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For: Shigematsu M, Kirino Y. tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins. Gene Regul Syst Bio 2015;9:27-33. [PMID: 26401098 PMCID: PMC4567038 DOI: 10.4137/grsb.s29411] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/28/2015] [Accepted: 07/09/2015] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
1
Ajmeriya S, Bharti DR, Kumar A, Rana S, Singh H, Karmakar S. In silico approach for the identification of tRNA-derived small non-coding RNAs in SARS-CoV infection. J Appl Genet 2024;65:403-413. [PMID: 38514586 DOI: 10.1007/s13353-024-00853-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
2
Zhang Y, Zhou H, Chen X, Wang N, Zhan Y, Huang Z, Ruan K, Qi Q, Deng M, Jiang Y. A novel tRNA-derived fragment tRF-3023b suppresses inflammation in RAW264.7 cells by targeting Cul4a through NF-κB signaling. Funct Integr Genomics 2024;24:9. [PMID: 38221594 DOI: 10.1007/s10142-024-01285-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/29/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024]
3
Mittal M, Dhingra A, Dawar P, Payton P, Rock CD. The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea). THE PLANT GENOME 2023;16:e20350. [PMID: 37351954 DOI: 10.1002/tpg2.20350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 06/24/2023]
4
Goldkamp AK, Li Y, Rivera RM, Hagen DE. Differentially expressed tRNA-derived fragments in bovine fetuses with assisted reproduction induced congenital overgrowth syndrome. Front Genet 2022;13:1055343. [PMID: 36457750 PMCID: PMC9705782 DOI: 10.3389/fgene.2022.1055343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/28/2022] [Indexed: 08/13/2023]  Open
5
Wijesinghe SN, Anderson J, Brown TJ, Nanus DE, Housmans B, Green JA, Hackl M, Choi KK, Arkill KP, Welting T, James V, Jones SW, Peffers MJ. The role of extracellular vesicle miRNAs and tRNAs in synovial fibroblast senescence. Front Mol Biosci 2022;9:971621. [PMID: 36213127 PMCID: PMC9537453 DOI: 10.3389/fmolb.2022.971621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022]  Open
6
An Expanded Landscape of Unusually Short RNAs in 11 Samples from Six Eukaryotic Organisms. Noncoding RNA 2022;8:ncrna8030034. [PMID: 35645341 PMCID: PMC9149858 DOI: 10.3390/ncrna8030034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 11/30/2022]  Open
7
Shigematsu M, Kirino Y. Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations. Biomolecules 2022;12:611. [PMID: 35625540 PMCID: PMC9138997 DOI: 10.3390/biom12050611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/15/2022] [Accepted: 04/15/2022] [Indexed: 12/18/2022]  Open
8
Kretschmer M, Gapp K. Deciphering the RNA universe in sperm in its role as a vertical information carrier. ENVIRONMENTAL EPIGENETICS 2022;8:dvac011. [PMID: 35633894 PMCID: PMC9134061 DOI: 10.1093/eep/dvac011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 05/21/2023]
9
Peng R, Santos HJ, Nozaki T. Transfer RNA-Derived Small RNAs in the Pathogenesis of Parasitic Protozoa. Genes (Basel) 2022;13:286. [PMID: 35205331 PMCID: PMC8872473 DOI: 10.3390/genes13020286] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 01/25/2023]  Open
10
Wu WS, Brown JS, Chen PH, Shiue SC, Lee DE, Lee HC. CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data. Noncoding RNA 2022;8:ncrna8010006. [PMID: 35076587 PMCID: PMC8788457 DOI: 10.3390/ncrna8010006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 12/24/2022]  Open
11
Li Z, Stanton BA. Transfer RNA-Derived Fragments, the Underappreciated Regulatory Small RNAs in Microbial Pathogenesis. Front Microbiol 2021;12:687632. [PMID: 34079534 PMCID: PMC8166272 DOI: 10.3389/fmicb.2021.687632] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 01/20/2023]  Open
12
Sun Z, Tan J, Zhao M, Peng Q, Zhou M, Zuo S, Wu F, Li X, Dong Y, Xie M, Yang Y, Zhou J, Liu X, He Q, He Z, Yu X, He Q. Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome. Sci Rep 2021;11:5226. [PMID: 33664286 PMCID: PMC7933247 DOI: 10.1038/s41598-021-83469-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 02/01/2021] [Indexed: 11/25/2022]  Open
13
Tong L, Zhang W, Qu B, Zhang F, Wu Z, Shi J, Chen X, Song Y, Wang Z. The tRNA-Derived Fragment-3017A Promotes Metastasis by Inhibiting NELL2 in Human Gastric Cancer. Front Oncol 2021;10:570916. [PMID: 33665159 PMCID: PMC7921707 DOI: 10.3389/fonc.2020.570916] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/30/2020] [Indexed: 12/24/2022]  Open
14
Avcilar-Kucukgoze I, Kashina A. Hijacking tRNAs From Translation: Regulatory Functions of tRNAs in Mammalian Cell Physiology. Front Mol Biosci 2020;7:610617. [PMID: 33392265 PMCID: PMC7773854 DOI: 10.3389/fmolb.2020.610617] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022]  Open
15
Pawar K, Shigematsu M, Sharbati S, Kirino Y. Infection-induced 5'-half molecules of tRNAHisGUG activate Toll-like receptor 7. PLoS Biol 2020;18:e3000982. [PMID: 33332353 PMCID: PMC7745994 DOI: 10.1371/journal.pbio.3000982] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/13/2020] [Indexed: 01/15/2023]  Open
16
Li PF, Guo SC, Liu T, Cui H, Feng D, Yang A, Cheng Z, Luo J, Tang T, Wang Y. Integrative analysis of transcriptomes highlights potential functions of transfer-RNA-derived small RNAs in experimental intracerebral hemorrhage. Aging (Albany NY) 2020;12:22794-22813. [PMID: 33203799 PMCID: PMC7746353 DOI: 10.18632/aging.103938] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/01/2020] [Indexed: 12/16/2022]
17
Gonçalves NP, Yan Y, Ulrichsen M, Venø MT, Poulsen ET, Enghild JJ, Kjems J, Vægter CB. Modulation of Small RNA Signatures in Schwann-Cell-Derived Extracellular Vesicles by the p75 Neurotrophin Receptor and Sortilin. Biomedicines 2020;8:E450. [PMID: 33114403 PMCID: PMC7694014 DOI: 10.3390/biomedicines8110450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]  Open
18
Maguire S, Lohman GJS, Guan S. A low-bias and sensitive small RNA library preparation method using randomized splint ligation. Nucleic Acids Res 2020;48:e80. [PMID: 32496547 PMCID: PMC7641310 DOI: 10.1093/nar/gkaa480] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/22/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022]  Open
19
Yan Y, Chang C, Su J, Venø MT, Kjems J. Osteoblastogenesis Alters Small RNA Profiles in EVs Derived from Bone Marrow Stem Cells (BMSCs) and Adipose Stem Cells (ASCs). Biomedicines 2020;8:biomedicines8100387. [PMID: 32998458 PMCID: PMC7599808 DOI: 10.3390/biomedicines8100387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022]  Open
20
Mo X, Du S, Chen X, Wang Y, Liu X, Zhang C, Zhu C, Ding L, Li Y, Tong Y, Ju Q, Qu D, Tan F, Wei F, Cai Q. Lactate Induces Production of the tRNAHis Half to Promote B-lymphoblastic Cell Proliferation. Mol Ther 2020;28:2442-2457. [PMID: 32966775 DOI: 10.1016/j.ymthe.2020.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/27/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022]  Open
21
Jia Y, Tan W, Zhou Y. Transfer RNA-derived small RNAs: potential applications as novel biomarkers for disease diagnosis and prognosis. ANNALS OF TRANSLATIONAL MEDICINE 2020;8:1092. [PMID: 33145311 PMCID: PMC7575943 DOI: 10.21037/atm-20-2797] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
22
Shigematsu M, Kirino Y. Oxidative stress enhances the expression of 2',3'-cyclic phosphate-containing RNAs. RNA Biol 2020;17:1060-1069. [PMID: 32397797 DOI: 10.1080/15476286.2020.1766861] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]  Open
23
Angelova MT, Dimitrova DG, Da Silva B, Marchand V, Jacquier C, Achour C, Brazane M, Goyenvalle C, Bourguignon-Igel V, Shehzada S, Khouider S, Lence T, Guerineau V, Roignant JY, Antoniewski C, Teysset L, Bregeon D, Motorin Y, Schaefer MR, Carré C. tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila. Nucleic Acids Res 2020;48:2050-2072. [PMID: 31943105 PMCID: PMC7038984 DOI: 10.1093/nar/gkaa002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 12/14/2022]  Open
24
Sala L, Chandrasekhar S, Vidigal JA. AGO unchained: Canonical and non-canonical roles of Argonaute proteins in mammals. Front Biosci (Landmark Ed) 2020;25:1-42. [PMID: 31585876 DOI: 10.2741/4793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
25
Peng Y, Zou J, Wang JH, Zeng H, Tan W, Yoshida S, Zhang L, Li Y, Zhou Y. Small RNA Sequencing Reveals Transfer RNA-derived Small RNA Expression Profiles in Retinal Neovascularization. Int J Med Sci 2020;17:1713-1722. [PMID: 32714074 PMCID: PMC7378657 DOI: 10.7150/ijms.46209] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022]  Open
26
Trolet A, Baldrich P, Criqui MC, Dubois M, Clavel M, Meyers BC, Genschik P. Cell Cycle-Dependent Regulation and Function of ARGONAUTE1 in Plants. THE PLANT CELL 2019;31:1734-1750. [PMID: 31189739 PMCID: PMC6713298 DOI: 10.1105/tpc.19.00069] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/07/2019] [Accepted: 06/07/2019] [Indexed: 05/04/2023]
27
Rigoutsos I, Londin E, Kirino Y. Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities. Curr Opin Biotechnol 2019;58:202-210. [PMID: 31323485 DOI: 10.1016/j.copbio.2019.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/09/2019] [Accepted: 05/27/2019] [Indexed: 01/03/2023]
28
tRNA-Derived Small Non-Coding RNAs as Novel Epigenetic Molecules Regulating Adipogenesis. Biomolecules 2019;9:biom9070274. [PMID: 31336727 PMCID: PMC6681357 DOI: 10.3390/biom9070274] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 06/29/2019] [Accepted: 07/08/2019] [Indexed: 12/17/2022]  Open
29
Zhang L, Liu S, Wang JH, Zou J, Zeng H, Zhao H, Zhang B, He Y, Shi J, Yoshida S, Zhou Y. Differential Expressions of microRNAs and Transfer RNA-derived Small RNAs: Potential Targets of Choroidal Neovascularization. Curr Eye Res 2019;44:1226-1235. [PMID: 31136199 DOI: 10.1080/02713683.2019.1625407] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
30
Roura Frigolé H, Camacho N, Castellví Coma M, Fernández-Lozano C, García-Lema J, Rafels-Ybern À, Canals A, Coll M, Ribas de Pouplana L. tRNA deamination by ADAT requires substrate-specific recognition mechanisms and can be inhibited by tRFs. RNA (NEW YORK, N.Y.) 2019;25:607-619. [PMID: 30737359 PMCID: PMC6467012 DOI: 10.1261/rna.068189.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/28/2019] [Indexed: 05/30/2023]
31
Telonis AG, Loher P, Magee R, Pliatsika V, Londin E, Kirino Y, Rigoutsos I. tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities. Cancer Res 2019;79:3034-3049. [PMID: 30996049 DOI: 10.1158/0008-5472.can-19-0789] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 01/26/2023]
32
Niaz S. The AGO proteins: an overview. Biol Chem 2019;399:525-547. [PMID: 29447113 DOI: 10.1515/hsz-2017-0329] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 02/05/2018] [Indexed: 12/21/2022]
33
Wang C, Zhao M, Wang J, Zhang D, Wang S, Zhao J. Expression analysis of transfer RNA‑derived fragments in the blood of patients with moyamoya disease: A preliminary study. Mol Med Rep 2019;19:3564-3574. [PMID: 30896793 PMCID: PMC6472122 DOI: 10.3892/mmr.2019.10024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 01/14/2019] [Indexed: 12/27/2022]  Open
34
Shigematsu M, Kawamura T, Kirino Y. Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome. Front Genet 2018;9:562. [PMID: 30538719 PMCID: PMC6277466 DOI: 10.3389/fgene.2018.00562] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/06/2018] [Indexed: 01/03/2023]  Open
35
Shen Y, Yu X, Zhu L, Li T, Yan Z, Guo J. Transfer RNA-derived fragments and tRNA halves: biogenesis, biological functions and their roles in diseases. J Mol Med (Berl) 2018;96:1167-1176. [PMID: 30232504 DOI: 10.1007/s00109-018-1693-y] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/30/2018] [Accepted: 09/05/2018] [Indexed: 12/15/2022]
36
He X, Li F, Bor B, Koyano K, Cen L, Xiao X, Shi W, Wong DTW. Human tRNA-Derived Small RNAs Modulate Host-Oral Microbial Interactions. J Dent Res 2018;97:1236-1243. [PMID: 29702004 DOI: 10.1177/0022034518770605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
37
Pliatsika V, Loher P, Magee R, Telonis AG, Londin E, Shigematsu M, Kirino Y, Rigoutsos I. MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res 2018;46:D152-D159. [PMID: 29186503 PMCID: PMC5753276 DOI: 10.1093/nar/gkx1075] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/18/2017] [Accepted: 10/27/2017] [Indexed: 12/16/2022]  Open
38
Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap. Methods Mol Biol 2018;1680:237-255. [PMID: 29030853 DOI: 10.1007/978-1-4939-7339-2_16] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
39
Telonis AG, Rigoutsos I. Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer. Cancer Res 2017;78:1140-1154. [PMID: 29229607 DOI: 10.1158/0008-5472.can-17-1947] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/19/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022]
40
Honda S, Kawamura T, Loher P, Morichika K, Rigoutsos I, Kirino Y. The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells. Nucleic Acids Res 2017. [PMID: 28645172 PMCID: PMC5587776 DOI: 10.1093/nar/gkx537] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
41
Loher P, Telonis AG, Rigoutsos I. MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data. Sci Rep 2017;7:41184. [PMID: 28220888 PMCID: PMC5318995 DOI: 10.1038/srep41184] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/15/2016] [Indexed: 12/21/2022]  Open
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Shigematsu M, Kirino Y. 5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves. RNA (NEW YORK, N.Y.) 2017;23:161-168. [PMID: 27879434 PMCID: PMC5238791 DOI: 10.1261/rna.058024.116] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
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Duechler M, Leszczyńska G, Sochacka E, Nawrot B. Nucleoside modifications in the regulation of gene expression: focus on tRNA. Cell Mol Life Sci 2016;73:3075-95. [PMID: 27094388 PMCID: PMC4951516 DOI: 10.1007/s00018-016-2217-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/25/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
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Pliatsika V, Loher P, Telonis AG, Rigoutsos I. MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. ACTA ACUST UNITED AC 2016;32:2481-9. [PMID: 27153631 PMCID: PMC4978933 DOI: 10.1093/bioinformatics/btw194] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/07/2016] [Indexed: 11/26/2022]
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Larriba E, del Mazo J. Role of Non-Coding RNAs in the Transgenerational Epigenetic Transmission of the Effects of Reprotoxicants. Int J Mol Sci 2016;17:452. [PMID: 27023531 PMCID: PMC4848908 DOI: 10.3390/ijms17040452] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/14/2022]  Open
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Berindan-Neagoe I, Calin GA, Francastel C, Hubé F, Santulli G. The Non-Coding RNA Journal Club: Highlights on Recent Papers—3. Noncoding RNA 2015. [PMCID: PMC5932552 DOI: 10.3390/ncrna1030285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
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