Other Related Tools and Databases

References

  1. Telonis AG, Loher P, Honda S, Jing Y, Palazzo J, Kirino Y, Rigoutsos I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015 Sep 22;6(28):24797-822. doi: 10.18632/oncotarget.4695. PubMed PMID: 26325506. [link]
  2. Pillai MM, Gillen AE, Yamamoto TM, Kline E, Brown J, Flory K, Hesselberth JR, Kabos P. HITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer. Breast Cancer Res Treat. 2014 Jul;146(1):85-97. doi: 10.1007/s10549-014-3004-9. Epub 2014 Jun 7. PubMed PMID: 24906430; PubMed Central PMCID: PMC4115274. [link]
  3. Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM; Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013 Sep 26;501(7468):506-11. doi: 10.1038/nature12531. Epub 2013 Sep 15. PubMed PMID: 24037378; PubMed Central PMCID: PMC3918453. [link]
  4. Rounge TB, Furu K, Skotheim RI, Haugen TB, Grotmol T, Enerly E. Profiling of the small RNA populations in human testicular germ cell tumors shows global loss of piRNAs. Mol Cancer. 2015 Aug 12;14:153. doi: 10.1186/s12943-015-0411-4. PubMed PMID: 26265322; PubMed Central PMCID: PMC4533958. [link]
  5. Sobala A, Hutvagner G. Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells. RNA Biol. 2013 Apr;10(4):553-63. doi: 10.4161/rna.24285. Epub 2013 Apr 1. PubMed PMID: 23563448; PubMed Central PMCID: PMC3710361. [link]
  6. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA. 2010 Apr;16(4):673-95. doi: 10.1261/rna.2000810. Epub 2010 Feb 24. PubMed PMID: 20181738; PubMed Central PMCID: PMC2844617. [link]
  7. Goodarzi H, Liu X, Nguyen HC, Zhang S, Fish L, Tavazoie SF. Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement. Cell. 2015 May 7;161(4):790-802. doi: 10.1016/j.cell.2015.02.053. PubMed PMID: 25957686; PubMed Central PMCID: PMC4457382. [link]
  8. Kumar P, Anaya J, Mudunuri SB, Dutta A. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol. 2014 Oct 1;12:78. doi: 10.1186/s12915-014-0078-0. PubMed PMID: 25270025; PubMed Central PMCID: PMC4203973. [link]
  9. Keam SP, Young PE, McCorkindale AL, Dang TH, Clancy JL, Humphreys DT, Preiss T, Hutvagner G, Martin DI, Cropley JE, Suter CM. The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells. Nucleic Acids Res. 2014 Aug;42(14):8984-95. doi: 10.1093/nar/gku620. Epub 2014 Jul 18. PubMed PMID: 25038252; PubMed Central PMCID: PMC4132735. [link]
  10. 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 Apr 10;9:157. doi: 10.1186/1471-2164-9-157. PubMed PMID: 18402656; PubMed Central PMCID: PMC2359750. [link]
  11. Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, Green PJ, Barton GJ, Hutvagner G. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA. 2009 Dec;15(12):2147-60. doi: 10.1261/rna.1738409. Epub 2009 Oct 22. PubMed PMID: 19850906; PubMed Central PMCID: PMC2779667. [link]
  12. Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 2008 Oct 15;22(20):2773-85. doi: 10.1101/gad.1705308. PubMed PMID: 18923076; PubMed Central PMCID: PMC2569885. [link]
  13. Liao JY, Ma LM, Guo YH, Zhang YC, Zhou H, Shao P, Chen YQ, Qu LH. Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers. PLoS One. 2010 May 14;5(5):e10563. doi: 10.1371/journal.pone.0010563. PubMed PMID: 20498841; PubMed Central PMCID: PMC2871053. [link]
  14. Yeung ML, Bennasser Y, Watashi K, Le SY, Houzet L, Jeang KT. Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid. Nucleic Acids Res. 2009 Oct;37(19):6575-86. doi: 10.1093/nar/gkp707. Epub 2009 Sep 3. PubMed PMID: 19729508; PubMed Central PMCID: PMC2770672. [link]
  15. Lee YS, Shibata Y, Malhotra A, Dutta A. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev. 2009 Nov 15;23(22):2639-49. doi: 10.1101/gad.1837609. PubMed PMID: 19933153; PubMed Central PMCID: PMC2779758. [link]
  16. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA. 2010 Apr;16(4):673-95. doi: 10.1261/rna.2000810. Epub 2010 Feb 24. PubMed PMID: 20181738; PubMed Central PMCID: PMC2844617. [link]
  17. Selitsky SR, Baran-Gale J, Honda M, Yamane D, Masaki T, Fannin EE, Guerra B, Shirasaki T, Shimakami T, Kaneko S, Lanford RE, Lemon SM, Sethupathy P. Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C. Sci Rep. 2015 Jan 8;5:7675. doi: 10.1038/srep07675. PubMed PMID: 25567797; PubMed Central PMCID: PMC4286764. [link]
  18. Li Y, Luo J, Zhou H, Liao JY, Ma LM, Chen YQ, Qu LH. Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia. Nucleic Acids Res. 2008 Nov;36(19):6048-55. doi: 10.1093/nar/gkn596. Epub 2008 Sep 27. PubMed PMID: 18820301; PubMed Central PMCID: PMC2577346. [link]
  19. Zhang Y, Zhang Y, Shi J, Zhang H, Cao Z, Gao X, Ren W, Ning Y, Ning L, Cao Y, Chen Y, Ji W, Chen ZJ, Chen Q, Duan E. Identification and characterization of an ancient class of small RNAs enriched in serum associating with active infection. J Mol Cell Biol. 2014 Apr;6(2):172-4. doi: 10.1093/jmcb/mjt052. Epub 2013 Dec 30. PubMed PMID: 24380870. [link]
  20. Peng H, Shi J, Zhang Y, Zhang H, Liao S, Li W, Lei L, Han C, Ning L, Cao Y, Zhou Q, Chen Q, Duan E. A novel class of tRNA-derived small RNAs extremely enriched in mature mouse sperm. Cell Res. 2012 Nov;22(11):1609-12. doi: 10.1038/cr.2012.141. Epub 2012 Oct 9. PubMed PMID: 23044802; PubMed Central PMCID: PMC3494397. [link]
  21. Loss-Morais G, Waterhouse PM, Margis R. Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets. Biol Direct. 2013 Feb 12;8:6. doi: 10.1186/1745-6150-8-6. PubMed PMID: 23402430; PubMed Central PMCID: PMC3574835. [link]
  22. Lalaouna D, Carrier MC, Semsey S, Brouard JS, Wang J, Wade JT, Massé E. A 3' external transcribed spacer in a tRNA transcript acts as a sponge for small RNAs to prevent transcriptional noise. Mol Cell. 2015 May 7;58(3):393-405. doi: 10.1016/j.molcel.2015.03.013. Epub 2015 Apr 16. PubMed PMID: 25891076. [link]
  23. Sobala A, Hutvagner G. Transfer RNA-derived fragments: origins, processing, and functions. Wiley Interdiscip Rev RNA. 2011 Nov-Dec;2(6):853-62. doi: 10.1002/wrna.96. Epub 2011 Jun 30. Review. PubMed PMID: 21976287. [link]
  24. Lodish H, Berk A, Zipursky SL, et al. New York: W. H. Freeman; 2000. [link]
  25. Kumar P, Mudunuri SB, Anaya J, Dutta A. tRFdb: a database for transfer RNA fragments. Nucleic Acids Res. 2015 Jan;43(Database issue):D141-5. doi: 10.1093/nar/gku1138. Epub 2014 Nov 11. PubMed PMID: 25392422; PubMed Central PMCID: PMC4383946. [link]
  26. Selitsky SR, Sethupathy P. tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data. BMC Bioinformatics. 2015 Nov 4;16:354. doi: 10.1186/s12859-015-0800-0. PubMed PMID: 26530785; PubMed Central PMCID: PMC4632369. [link]
  27. Dhahbi JM. 5' tRNA Halves: The Next Generation of Immune Signaling Molecules. Front Immunol. 2015 Feb 19;6:74. doi: 10.3389/fimmu.2015.00074. eCollection 2015. Review. PubMed PMID: 25745425; PubMed Central PMCID: PMC4333838. [link]
  28. Wang Q, Lee I, Ren J, Ajay SS, Lee YS, Bao X. Identification and functional characterization of tRNA-derived RNA fragments (tRFs) in respiratory syncytial virus infection. Mol Ther. 2013 Feb;21(2):368-79. doi: 10.1038/mt.2012.237. Epub 2012 Nov 27. PubMed PMID: 23183536; PubMed Central PMCID: PMC3594034. [link]
  29. Baglio SR, Rooijers K, Koppers-Lalic D, Verweij FJ, Pérez Lanzón M, Zini N, Naaijkens B, Perut F, Niessen HW, Baldini N, Pegtel DM. Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species. Stem Cell Res Ther. 2015 Jul 1;6:127. doi: 10.1186/s13287-015-0116-z. PubMed PMID: 26129847; PubMed Central PMCID: PMC4529699. [link]
  30. Saikia M, Krokowski D, Guan BJ, Ivanov P, Parisien M, Hu GF, Anderson P, Pan T, Hatzoglou M. Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J Biol Chem. 2012 Dec 14;287(51):42708-25. doi: 10.1074/jbc.M112.371799. Epub 2012 Oct 19. PubMed PMID: 23086926; PubMed Central PMCID: PMC3522271. [link]
  31. Nolte-'t Hoen EN, Buermans HP, Waasdorp M, Stoorvogel W, Wauben MH, 't Hoen PA. Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res. 2012 Oct;40(18):9272-85. doi: 10.1093/nar/gks658. Epub 2012 Jul 19. PubMed PMID: 22821563; PubMed Central PMCID: PMC3467056.
    32. [link]
  32. Zheng LL, Wen YZ, Yang JH, Liao JY, Shao P, Xu H, Zhou H, Wen JZ, Lun ZR, Ayala FJ, Qu LH. Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei. RNA. 2013 Jul;19(7):863-75. doi: 10.1261/rna.035683.112. Epub 2013 May 23. PubMed PMID: 23704326; PubMed Central PMCID: PMC3683921.
    33. [link]
  33. Keam SP, Hutvagner G. tRNA-Derived Fragments (tRFs): Emerging New Roles for an Ancient RNA in the Regulation of Gene Expression. Life (Basel). 2015 Nov 27;5(4):1638-51. doi: 10.3390/life5041638. Review. PubMed PMID: 26703738. [link]
  34. Garcia-Silva MR, Sanguinetti J, Cabrera-Cabrera F, Franzén O, Cayota A. A particular set of small non-coding RNAs is bound to the distinctive Argonaute protein of Trypanosoma cruzi: insights from RNA-interference deficient organisms. Gene. 2014 Apr 1;538(2):379-84. doi: 10.1016/j.gene.2014.01.023. Epub 2014 Jan 23. PubMed PMID: 24463018. [link]
  35. Garcia-Silva MR, Cabrera-Cabrera F, das Neves RF, Souto-Padrón T, de Souza W, Cayota A. Gene expression changes induced by Trypanosoma cruzi shed microvesicles in mammalian host cells: relevance of tRNA-derived halves. Biomed Res Int. 2014;2014:305239. doi: 10.1155/2014/305239. Epub 2014 Apr 9. PubMed PMID: 24812611; PubMed Central PMCID: PMC4000953. [link]
  36. Blanco S, Dietmann S, Flores JV, Hussain S, Kutter C, Humphreys P, Lukk M, Lombard P, Treps L, Popis M, Kellner S, Hölter SM, Garrett L, Wurst W, Becker L, Klopstock T, Fuchs H, Gailus-Durner V, Hrabĕ de Angelis M, Káradóttir RT, Helm M, Ule J, Gleeson JG, Odom DT, Frye M. Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. EMBO J. 2014 Sep 17;33(18):2020-39. doi: 10.15252/embj.201489282. Epub 2014 Jul 25. PubMed PMID: 25063673; PubMed Central PMCID: PMC4195770. [link]
  37. Schopman NC, Heynen S, Haasnoot J, Berkhout B. A miRNA-tRNA mix-up: tRNA origin of proposed miRNA. RNA Biol. 2010 Sep-Oct;7(5):573-6. doi: 10.4161/rna.7.4.13141. Epub 2010 Sep 1. PubMed PMID: 20818168. [link]
  38. Keam SP, Sobala A, Humphreys DT, Suter CM, Hutvagner G. Computational analysis, biochemical purification, and detection of tRNA-derived small RNA fragments. Methods Mol Biol. 2014;1173:157-67. doi: 10.1007/978-1-4939-0931-5_14. PubMed PMID: 24920368. [link]
  39. Hirose Y, Ikeda KT, Noro E, Hiraoka K, Tomita M, Kanai A. Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp). BMC Genet. 2015 Jul 14;16:83. doi: 10.1186/s12863-015-0245-5. PubMed PMID: 26168920; PubMed Central PMCID: PMC4501094. [link]
  40. Thompson DM, Lu C, Green PJ, Parker R. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA. 2008 Oct;14(10):2095-103. doi: 10.1261/rna.1232808. Epub 2008 Aug 21. PubMed PMID: 18719243; PubMed Central PMCID: PMC2553748. [link]
  41. Lee SR, Collins K. Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. J Biol Chem. 2005 Dec 30;280(52):42744-9. Epub 2005 Nov 3. PubMed PMID: 16272149. [link]
  42. Garcia-Silva MR, Frugier M, Tosar JP, Correa-Dominguez A, Ronalte-Alves L, Parodi-Talice A, Rovira C, Robello C, Goldenberg S, Cayota A. A population of tRNA-derived small RNAs is actively produced in Trypanosoma cruzi and recruited to specific cytoplasmic granules. Mol Biochem Parasitol. 2010 Jun;171(2):64-73. doi: 10.1016/j.molbiopara.2010.02.003. Epub 2010 Feb 13. PubMed PMID: 20156490. [link]
  43. Tomita K, Ogawa T, Uozumi T, Watanabe K, Masaki H. A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops. Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8278-83. PubMed PMID: 10880568; PubMed Central PMCID: PMC26938. [link]
  44. Dhahbi JM, Spindler SR, Atamna H, Yamakawa A, Boffelli D, Mote P, Martin DI. 5' tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction. BMC Genomics. 2013 May 2;14:298. doi: 10.1186/1471-2164-14-298. PubMed PMID: 23638709; PubMed Central PMCID: PMC3654920. [link]
  45. Cozen AE, Quartley E, Holmes AD, Hrabeta-Robinson E, Phizicky EM, Lowe TM. ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat Methods. 2015 Sep;12(9):879-84. doi: 10.1038/nmeth.3508. Epub 2015 Aug 3. PubMed PMID: 26237225; PubMed Central PMCID: PMC4553111. [link]
  46. Casas E, Cai G, Neill JD. Characterization of circulating transfer RNA-derived RNA fragments in cattle. Front Genet. 2015 Aug 24;6:271. doi: 10.3389/fgene.2015.00271. eCollection 2015. PubMed PMID: 26379699; PubMed Central PMCID: PMC4547532. [link]
  47. Venkatesh T, Suresh PS, Tsutsumi R. tRFs: miRNAs in disguise. Gene. 2015 Dec 29. pii: S0378-1119(15)01570-X. doi: 10.1016/j.gene.2015.12.058. [Epub ahead of print] Review. PubMed PMID: 26743126. [link]
  48. Abbott Jamie A, Francklyn Chris S, Robey-Bond Susan M. Transfer RNA and human disease. Frontiers in Genetics. 2014 (5):00158 . doi: 10.3389/fgene.2014.00158 [link]
  49. Couvillion MT, Sachidanandam R, Collins K. A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo. Genes Dev. 2010 Dec 15;24(24):2742-7. doi: 10.1101/gad.1996210. Epub 2010 Nov 24. PubMed PMID: 21106669; PubMed Central PMCID: PMC3003190. [link]
  50. Thompson DM, Parker R. Stressing out over tRNA cleavage. Cell. 2009 Jul 23;138(2):215-9. doi: 10.1016/j.cell.2009.07.001. PubMed PMID: 19632169. [link]
  51. Chen Q, Yan M, Cao Z, Li X, Zhang Y, Shi J, Feng GH, Peng H, Zhang X, Zhang Y, Qian J, Duan E, Zhai Q, Zhou Q. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science. 2016 Jan 22;351(6271):397-400. doi: 10.1126/science.aad7977. Epub 2015 Dec 31. PubMed PMID: 26721680. [link]
  52. Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, Bing XY, Belleannee C, Kucukural A, Serra RW, Sun F, Song L, Carone BR, Ricci EP, Li XZ, Fauquier L, Moore MJ, Sullivan R, Mello CC, Garber M, Rando OJ. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science. 2016 Jan 22;351(6271):391-6. doi: 10.1126/science.aad6780. Epub 2015 Dec 31. PubMed PMID: 26721685. [link]