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PNPASE Regulates RNA Import into Mitochondria
Open accessAbstract
RNA import into mammalian mitochondria is considered essential for replication, transcription, and translation of the mitochondrial genome but the pathway(s) and factors that control this import are poorly understood. Previously, we localized polynucleotide phosphorylase (PNPASE), a 3' --> 5' exoribonuclease and poly-A polymerase, in the mitochondrial intermembrane space, a location lacking resident RNAs. Here, we show a new role for PNPASE in regulating the import of nuclear-encoded RNAs into the mitochondrial matrix. PNPASE reduction impaired mitochondrial RNA processing and polycistronic transcripts accumulated. Augmented import of RNase P, 5S rRNA, and MRP RNAs depended on PNPASE expression and PNPASE-imported RNA interactions were identified. PNPASE RNA processing and import activities were separable and a mitochondrial RNA targeting signal was isolated that enabled RNA import in a PNPASE-dependent manner. Combined, these data strongly support an unanticipated role for PNPASE in mediating the translocation of RNAs into mitochondria.
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“PNPASE orchestrates the import of specific nucleus-encoded RNAs into the mitochondria through its recognition of distinct RNA stem-loop structures”
From The mitochondrial long non-coding RNA lncMtloop regulates mitochondrial transcription and suppresses Alzheimer’s disease (2024) · cites this paper as Wang et al, 2010
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“PNPASE emerged as a key player in the RNA import machinery of mammalian mitochondria (Wang et al, 2010; Wang et al, 2012a).”
From The mitochondrial long non-coding RNA lncMtloop regulates mitochondrial transcription and suppresses Alzheimer’s disease (2024) · cites this paper as Wang et al, 2010
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“PNPT1, which is implicated in both RNA degradation (Borowski et al., 2013) and 5S rRNA, RNase P RNA and MRP RNA import (Wang et al., 2010a), has also been recently associated with hearing loss and respiratory chain deficiency (Vedrenne et al., 2012; von Ameln et al., 2012).”
BackgroundResultvon Ameln, S., Wang, G., Boulouiz, R., Rutherford, M., Smith, G. M., Li, Y., Pogoda, H.-M., Nürnberg, G., Stiller, B., Volk, A., et al. (2012) · American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.09.002 · Cited by 99
Self-citationMitochondrial poly(A) polymerase and polyadenylation
Chang, J., & Tong, L. (2011) · Biochimica et Biophysica Acta · doi:10.1016/j.bbagrm.2011.10.012 · Cited by 98
“PNPase has an important role in maintaining mitochondrial homeostasis, and is also required for importing nuclear-encoded RNA into the mitochondria [16].”
Adapting CRISPR/Cas9 System for Targeting Mitochondrial Genome
Hussain, S.-R. A., YALVAÇ, M. E., Khoo, B. S., Eckardt, S., & McLaughlin, K. J. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.627050 · Cited by 105
“Furthermore, this delivery system has been previously reported to mediate the targeted transfer of recombinant RNAs into the mitochondria (Wang et al., 2010; Comte et al., 2013).”
BackgroundTelomerase and telomeres in aging theory and chronographic aging theory (Review)
Razgonova, M., Zakharenko, A., Golokhvast, K., Thanasoula, M., Sarandi, E., Nikolouzakis, K., Fragkiadaki, P., Tsoukalas, D., Spandidos, D., & Tsatsakis, A. (2020) · Molecular Medicine Reports · doi:10.3892/mmr.2020.11274 · Cited by 89
“Wang et al (60) (2010) investigated the import functions of some lncrnas in mitochondria, showing that one of the rnas, the rna component of the telomerase (Terc), is processed in mitochondria and then exported out of mitochondria.”
Interplay of mitochondrial metabolism and microRNAs
Geiger, J., & Dalgaard, L. T. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2342-7 · Cited by 101
Mitochondria, Telomeres and Telomerase Subunits
Zheng, Q., Huang, J., & Wang, G. (2019) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00274 · Cited by 118
Self-citationBiochemical functional predictions for protein structures of unknown or uncertain function
Mills, C. L., Beuning, P., & Ondrechen, M. (2015) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2015.02.003 · Cited by 91
“These functions include hydrolyzing single-stranded RNA [147], facilitating the import of RNAs into the mitochondrial matrix [148], and responding to oxidative stress [149].”
BackgroundNuclear localization of the mitochondrial ncRNAs in normal and cancer cells
Landerer, E., Villegas, J., Burzio, V. A., Oliveira, L., Villota, C., López, C., Restovic, F., Martínez, R., Castillo, O., & Burzio, L. (2011) · Cellular Oncology · doi:10.1007/s13402-011-0018-8 · Cited by 91
Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria
Pietras, Z., Wojcik, M. A., Borowski, L. S., Szewczyk, M., Kuliński, T. M., Cysewski, D., Stepien, P., Dziembowski, A., & Szczęsny, R. (2018) · Nature Communications · doi:10.1038/s41467-018-05007-9 · Cited by 90
MicroRNA-214 promotes chronic kidney disease by disrupting mitochondrial oxidative phosphorylation.
Bai, M., Chen, H., Ding, D., Song, R., Lin, J., Zhang, Y., Guo, Y., Chen, S., Ding, G., Zhang, Y., et al. (2019) · Kidney International · doi:10.1016/j.kint.2018.12.028 · Cited by 87
Self-citationPNPT1 Release from Mitochondria during Apoptosis Triggers Decay of Poly(A) RNAs.
Liu, X., Fu, R., Pan, Y.-D., Meza-Sosa, K., Zhang, Z.-B., & Lieberman, J. (2018) · Cell · doi:10.1016/j.cell.2018.04.017 · Cited by 86
“In mammalian cells, PNPT1 is located in the IMS, where it is responsible for importing some chromosomally encoded RNAs and possibly post-transcriptionally processing them (Wang et al., 2010).”
BackgroundInfluentialKaricheva, O., Kolesnikova, O., Schirtz, T., Vysokikh, M., Mager-Heckel, A., Lombès, A., Boucheham, A., Krasheninnikov, I., Martin, R., Entelis, N., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr546 · Cited by 86
PNPASE and RNA trafficking into mitochondria
Wang, G., Shimada, E., Koehler, C. M., & Teitell, M. A. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2011.10.001 · Cited by 84
“Since PNPT1 knockout is embryonic lethal and hepatocytes or mouse embryonic fibroblasts (MEFs) devoid of PNPASE expression cannot be propagated [11], it might be that all primary mammalian cell types require some level of PNPASE expression.”
BackgroundInfluentialSelf-citationPowell, C. A., Nicholls, T. J. J., & Minczuk, M. A. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00079 · Cited by 71
“…the mitochondrial matrix, namely RNase P RNA (the RNA component of the nuclear RNase P ribozyme, suggested to constitute an additional mitochondrial RNase P activity), MRP RNA (hypothesized to be involved in primer formation for mtDNA replication) and 5S cytosolic ribosomal RNA (Wang et al., 2010).”
BackgroundSilva, S. D. R., Camino, L. P., & Aguilera, A. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1807258115 · Cited by 88
“In particular, SUV3 and PNPT1 homozygous KO mice are embryonic lethal (39, 40), and SUV3 heterozygous mice show increased tumor development and premature aging phenotypes (40), serving the idea that it might act as a tumor suppressor gene.”
BackgroundExploring the mitochondrial microRNA import pathway through Polynucleotide Phosphorylase (PNPase)
Shepherd, D. L., Hathaway, Q. A., Pinti, M. V., Nichols, C. E., Durr, A. J., Sreekumar, S., Hughes, K. M., Stine, S. M., Martínez, I., & Hollander, J. M. (2017) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2017.06.012 · Cited by 92
“PNPase has been established to play an important role in the import of nuclear RNA (75, 78, 92); however, evaluating its role in miRNA transport could provide the first mechanistic view of miRNA import into the mitochondria.”
BackgroundGórna, M. W., Carpousis, A. J., & Luisi, B. F. (2011) · Quarterly Reviews of Biophysics · doi:10.1017/s003358351100014x · Cited by 86
Pnpt1 mediates NLRP3 inflammasome activation by MAVS and metabolic reprogramming in macrophages
Hsu, C. G., Li, W., Sowden, M. P., Chávez, C. L., & Berk, B. C. (2023) · Cellular and Molecular Immunology · doi:10.1038/s41423-022-00962-2 · Cited by 84
“Pnpt1 deletion increases inflammasome activation independent of mitochondrial ROS Pnpt1 is located in the mitochondrial intermembrane space and regulates the expression of electron transport chain components [6], and Pnpt1 mutations impair mitochondrial function [8, 9].”
BackgroundImport of Non-Coding RNAs into Human Mitochondria: A Critical Review and Emerging Approaches
Jeandard, D., Smirnova, A., Tarassov, I., Barrey, É., Smirnov, A., & Entelis, N. (2019) · Cells · doi:10.3390/cells8030286 · Cited by 90
“In this study, the import of hTERC was initially suspected based on the presence of a region similar to a short stem-loop that, in H1 RNA and RMRP, facilitates the mitochondrial localization of RNAs (see Figure 3c below) [19].”
BackgroundInfluentialMitochondrial Trafficking and Processing of Telomerase RNA TERC
Cheng, Y., Liu, P., Zheng, Q., Gao, G., Yuan, J., Wang, P., Huang, J., Xie, L., Lu, X., Tong, T., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.08.003 · Cited by 87
Self-citationLin, C.-L., Wang, Y.-T., Yang, W.-Z., Hsiao, Y., & Yuan, H. S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1281 · Cited by 74
“It is intriguing why some RNAs, such as RNase P, 5S rRNA and MRP RNA, are bound and translocated by hPNPase, whereas some other RNAs, such as c-myc mRNA, are digested by hPNPase (15,16,18,19).”
BackgroundA microRNA’s journey to the center of the mitochondria
Macgregor-Das, A. M., & Das, S. (2018) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00714.2017 · Cited by 76
Mitochondrial MicroRNAs in Aging and Neurodegenerative Diseases
John, A. A., Kubosumi, A., & Reddy, P. H. (2020) · Cells · doi:10.3390/cells9061345 · Cited by 84
“The PNPase enzyme, a 3′ to 5′ exoribonuclease and poly‐A polymerase found in the mitochondrial intermembrane space, regulates the entry of miRNA into the mitochondria to maintain homeostasis [14].”
BackgroundMitochondrial Epigenetics: Non-Coding RNAs as a Novel Layer of Complexity
Cavalcante, G. C., de Magalhães, L. L., Ribeiro‐dos‐Santos, Â., & Vidal, A. F. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21051838 · Cited by 77
“1 lncRNA NA Nuclear Anterograde RNA transport NA Yeast and mammalian [64]”
BackgroundComte, C., Tonin, Y., Heckel, A., Boucheham, A., Smirnov, A., Auré, K., Lombès, A., Martin, R. P., Entelis, N., & Tarassov, I. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks965 · Cited by 83
Lightowlers, R. N., Rozanska, A., & Chrzanowska-Lightowlers, Z. M. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.05.054 · Cited by 70
“Interested readers are recommended to consult this work [60].”
BackgroundSelf-citationNon-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization
Zhu, X., Xie, X., Das, H., Tan, B. G., Shi, Y., Al-Behadili, A., Peter, B., Motori, E., Valenzuela, S., Posse, V., et al. (2022) · Cell · doi:10.1016/j.cell.2022.05.006 · Cited by 69
“The more pronounced effect of SUV3 on 7S RNA most likely reflects the multiple and somewhat complex roles that SUV3 and PNPase play in vivo (Borowski et al., 2013; Wang et al., 2010).”
ncRNAs: New Players in Mitochondrial Health and Disease?
Gušić, M., & Prokisch, H. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00095 · Cited by 75
REXO2 Is an Oligoribonuclease Active in Human Mitochondria
Bruni, F., Gramegna, P., Oliveira, J. M. A., Lightowlers, R. N., & Chrzanowska‐Lightowlers, Z. M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064670 · Cited by 64
“The latter has been localized to the mitochondrial matrix [44] and the IMS [45] mediating translocation of several RNAs into mitochondria [46].”
BackgroundSelf-citationHardwick, S., Gubbey, T., Hug, I., Jenal, U., & Luisi, B. (2012) · Open Biology · doi:10.1098/rsob.120028 · Cited by 68
“Human PNPase contributes to global changes in gene expression associated with terminal differentiation [14] and to the transport of RNA into the mitochondrion [15].”
BackgroundMitochondrial Gene Expression and Beyond—Novel Aspects of Cellular Physiology
Kotrys, A. V., & Szczęsny, R. J. (2019) · Cells · doi:10.3390/cells9010017 · Cited by 84
“Indeed, a pool of PNPase is found in the mitochondrial intermembrane space [94,96,189], where it could take part in importing RNA.”
BackgroundInfluentialMitochondrial miRNAs (MitomiRs): Their potential roles in breast and other cancers
Ertürk, E., Onur, O. E., Akgün, O., Tuna, G., Yıldız, Y., & Arı, F. (2022) · Mitochondrion · doi:10.1016/j.mito.2022.08.002 · Cited by 67
Mechanisms of the Metabolic Shift during Somatic Cell Reprogramming
Nishimura, K., Fukuda, A., & Hisatake, K. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20092254 · Cited by 71
“PnPase is an RNAase localized in the intermembrane space of mitochondria [92] and facilitates RNA imports into mitochondria to maintain their homeostasis [93].”
BackgroundPolynucleotide Phosphorylase Activity May Be Modulated by Metabolites in Escherichia coli
Nurmohamed, S., Vincent, H. A., Titman, C., Chandran, V., Pears, M. R., Du, D., Griffin, J., Callaghan, A. J., & Luisi, B. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.200741 · Cited by 64
Mitochondrial noncoding RNA transport
Kim, K. M., Noh, J. H., Abdelmohsen, K., & Gorospe, M. (2017) · BMB Reports · doi:10.5483/bmbrep.2017.50.4.013 · Cited by 69
“Only a few noncoding transcripts are selectively transported into the mitochondrial matrix (17, 24).”
BackgroundOrganellar non-coding RNAs: Emerging regulation mechanisms
Dietrich, A., Wallet, C., Iqbal, R. K., Gualberto, J. M., & Weber‐Lotfi, F. (2015) · Biochimie · doi:10.1016/j.biochi.2015.06.027 · Cited by 64
Mucosal effects of tenofovir 1% gel
Hladik, F., Burgener, A. D., Ballweber, L., Gottardo, R., Fourati, S., Dai, J. Y., Cameron, M., Vojtech, L., Strobl, J., Hughes, S., et al. (2014) · bioRxiv · doi:10.1101/008607 · Cited by 61
“PNPASE regulates nucleus-encoded RNA import into mitochondria (Wang et al., 2010).”
BackgroundInfluentialMitochondrial DNA deletions in Alzheimer's brains: A review
Phillips, N., Simpkins, J. W., & Roby, R. K. (2013) · Alzheimer s & Dementia · doi:10.1016/j.jalz.2013.04.508 · Cited by 62
“There is some recent evidence for RNA import into the mitochondria [15].”
BackgroundInsights Into Exosomal Non-Coding RNAs Sorting Mechanism and Clinical Application
Qiu, Y., Li, P., Zhang, Z., & Wu, M. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.664904 · Cited by 66
Subcellular Heterogeneity of the microRNA Machinery
Trabucchi, M., & Matégot, R. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.10.006 · Cited by 74
miR-378a: a new emerging microRNA in metabolism
Machado, I. F., Teodoro, J. S., Palmeira, C. M., & Rolo, A. P. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-019-03375-z · Cited by 72
“In addition, polynucleotide phosphorylase (PNPase), that is located in the mitochondrial intermembrane space and is best known for the degradation of RNA molecules, has emerged as a potential player of mitochondrial RNA [54] and miRNA [8] import mechanisms.”
BackgroundRole of microRNA in metabolic shift during heart failure
Pinti, M. V., Hathaway, Q. A., & Hollander, J. M. (2016) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00341.2016 · Cited by 59
Regulating microRNA expression: at the heart of diabetes mellitus and the mitochondrion
Hathaway, Q. A., Pinti, M. V., Durr, A. J., Waris, S. A., Shepherd, D. L., & Hollander, J. M. (2017) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00520.2017 · Cited by 69
“(150, 151) demonstrated the importance Citric Acid Cycle”
BackgroundBandyra, K., Sinha, D., Syrjänen, J. L., Luisi, B. F., & Lay, N. R. D. (2016) · RNA · doi:10.1261/rna.052886.115 · Cited by 60
“…PNPase, with 40% identity to the E. coli homolog, binds the ribozymes RNase P and MRP, as well as 5S RNA and transports them into the mitochondria (Wang et al. 2010), suggesting that PNPase can bind RNAs without degrading them, and binding of the RNA by this enzyme in itself plays an important…”
Direct evidence of CRISPR-Cas9-mediated mitochondrial genome editing
Bi, R., Li, Y., Xu, M., Zheng, Q.-Z., Zhang, D.-F., Li, X., Ma, G., Xiang, B., Zhu, X., Zhao, H., et al. (2022) · Innovation (Cambridge (Mass.)) · doi:10.1016/j.xinn.2022.100329 · Cited by 56
Defective mitochondrial RNA processing due to PNPT1 variants causes Leigh syndrome
Matilainen, S., Carroll, C., Richter, U., Euro, L., Pohjanpelto, M., Paetau, A., Isohanni, P., & Suomalainen, A. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx221 · Cited by 56
Sieber, F., Duchêne, A., & Maréchal‐Drouard, L. (2011) · International review of cytology · doi:10.1016/b978-0-12-386043-9.00004-9 · Cited by 54
Defects of mitochondrial RNA turnover lead to the accumulation of double-stranded RNA in vivo
Pajak, A., Laine, I., Clemente, P., Fissi, N. E., Schober, F. A., Maffezzini, C., Calvo‐Garrido, J., Wibom, R., Filograna, R., Dhir, A., et al. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008240 · Cited by 55
Mitochondria Encoded Non-coding RNAs in Cell Physiology
Liu, X., & Shan, G. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.713729 · Cited by 60
Leber Hereditary Optic Neuropathy: Exemplar of an mtDNA Disease
Wallace, D. C., & Lott, M. T. (2017) · Handbook of experimental pharmacology · doi:10.1007/164_2017_2 · Cited by 64
“The imported nuclear-coded RNAs include components of the RNase P and the MRP enzymes, the 5S rRNA, and perhaps tRNAs (Wang et al. 2010, 2012a).”
BackgroundAdvancing organelle genome transformation and editing for crop improvement
Li, S., Chang, L., & Zhang, J. (2021) · Plant Communications · doi:10.1016/j.xplc.2021.100141 · Cited by 52
“(2020) demonstrated that gRNA could be efficiently imported to the mitochondria of mammalian cells with an additional 20-bp stem–loop element of nuclear RNase P in a polynucleotide phosphorylase-dependent manner (Wang et al., 2010).”
BackgroundSelf-citation
Metadata
- Authors
- Wang, G., Chen, H.-W., Oktay, Y., Zhang, J., Allen, E. L., Smith, G. M., Fan, K. C., Hong, J. S., French, S. W., McCaffery, J. M., Lightowlers, R. N., Morse, H. C., Koehler, C. M., & Teitell, M. A.
- Affiliations
- University of California, Los Angeles (US)
- University of California, Irvine (US)
- Johns Hopkins University (US)
- Newcastle University (GB)
- National Institutes of Health (US)
- California NanoSystems Institute (US)
- Corresponding author
- Koehler, Carla M.
- Teitell, Michael A.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2010-08
- Volume
- 142
- Issue
- 3
- Pages
- 456-467
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC2921675
- OpenAlex
- W2154990937
- Cited by
- 366
- References
- 42
- Citations by year
- 2026: 16 · 2025: 21 · 2024: 25 · 2023: 17 · 2022: 31 · 2021: 28 · 2020: 24 · 2019: 27 · 2018: 26 · 2017: 18 · 2016: 20 · 2015: 22 · 2014: 14 · 2013: 26 · 2012: 26
- FWCI
- 9.91
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 1081 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- Wellcome Trust (074454)
- National Institutes of Health
- National Eye Institute (PN2EY018228)
- National Cancer Institute (R01CA107300, R01 CA90571, K22CA120147, R01CA090571, R01CA156674)
- National Institute of General Medical Sciences (R01GM073981, R01GM061721)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- polynucleotide phosphorylase, mitochondrial RNA import, mitochondrial intermembrane space, mitochondrial matrix, mitochondrial RNA processing, polycistronic transcripts, RNase P, 5S rRNA, 3'-5' exoribonuclease, poly(A) polymerase
- MeSH terms
- Animals, Cell Line, Humans, Mice, Inbred C57BL, Mitochondria, Polyribonucleotide Nucleotidyltransferase, RNA, RNA Processing, Post-Transcriptional, Saccharomyces cerevisiae, Ribonuclease P, Mice, Gene Knockout Techniques
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