know yet what its physiological roles are and what cellular RNAs are its genuine targets. In this paper, we analyzed the effects of the Y4RNAfr on cell viability and transcriptomes using HL60, RPMI-8226, and HEK293 cells, and Y4RNAfr-binding RNAs in A549 cells. Although the Y4RNAfr hardly affected the viability of HL60, RPMI-8226, and HEK293 cells, it significantly affected their transcriptome. The DAVID analysis for > 2-fold upregulated and downregulated genes suggested that the Y4RNAfr may affect various KEGG pathways. We obtained 108 Y4RNAfr-binding RNAs in A549 cells, searched potential secondary structures of complexes between theY4RNAfr and its binding RNAs for the pre-tRNA-like structure, and found many such structures. One of the five best fitted structures was for the MKI67 mRNA, suggesting that the Y4RNAfr can decrease the cellular MKI67 level through guiding the cleavage of the MKI67 mRNA by tRNase ZL. This may be one of the underlying mechanisms for the reported observation that the Y4RNAfr suppresses the proliferation of A549 cells.
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Affiliation(s)
- Sho Ninomiya
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Tatsuya Ishikawa
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Masayuki Takahashi
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, 956-8603, Japan
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The Y4-RNA fragment, a potential diagnostic marker, exists in saliva. Noncoding RNA Res 2017; 2:122-128. [PMID: 30159430 PMCID: PMC6096425 DOI: 10.1016/j.ncrna.2017.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 01/07/2023] Open
Abstract
The 94-nt full-length Y4-RNA is thought to have roles in the initiation of DNA replication and RNA quality control. Although its 31/32-nt fragment also exists abundantly in plasma, little is known about its physiological role. Since the 31/32-nt Y4-RNA fragment in sera is reported to be more abundant in patients with coronary artery disease than healthy persons, the fragment may have a potential for a diagnostic and/or prognostic biomarker for some diseases regardless of its functionality. As a step toward further investigation of its potential utility, we examined if the 31/32-nt Y4-RNA fragment also exists in saliva that can be obtained noninvasively, and showed that, in addition to the 31/32-nt fragment, 14- and 11-nt Y4-RNA fragments are present in all saliva RNA samples from four healthy persons. We established a PCR method to accurately quantitate the amount of the 31/32-nt Y4-RNA fragment, and estimated its amount in saliva of healthy persons to be 0.06 ± 0.04 fmol per nanogram of saliva RNA. We also tried to develop an easier quantitation method using a DNA molecular beacon.
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Haino A, Ishikawa T, Seki M, Nashimoto M. TRUE Gene Silencing: Screening of a Heptamer-type Small Guide RNA Library for Potential Cancer Therapeutic Agents. J Vis Exp 2016:53879. [PMID: 27285342 PMCID: PMC4927757 DOI: 10.3791/53879] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
TRUE gene silencing (termed after tRNase Z(L)-utilizing efficacious gene silencing) is one of the RNA-directed gene silencing technologies, which utilizes an artificial small guide RNA (sgRNA) to guide tRNA 3' processing endoribonuclease, tRNase Z(L), to recognize a target RNA. sgRNAs can be taken up by cells without any transfection reagents and can downregulate their target RNA levels and/or induce apoptosis in human cancer cells. We have screened an sgRNA library containing 156 heptamer-type sgRNAs for the effect on viability of human myeloma and leukemia cells, and found that 20 of them can efficiently induce apoptosis in at least one of the cancer cell lines. Here we present a protocol for screening of a heptamer-type sgRNA library for potential therapeutic drugs against blood cancers. The protocol includes how to construct the sgRNA library, how to assess the effect of each sgRNA on cell viability, and how to further evaluate the effective sgRNAs by flow cytometry. Around 2,000 hits would be expected to be obtained by screening the full-scale sgRNA library composed of 16,384 heptamers.
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Affiliation(s)
- Arisa Haino
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences
| | - Tatsuya Ishikawa
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences;
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Ninomiya S, Kawano M, Abe T, Ishikawa T, Takahashi M, Tamura M, Takahashi Y, Nashimoto M. Potential small guide RNAs for tRNase ZL from human plasma, peripheral blood mononuclear cells, and cultured cell lines. PLoS One 2015; 10:e0118631. [PMID: 25730316 PMCID: PMC4346264 DOI: 10.1371/journal.pone.0118631] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/09/2015] [Indexed: 11/18/2022] Open
Abstract
Several pieces of evidence suggest that small RNA degradation products together with tRNase ZL appear to form another layer of the whole gene regulatory network. The degraded RNA such as a 5'-half-tRNA and an rRNA fragment function as small guide RNA (sgRNA) to guide the enzyme to target RNA. We were curious whether there exist RNAs in plasma that can function as sgRNAs for tRNase ZL, whether these RNAs are working as signaling molecules between cells to fulfill physiological roles, and whether there are any differences in plasma sgRNA species and levels between normal and pathological conditions. Here, we analyzed small plasma RNAs from three healthy persons and three multiple myeloma patients for potential sgRNAs by deep sequencing. We also examined small RNAs from peripheral blood mononuclear cells (PBMC) of three healthy persons and three myeloma patients and from various cultured human cell lines for sgRNAs. We found that read-number distribution patterns of plasma and PBMC RNAs differ between persons in the range of 5-40 nt and that there are many RNA species that exist significantly more or less abundantly in the plasma or PBMC of the myeloma patients than those of the healthy persons. Furthermore, we found that there are many potential sgRNAs in the 5-40-nt RNAs and that, among them, a 31-nt RNA fragment derived from 94-nt Y4-RNA, which can function as a 5'-half-tRNA-type sgRNA, is overwhelmingly abundant in the plasma of 2/3 of the examinees. These observations suggest that the gene regulatory network via tRNase ZL and sgRNA may be extended intercellularly.
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Affiliation(s)
- Sho Ninomiya
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Mitsuoki Kawano
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
- Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Takashi Abe
- Department of Information Engineering, Niigata University, Niigata, Japan
| | - Tatsuya Ishikawa
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masayuki Takahashi
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masato Tamura
- Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Yoshiaki Takahashi
- Laboratory of Biochemistry, Niigata University Graduate School of Health Sciences, Niigata, Japan
| | - Masayuki Nashimoto
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
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Takahashi M, Elbarbary RA, Watanabe N, Goto A, Kamiya D, Watabe Y, Uchiyama T, Narita M, Takahashi M, Takahashi Y, Ishihara N, Miyazawa T, Yoshida T, Kawano M, Tamura M, Nashimoto M. Screening of a heptamer-type sgRNA library for potential therapeutic agents against hematological malignancies. Leuk Res 2014; 38:808-15. [PMID: 24768135 DOI: 10.1016/j.leukres.2014.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 01/11/2023]
Abstract
tRNase-Z(L)-utilizing efficacious (TRUE) gene silencing is an RNA-mediated gene expression control technology that has therapeutic potential. This technology is based on the property of tRNase Z(L) that it can cleave any target RNA at any desired site under the direction of an appropriate artificial small guide RNA (sgRNA). To search for novel potential therapeutic sgRNAs for hematological malignancies, we screened a library composed of 156 sgRNAs, and found that 20 sgRNAs can efficiently induce apoptosis in leukemia and/or myeloma cells. Furthermore, we demonstrated that 4 of the 20 sgRNAs can reduce growth rates of HL60 cells in mouse xenograft models.
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Affiliation(s)
- Masayuki Takahashi
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan
| | - Reyad A Elbarbary
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan
| | - Norihiro Watanabe
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan; Laboratory of Hematology and Oncology, Niigata University Graduate School of Health Sciences, Asahimachi-dori 746-2, Chuoku, Niigata, Niigata 951-8518, Japan
| | - Atsushi Goto
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan
| | - Daichi Kamiya
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan
| | - Yoshihiro Watabe
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan
| | - Takayoshi Uchiyama
- Laboratory of Hematology and Oncology, Niigata University Graduate School of Health Sciences, Asahimachi-dori 746-2, Chuoku, Niigata, Niigata 951-8518, Japan
| | - Miwako Narita
- Laboratory of Hematology and Oncology, Niigata University Graduate School of Health Sciences, Asahimachi-dori 746-2, Chuoku, Niigata, Niigata 951-8518, Japan
| | - Masuhiro Takahashi
- Laboratory of Hematology and Oncology, Niigata University Graduate School of Health Sciences, Asahimachi-dori 746-2, Chuoku, Niigata, Niigata 951-8518, Japan
| | - Yoshiaki Takahashi
- Laboratory of Biochemistry, Niigata University Graduate School of Health Sciences, Asahimachi-dori 746-2, Chuoku, Niigata, Niigata 951-8518, Japan
| | - Noriko Ishihara
- Department of Clinical Pathology, Saiseikai Niigata Daini Hospital, Terachi 280-7, Nishiku, Niigata, Niigata 950-1104, Japan
| | - Tatsuya Miyazawa
- Biologics Research Laboratories, Kyowa Hakko Kirin Co., Ltd., Asahimachi 3-6-6, Machida, Tokyo 194-8533, Japan
| | - Tetsuo Yoshida
- Biologics Research Laboratories, Kyowa Hakko Kirin Co., Ltd., Asahimachi 3-6-6, Machida, Tokyo 194-8533, Japan
| | - Mitsuoki Kawano
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan; Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, North 13, West 7, Sapporo, Hokkaido 060-8586, Japan
| | - Masato Tamura
- Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, North 13, West 7, Sapporo, Hokkaido 060-8586, Japan
| | - Masayuki Nashimoto
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akihaku, Niigata, Niigata 956-8603, Japan.
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Induction of apoptosis of leukemic cells by TRUE gene silencing using small guide RNAs targeting the WT1 mRNA. Leuk Res 2013; 37:580-5. [PMID: 23403166 DOI: 10.1016/j.leukres.2013.01.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 01/08/2013] [Accepted: 01/18/2013] [Indexed: 12/29/2022]
Abstract
TRUE gene silencing is a technology to eliminate specific cellular RNAs by using tRNase Z(L) and small guide RNA (sgRNA). Here we investigated how WT1-mRNA-targeting sgRNAs affect leukemic cells. We showed that sgRNA can be easily taken up by cells without any transfection reagents, and that the naked sgRNAs targeting the WT1 mRNA can reduce its mRNA levels and WT1 protein amounts in the WT1-expressing leukemic cells. Concomitantly, these sgRNAs efficiently induced apoptosis in these cells but not in WT1-nonexpressing cells. We also demonstrated that the reduction in the WT1 mRNA level is caused by its cleavage by tRNase Z(L).
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Takahashi M, Elbarbary RA, Nakashima A, Abe M, Watanabe N, Narita M, Takahashi M, Tamura M, Yoshida T, Nashimoto M. A naked RNA heptamer targeting the human Bcl-2 mRNA induces apoptosis of HL60 leukemia cells. Cancer Lett 2013; 328:362-8. [PMID: 23092557 DOI: 10.1016/j.canlet.2012.10.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 10/03/2012] [Accepted: 10/16/2012] [Indexed: 12/13/2022]
Abstract
tRNase Z(L)-utilizing efficacious gene silencing is a gene control technology, which is based on the property that tRNase Z(L) can cleave any target RNA under the direction of an appropriate small guide RNA (sgRNA). To find therapeutic sgRNAs to cure hematological malignancies, we investigated behavior of heptamer-type sgRNA. We demonstrated that a heptamer, mh1(Bcl-2), which targets the human Bcl-2 mRNA, can be taken up by cells without any transfection reagents and that it can induce apoptosis of the leukemia cells. Mouse xenograft experiments showed that a median survival of the mh1(Bcl-2)-treated mice was longer than that of the control mice.
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Affiliation(s)
- Masayuki Takahashi
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
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11
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Kato K, Senoki T, Takaku H. Inhibition of HIV-1 replication by RNA with a microRNA-like function. Int J Mol Med 2013; 31:252-8. [PMID: 23128354 DOI: 10.3892/ijmm.2012.1170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 10/11/2012] [Indexed: 11/06/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) replication is suppressed by a small guide RNA (sgRNA) that targets the packaging signal of HIV-1 RNA. We unintentionally produced a plasmid with the reverse sequence of the sgRNA and its terminator (pR-Ψ-sgRNA-ter). Both sgRNA and R-Ψ-sgRNA suppress HIV-1, but the mechanism by which R-Ψ-sgRNA suppresses HIV is not clear. To evaluate whether the suppressive effect is caused by an RNA interference or microRNA (miRNA)-like mechanism, R-Ψ-sgRNA was synthesized in vitro and treated with the Dicer enzyme, an important enzyme for RNA interference and miRNA. The RNA was cleaved into fragments of approximately 24 nucleotides (nt). We analyzed the sequence of the RNA fragments and predicted the RNA secondary structure of R-Ψ-sgRNA to determine the region recognized by the Dicer enzyme. The lengths of the R-Ψ-sgRNA fragments ranged from 48 to 140 nt, and were predicted to form double strands, including mismatches, in this region. An HIV-1 p24 assay indicated that the R-Ψ-sgRNA fragments suppressed HIV-1 replication. These findings suggest that R-Ψ-sgRNA acts as a miRNA to inhibit HIV-1.
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Affiliation(s)
- Keijiro Kato
- Department of Life and Environmental Science, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan
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Garcia-Silva MR, Cabrera-Cabrera F, Güida MC, Cayota A. Novel aspects of tRNA-derived small RNAs with potential impact in infectious diseases. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.45a002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Takahashi M, Elbarbary RA, Abe M, Sato M, Yoshida T, Yamada Y, Tamura M, Nashimoto M. Elimination of specific miRNAs by naked 14-nt sgRNAs. PLoS One 2012; 7:e38496. [PMID: 22675569 PMCID: PMC3366928 DOI: 10.1371/journal.pone.0038496] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 05/09/2012] [Indexed: 01/02/2023] Open
Abstract
tRNase Z(L)-utilizing efficacious gene silencing (TRUE gene silencing) is a newly developed technology to suppress mammalian gene expression. TRUE gene silencing works on the basis of a unique enzymatic property of mammalian tRNase Z(L), which is that it can recognize a pre-tRNA-like or micro-pre-tRNA-like complex formed between target RNA and artificial small guide RNA (sgRNA) and can cleave any target RNA at any desired site. There are four types of sgRNA, 5'-half-tRNA, RNA heptamer, hook RNA, and ~14-nt linear RNA. Here we show that a 14-nt linear-type sgRNA against human miR-16 can guide tRNase Z(L) cleavage of miR-16 in vitro and can downregulate the miR-16 level in HEK293 cells. We also demonstrate that the 14-nt sgRNA can be efficiently taken up without any transfection reagents by living cells and can exist stably in there for at least 24 hours. The naked 14-nt sgRNA significantly reduced the miR-16 level in HEK293 and HL60 cells. Three other naked 14-nt sgRNAs against miR-142-3p, miR-206, and miR-19a/b are also shown to downregulate the respective miRNA levels in various mammalian cell lines. Our observations suggest that in general we can eliminate a specific cellular miRNA at least by ~50% by using a naked 14-nt sgRNA on the basis of TRUE gene silencing.
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Affiliation(s)
- Masayuki Takahashi
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Reyad A. Elbarbary
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Mayumi Abe
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Mari Sato
- Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Tetsuo Yoshida
- Biologics Research Laboratories, Kyowa Hakko Kirin Company Limited, Machida, Japan
| | - Yoji Yamada
- Biologics Research Laboratories, Kyowa Hakko Kirin Company Limited, Machida, Japan
| | - Masato Tamura
- Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Masayuki Nashimoto
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
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14
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Sano T, Takahashi M, Nozaki T, Takahashi Y, Tamura M, Nashimoto M. Expanding the utility of heptamer-type sgRNA for TRUE gene silencing. Biochem Biophys Res Commun 2011; 416:427-32. [PMID: 22142845 DOI: 10.1016/j.bbrc.2011.11.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 11/17/2011] [Indexed: 12/22/2022]
Abstract
tRNase Z(L)-utilizing efficacious gene silencing (TRUE gene silencing) is a novel technology for suppressing gene expression. TRUE gene silencing is based on a unique enzymatic property of mammalian tRNase Z(L), which is that it can cleave any target RNA at any desired site by recognizing a pre-tRNA-like or micro-pre-tRNA-like complex formed between the target RNA and artificial small guide RNA (sgRNA). sgRNA is divided into four groups, 5'-half-tRNA, RNA heptamer, hook RNA, and ∼14-nt linear RNA. One of the final destinations of TRUE gene silencing is to generate cancer therapeutic sgRNAs, and from a pharmacological point of view, heptamer-type sgRNA appears to be the most appropriate for this purpose. In this paper, we present two strategies to expand the utility of heptamer-type sgRNA: one is about locked nucleic acid (LNA) modifications of heptamers and the other is about usage of double heptamers. We showed that RNA heptamers with LNA modifications can work as sgRNA in vitro and in vivo. We also demonstrated that two consecutively aligned heptamers can guide target RNA cleavage by human tRNase Z(L) as efficiently as a corresponding 14-nt sgRNA in vitro and that a double heptamer can work much better than a 14-nt sgRNA in vivo.
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Affiliation(s)
- Takako Sano
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
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15
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Sugiyama R, Hayafune M, Habu Y, Yamamoto N, Takaku H. HIV-1 RT-dependent DNAzyme expression inhibits HIV-1 replication without the emergence of escape viruses. Nucleic Acids Res 2011; 39:589-98. [PMID: 20833635 PMCID: PMC3025543 DOI: 10.1093/nar/gkq794] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 08/18/2010] [Accepted: 08/23/2010] [Indexed: 12/12/2022] Open
Abstract
DNAzymes are easier to prepare and less sensitive to chemical and enzymatic degradation than ribozymes; however, a DNA enzyme expression system has not yet been developed. In this study, we exploited the mechanism of HIV-1 reverse transcription (RT) in a DNA enzyme expression system. We constructed HIV-1 RT-dependent lentiviral DNAzyme expression vectors including the HIV-1 primer binding site, the DNA enzyme, and either a native tRNA (Lys-3), tR(M)DtR(L), or one of two truncated tRNAs (Lys-3), tR(M)DΔARMtR(L) or tR(M)D3'-endtR(L). Lentiviral vector-mediated DNAzyme expression showed high levels of inhibition of HIV-1 replication in SupT1 cells. We also demonstrated the usefulness of this approach in a long-term assay, in which we found that the DNAzymes prevented escape from inhibition of HIV. These results suggest that HIV-1 RT-dependent lentiviral vector-derived DNAzymes prevent the emergence of escape mutations.
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Affiliation(s)
- Ryuichi Sugiyama
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Masaaki Hayafune
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yuichiro Habu
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Norio Yamamoto
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hiroshi Takaku
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
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16
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Elbarbary RA, Takaku H, Uchiumi N, Tamiya H, Abe M, Nishida H, Nashimoto M. Human cytosolic tRNase ZL can downregulate gene expression through miRNA. FEBS Lett 2009; 583:3241-6. [PMID: 19751732 DOI: 10.1016/j.febslet.2009.09.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 08/28/2009] [Accepted: 09/07/2009] [Indexed: 12/19/2022]
Abstract
A long form of tRNase Z (tRNase ZL) can cleave any target RNA at any desired site under the direction of artificial small guide RNA including approximately 25-nucleotide hook-shaped RNA. Here we show that human miR-103 can form a hook structure to guide target RNA cleavage by human cytosolic tRNase ZL in vitro. In vivo analyses using luciferase mRNAs modified to contain miR-103 target sequences in their 3' untranslated regions indicated that miR-103 downregulates gene expression through directing mRNA cleavage by tRNase ZL. The present data suggest the possibility that human cytosolic tRNase ZL modulates gene expression through a subset of microRNAs in the cells.
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Affiliation(s)
- Reyad A Elbarbary
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata 956-8603, Japan
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17
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Elbarbary RA, Takaku H, Uchiumi N, Tamiya H, Abe M, Takahashi M, Nishida H, Nashimoto M. Modulation of gene expression by human cytosolic tRNase Z(L) through 5'-half-tRNA. PLoS One 2009; 4:e5908. [PMID: 19526060 PMCID: PMC2691602 DOI: 10.1371/journal.pone.0005908] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 05/19/2009] [Indexed: 01/10/2023] Open
Abstract
A long form (tRNase Z(L)) of tRNA 3' processing endoribonuclease (tRNase Z, or 3' tRNase) can cleave any target RNA at any desired site under the direction of artificial small guide RNA (sgRNA) that mimics a 5'-half portion of tRNA. Based on this enzymatic property, a gene silencing technology has been developed, in which a specific mRNA level can be downregulated by introducing into cells a synthetic 5'-half-tRNA that is designed to form a pre-tRNA-like complex with a part of the mRNA. Recently 5'-half-tRNA fragments have been reported to exist stably in various types of cells, although little is know about their physiological roles. We were curious to know if endogenous 5'-half-tRNA works as sgRNA for tRNase Z(L) in the cells. Here we show that human cytosolic tRNase Z(L) modulates gene expression through 5'-half-tRNA. We found that 5'-half-tRNA(Glu), which co-immunoprecipitates with tRNase Z(L), exists predominantly in the cytoplasm, functions as sgRNA in vitro, and downregulates the level of a luciferase mRNA containing its target sequence in human kidney 293 cells. We also demonstrated that the PPM1F mRNA is one of the genuine targets of tRNase Z(L) guided by 5'-half-tRNA(Glu). Furthermore, the DNA microarray data suggested that tRNase Z(L) is likely to be involved in the p53 signaling pathway and apoptosis.
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Affiliation(s)
- Reyad A. Elbarbary
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Hiroaki Takaku
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Naoto Uchiumi
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Hiroko Tamiya
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Mayumi Abe
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masayuki Takahashi
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Hiroshi Nishida
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masayuki Nashimoto
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
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18
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Elbarbary RA, Takaku H, Tamura M, Nashimoto M. Inhibition of vascular endothelial growth factor expression by TRUE gene silencing. Biochem Biophys Res Commun 2009; 379:924-7. [PMID: 19135977 DOI: 10.1016/j.bbrc.2008.12.173] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Accepted: 12/24/2008] [Indexed: 10/21/2022]
Abstract
Pathogenic angiogenesis in various diseases including cancer, autoimmune diseases, and age-related macular degeneration is thought to be regressed with anti-angiogenic drugs. TRUE gene silencing is a new technology to eliminate a specific mRNA using synthetic sgRNA and cellular tRNase Z(L). To discover anti-angiogenic sgRNAs, we applied TRUE silencing to the VEGF gene. We examined eight sgRNAs for efficacy in targeting exogenous human VEGF mRNA. Many of them worked efficiently in 293 and HeLa cells. Two of them downregulated the endogenous VEGF gene expression in HeLa cells very efficiently, and the efficacy of these two sgRNAs surpassed that of siRNA extremely.
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Affiliation(s)
- Reyad A Elbarbary
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Niigata, Niigata 956-8603, Japan
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19
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Fu H, Feng J, Liu Q, Sun F, Tie Y, Zhu J, Xing R, Sun Z, Zheng X. Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett 2008; 583:437-42. [DOI: 10.1016/j.febslet.2008.12.043] [Citation(s) in RCA: 322] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 12/05/2008] [Accepted: 12/17/2008] [Indexed: 10/21/2022]
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Abstract
This chapter describes the major gene therapeutic approaches for viral infections. The vast majority of published approaches target severe chronic viral infections such as hepatitis B or C and HIV infection. Two basic gene therapy strategies are introduced here. The first involves the expression of a protein or an RNA that inhibits viral replication by targeting crucial steps of the viral life cycle or by interfering with a cellular factor required for virus replication. The major limitation of this approach is that primary levels of gene modification have generally not been sufficient to reduce the availability of target cells permissive for virus replication to a level that significantly decreases overall viral load. Thus, investigators have banked on the expectation that gene-protected cells have a sufficient selective advantage to accumulate and gain prevalence over time, a prediction that so far could not be confirmed in clinical trials. In vivo levels of gene modification can be improved, however, by introducing an additional selectable marker. In addition, a secreted antiviral gene product that exerts a bystander effect could significantly reduce overall virus replication despite relatively low levels of gene modification. In addition to these direct antiviral approaches, several strategies have been developed that employ or aim to enhance host immune responses. The innate immune response has been enhanced, for example, by the in vivo expression of interferons. Alternatively, T cells can be grafted with recombinant receptors to boost adaptive virus-specific immunity. These approaches are especially promising for chronic virus infection, where natural immune responses are evidently not sufficient to effectively control virus replication.
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21
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Yang Y, Wu C, Wu J, Nerurkar VR, Yanagihara R, Lu Y. Inhibition of West Nile Virus replication by retrovirus-delivered small interfering RNA in human neuroblastoma cells. J Med Virol 2008; 80:930-6. [PMID: 18360908 DOI: 10.1002/jmv.21164] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
West Nile virus (WNV) has been responsible for the largest outbreaks of arboviral encephalitis in U.S. history. No specific drug is currently available for the effective treatment of WNV infection. To exploit RNA interference as a potential therapeutic approach, a Moloney murine leukemia virus-based retrovirus vector was used to effectively deliver WNV-specific small interfering RNA (siRNA) into human neuroblastoma HTB-11 cells. Viral plaque assays demonstrated that transduced cells were significantly refractory to WNV replication, as compared to untransduced control cells (P < 0.05), which correlated with the reduced expression of target viral genes and respective viral proteins. Therefore, retrovirus-mediated delivery of siRNA for gene silencing can be used to study the specific functions of viral genes associated with replication and may have potential therapeutic applications.
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Affiliation(s)
- Yongbo Yang
- Department of Public Health Sciences, John A. Burns School of Medicine, University of Hawai'i, Honolulu, Hawaii, USA
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22
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Scherer L, Weinberg MS, Rossi JJ. RNA Based Therapies for Treatment of HIV Infection. THERAPEUTIC OLIGONUCLEOTIDES 2008. [DOI: 10.1039/9781847558275-00316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lisa Scherer
- Division of Molecular Biology City of Hope Beckman Research Institute Duarte CA
| | - Marc S. Weinberg
- Department of Molecular Medicine and Hematology University of the Witwatersrand Medical School Wits South Africa
| | - John J. Rossi
- Division of Molecular Biology City of Hope Beckman Research Institute Duarte CA
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23
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Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y. Hidden layers of human small RNAs. BMC Genomics 2008. [PMID: 18402656 DOI: 10.1186/1471-12164-9-157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the possible existence of yet undiscovered types of small RNAs in higher organisms, many studies to profile small RNA have focused on miRNA and/or siRNA rather than on the exploration of additional classes of RNAs. RESULTS Here, we explored human small RNAs by unbiased sequencing of RNAs with sizes of 19-40 nt. We provide substantial evidences for the existence of independent classes of small RNAs. Our data shows that well-characterized non-coding RNA, such as tRNA, snoRNA, and snRNA are cleaved at sites specific to the class of ncRNA. In particular, tRNA cleavage is regulated depending on tRNA type and tissue expression. We also found small RNAs mapped to genomic regions that are transcribed in both directions by bidirectional promoters, indicating that the small RNAs are a product of dsRNA formation and their subsequent cleavage. Their partial similarity with ribosomal RNAs (rRNAs) suggests unrevealed functions of ribosomal DNA or interstitial rRNA. Further examination revealed six novel miRNAs. CONCLUSION Our results underscore the complexity of the small RNA world and the biogenesis of small RNAs.
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Affiliation(s)
- Hideya Kawaji
- Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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24
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Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y. Hidden layers of human small RNAs. BMC Genomics 2008; 9:157. [PMID: 18402656 PMCID: PMC2359750 DOI: 10.1186/1471-2164-9-157] [Citation(s) in RCA: 232] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 04/10/2008] [Indexed: 01/09/2023] Open
Abstract
Background Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the possible existence of yet undiscovered types of small RNAs in higher organisms, many studies to profile small RNA have focused on miRNA and/or siRNA rather than on the exploration of additional classes of RNAs. Results Here, we explored human small RNAs by unbiased sequencing of RNAs with sizes of 19–40 nt. We provide substantial evidences for the existence of independent classes of small RNAs. Our data shows that well-characterized non-coding RNA, such as tRNA, snoRNA, and snRNA are cleaved at sites specific to the class of ncRNA. In particular, tRNA cleavage is regulated depending on tRNA type and tissue expression. We also found small RNAs mapped to genomic regions that are transcribed in both directions by bidirectional promoters, indicating that the small RNAs are a product of dsRNA formation and their subsequent cleavage. Their partial similarity with ribosomal RNAs (rRNAs) suggests unrevealed functions of ribosomal DNA or interstitial rRNA. Further examination revealed six novel miRNAs. Conclusion Our results underscore the complexity of the small RNA world and the biogenesis of small RNAs.
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Affiliation(s)
- Hideya Kawaji
- Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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25
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Scherer LJ, Frank R, Rossi JJ. Optimization and characterization of tRNA-shRNA expression constructs. Nucleic Acids Res 2007; 35:2620-8. [PMID: 17426139 PMCID: PMC1885648 DOI: 10.1093/nar/gkm103] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 01/12/2007] [Accepted: 02/06/2007] [Indexed: 12/05/2022] Open
Abstract
Expression of short hairpin RNAs via the use of PolIII-based transcription systems has proven to be an effective mechanism for triggering RNAi in mammalian cells. The most popular promoters for this purpose are the U6 and H1 promoters since they are easily manipulated for expression of shRNAs with defined start and stop signals. Multiplexing (the use of siRNAs against multiple targets) is one strategy that is being developed by a number of laboratories for the treatment of HIV infection since it increases the likelihood of suppressing the emergence of resistant virus in applications. In this context, the development of alternative small PolIII promoters other than U6 and H1 would be useful. We describe tRNA(Lys3)-shRNA chimeric expression cassettes which produce siRNAs with comparable efficacy and strand selectivity to U6-expressed shRNAs, and show that their activity is consistent with processing by endogenous 3' tRNAse. In addition, our observations suggest general guidelines for expressing effective tRNA-shRNAs with the potential for graded response, to minimize toxicities associated with competition for components of the endogenous RNAi pathway in cells.
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MESH Headings
- Base Sequence
- Cell Line
- Gene Products, rev/genetics
- Gene Products, tat/genetics
- Genetic Vectors
- HIV-1/genetics
- Humans
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA Interference
- RNA, Small Interfering/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Untranslated/biosynthesis
- RNA, Untranslated/chemistry
- RNA, Untranslated/metabolism
- rev Gene Products, Human Immunodeficiency Virus
- tat Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Lisa J. Scherer
- Department of Molecular Biology and Division of Hematology & Hematopoietic Cell Transplantation and Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1450 E. Duarte Road, Duarte, California 91010, USA
| | - Richard Frank
- Department of Molecular Biology and Division of Hematology & Hematopoietic Cell Transplantation and Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1450 E. Duarte Road, Duarte, California 91010, USA
| | - John J. Rossi
- Department of Molecular Biology and Division of Hematology & Hematopoietic Cell Transplantation and Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1450 E. Duarte Road, Duarte, California 91010, USA
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26
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Nakashima A, Nashimoto M, Tamura M. TRUE Gene Silencing : Unique Gene Silencing by the tRNA Maturase tRNase ZL under the Direction of Small-guide RNA. J Oral Biosci 2007. [DOI: 10.1016/s1349-0079(07)80016-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Nakashima A, Takaku H, Shibata HS, Negishi Y, Takagi M, Tamura M, Nashimoto M. Gene silencing by the tRNA maturase tRNase ZL under the direction of small-guide RNA. Gene Ther 2007; 14:78-85. [PMID: 16885998 DOI: 10.1038/sj.gt.3302841] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Revised: 05/30/2006] [Accepted: 06/28/2006] [Indexed: 11/08/2022]
Abstract
We have been developing a unique system for the downregulation of a gene expression through cutting a specific mRNA by the long form of tRNA 3'-processing endoribonuclease (tRNase Z(L)) under the direction of small-guide RNA (sgRNA). However, the efficacy of this system and the involvement of tRNase Z(L) in the living cells were not clear. Here we show, by targeting the exogenous luciferase gene, that the efficacy of the sgRNA/tRNase Z(L) method can become comparable to that of the RNA interference technology and that the gene silencing is owing to tRNase Z(L) directed by sgRNA not owing to a simple antisense effect. We also show that tRNase Z(L) together with sgRNA can downregulate expression of the endogenous human genes Bcl-2 and glycogen synthase kinase-3beta by degrading their mRNAs in cell culture. Furthermore, we demonstrate that a gene expression in the livers of postnatal mice can be inhibited by an only seven-nucleotide sgRNA. These data suggest that sgRNA might be utilized as therapeutic agents to treat diseases such as cancers and AIDS.
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Affiliation(s)
- A Nakashima
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Niigata, Japan
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28
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Effects of recombinant retroviral vector mediated human insulin like growth factor-1 gene transfection on skeletal muscle growth in rat. Chin Med J (Engl) 2006. [DOI: 10.1097/00029330-200612010-00009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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29
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Ikeda M, Habu Y, Miyano-Kurosaki N, Takaku H. Suppression of HIV-1 replication by a combination of endonucleolytic ribozymes (RNase P and tRNnase ZL). NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:427-37. [PMID: 16838836 DOI: 10.1080/01457630600684120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We examined the combinatorial action of RNase P and tRNase ZL-mediated specific inhibition of HIV-1 in cultured cells. We designed two short extra guide sequences (sEGS) that specifically recognize the tat and vifregions of HIV-1 mRNA and mediate the subsequent cleavage of hybridized mRNA by the RNase P and tRNase ZL components. We constructed an RNase P and tRNase ZL-associated vif and tat sEGS expression vector; which used the RNA-polymerase III dependent U6 promoter, as an expression cassette for EGS. Together, the RNase P and tRNase ZL-associated sEGS molecules allow more efficient suppression of HIV-1 mRNA production when separately applied. The possibilities offered by the vector to encode sEGS will provide a powerful tool for gene therapy.
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Affiliation(s)
- Masahiro Ikeda
- Department of Life and Environmental Science, Faculty of Engineering, Chiba Institute of Technology, Narashino, Chiba, Japan
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30
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Kaneko H, Suzuki H, Abe T, Miyano-Kurosaki N, Takaku H. Inhibition of HIV-1 replication by vesicular stomatitis virus envelope glycoprotein pseudotyped baculovirus vector-transduced ribozyme in mammalian cells. Biochem Biophys Res Commun 2006; 349:1220-7. [PMID: 16979590 DOI: 10.1016/j.bbrc.2006.08.184] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Accepted: 08/25/2006] [Indexed: 11/18/2022]
Abstract
The baculovirus has recently emerged as a promising vector for in vivo gene therapy. To investigate its potential as a delivery vector for an anti-virus ribozyme targeting HIV-1, we constructed recombinant baculovirus vectors bearing a ribozyme-synthesizing cassette driven by the tRNA(i)(Met) promoter with enhanced transduction efficiency by displaying vesicular stomatitis virus glycoprotein (VSV-G) on the viral envelope. Transduction of HeLa CD4(+) cells with a recombinant baculovirus delivering the HIV-1 U5 gene-specific ribozyme dramatically suppressed HIV-1 expression in this cell line. The VSV-G pseudotyped baculovirus vector-transduced ribozyme potently inhibited HIV-1 replication compared to a recombinant baculovirus vector-transduced ribozyme lacking VSV-G. The use of a baculovirus vector might be beneficial for application in gene therapy.
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Affiliation(s)
- Hiroyasu Kaneko
- Department of Life and Environmental Science, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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31
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von Laer D, Hasselmann S, Hasselmann K. Gene therapy for HIV infection: what does it need to make it work? J Gene Med 2006; 8:658-67. [PMID: 16598816 DOI: 10.1002/jgm.908] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The efficacy of antiviral drug therapy for HIV infection is limited by toxicity and viral resistance. Thus, alternative therapies need to be explored. Several gene therapeutic strategies for HIV infection have been developed, but in clinical testing therapeutically effective levels of the transgene product were not achieved. This review focuses on the determinants of therapeutic efficacy and discusses the potential and also the limits of current gene therapy approaches for HIV infection.
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Affiliation(s)
- Dorothee von Laer
- Georg-Speyer-Haus, Paul-Ehrlich-Strasse 42, Frankfurt a.M., Germany.
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Nagawa T, Habu Y, Matsumoto N, Miyano-Kurosaki N, Takaku H. Long-term transgene expression and inhibition of HIV-1 replication by a Cre/loxP-EBNA-1/oriP HIV-1-dependent ribozyme vector: Applications for HIV-1 gene therapy. JOURNAL OF RNAI AND GENE SILENCING : AN INTERNATIONAL JOURNAL OF RNA AND GENE TARGETING RESEARCH 2006; 2:146-53. [PMID: 19771216 PMCID: PMC2737208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 12/10/2005] [Accepted: 12/15/2005] [Indexed: 11/08/2022]
Abstract
The cleavage of target mRNA by ribozymes is being exploited as a means of gene silencing in nucleic-acid-based therapies. We previously established an HIV-1-dependent ribozyme-expression vector system, based on Cre-loxP technology with an LTR-gag-p17 promoter as a molecular switch for use in acute HIV-1 infection. The simultaneous expression of the Cre protein and loxP homologous recombination induced a high level of HIV-1-replication inhibition, but ribozyme expression was transient. In the current study, we overcame this limitation by inserting EBNA-1 and oriP genes from the Epstein-Barr virus (EBV) into the vector. When this plasmid was introduced into HeLa CD4(+) cells, we observed long-term expression of both the EGFP reporter gene and the ribozyme. Moreover, HIV-1 replication was inhibited in the long-term in transfected cells. These data suggest that the HIV-1-dependent ribozyme-expression vector containing EBNA-1/oriP sequences would be a useful tool in HIV-1 gene therapy applications.
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Affiliation(s)
| | - Yuichiro Habu
- High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan,Japanese Foundation for AIDS Prevention, Toranomon, Minato-ku, Tokyo, 105-0001, Japan
| | | | - Naoko Miyano-Kurosaki
- Department of Life and Environmental Sciences,High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Hiroshi Takaku
- Department of Life and Environmental Sciences,High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan,Correspondence to: Hiroshi Takaku, , Tel: +81 47 478 0407, Fax: +81 47 471 8764
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