TRNAviz: Explore and Visualize TRNA Sequence Features

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 May 26

PMID 31127306

Citations 18

Authors

Brian Y Lin

Patricia P Chan

Todd M Lowe

Affiliations

Soon will be listed here.

Abstract

Transfer RNAs (tRNAs) are ubiquitous across the tree of life. Although tRNA structure is highly conserved, there is still significant variation in sequence features between clades, isotypes and even isodecoders. This variation not only impacts translation, but as shown by a variety of recent studies, nontranslation-associated functions are also sensitive to small changes in tRNA sequence. Despite the rapidly growing number of sequenced genomes, there is a lack of tools for both small- and large-scale comparative genomics analysis of tRNA sequence features. Here, we have integrated over 150 000 tRNAs spanning all domains of life into tRNAviz, a web application for exploring and visualizing tRNA sequence features. tRNAviz implements a framework for determining consensus sequence features and can generate sequence feature distributions by isotypes, clades and anticodons, among other tRNA properties such as score. All visualizations are interactive and exportable. The web server is publicly available at http://trna.ucsc.edu/tRNAviz/.

Citing Articles

Automated orthogonal tRNA generation.

Spinck M, Guppy A, Chin J Nat Chem Biol. 2024; .

PMID: 39706894 DOI: 10.1038/s41589-024-01782-3.

Optimization of ACE-tRNAs function in translation for suppression of nonsense mutations.

Porter J, Ko W, Sorensen E, Lueck J Nucleic Acids Res. 2024; 52(22):14112-14132.

PMID: 39673265 PMC: 11662937. DOI: 10.1093/nar/gkae1112.

AcrIIIA1 is a protein-RNA anti-CRISPR complex that targets core Cas and accessory nucleases.

Chou-Zheng L, Howell O, Boyle T, Hossain M, Walker F, Sheriff E Nucleic Acids Res. 2024; 52(22):13490-13514.

PMID: 39551936 PMC: 11662646. DOI: 10.1093/nar/gkae1006.

AARS Online: A collaborative database on the structure, function, and evolution of the aminoacyl-tRNA synthetases.

Douglas J, Cui H, Perona J, Vargas-Rodriguez O, Tyynismaa H, Carreno C IUBMB Life. 2024; 76(12):1091-1105.

PMID: 39247978 PMC: 11580382. DOI: 10.1002/iub.2911.

Genomic factors shaping codon usage across the Saccharomycotina subphylum.

Zavala B, Dineen L, Fisher K, Opulente D, Harrison M, Wolters J G3 (Bethesda). 2024; 14(11).

PMID: 39213398 PMC: 11540330. DOI: 10.1093/g3journal/jkae207.

References

Juhling F, Morl M, Hartmann R, Sprinzl M, Stadler P, Putz J . tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 2008; 37(Database issue):D159-62. PMC: 2686557. DOI: 10.1093/nar/gkn772. View

Phizicky E, Hopper A . tRNA processing, modification, and subcellular dynamics: past, present, and future. RNA. 2015; 21(4):483-5. PMC: 4371247. DOI: 10.1261/rna.049932.115. View

Giege R, Sissler M, Florentz C . Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res. 1998; 26(22):5017-35. PMC: 147952. DOI: 10.1093/nar/26.22.5017. View

Raina M, Ibba M . tRNAs as regulators of biological processes. Front Genet. 2014; 5:171. PMC: 4052509. DOI: 10.3389/fgene.2014.00171. View

Schimmel P . The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat Rev Mol Cell Biol. 2017; 19(1):45-58. DOI: 10.1038/nrm.2017.77. View

Steinberg S, Misch A, Sprinzl M . Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1993; 21(13):3011-5. PMC: 309727. DOI: 10.1093/nar/21.13.3011. View

Letunic I, Bork P . Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016; 44(W1):W242-5. PMC: 4987883. DOI: 10.1093/nar/gkw290. View

Anderson P, Ivanov P . tRNA fragments in human health and disease. FEBS Lett. 2014; 588(23):4297-304. PMC: 4339185. DOI: 10.1016/j.febslet.2014.09.001. View

de Crecy-Lagard V, Marck C, Brochier-Armanet C, Grosjean H . Comparative RNomics and modomics in Mollicutes: prediction of gene function and evolutionary implications. IUBMB Life. 2007; 59(10):634-58. DOI: 10.1080/15216540701604632. View

10.

Phizicky E, Alfonzo J . Do all modifications benefit all tRNAs?. FEBS Lett. 2009; 584(2):265-71. PMC: 2794898. DOI: 10.1016/j.febslet.2009.11.049. View

11.

Goodenbour J, Pan T . Diversity of tRNA genes in eukaryotes. Nucleic Acids Res. 2006; 34(21):6137-46. PMC: 1693877. DOI: 10.1093/nar/gkl725. View

12.

Marck C, Grosjean H . tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA. 2002; 8(10):1189-232. PMC: 1370332. DOI: 10.1017/s1355838202022021. View

13.

Eddy S, Durbin R . RNA sequence analysis using covariance models. Nucleic Acids Res. 1994; 22(11):2079-88. PMC: 308124. DOI: 10.1093/nar/22.11.2079. View

14.

Ishimura R, Nagy G, Dotu I, Zhou H, Yang X, Schimmel P . RNA function. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration. Science. 2014; 345(6195):455-9. PMC: 4281038. DOI: 10.1126/science.1249749. View

15.

Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View

16.

Abe T, Ikemura T, Sugahara J, Kanai A, Ohara Y, Uehara H . tRNADB-CE 2011: tRNA gene database curated manually by experts. Nucleic Acids Res. 2010; 39(Database issue):D210-3. PMC: 3013639. DOI: 10.1093/nar/gkq1007. View

17.

Rajendran V, Kalita P, Shukla H, Kumar A, Tripathi T . Aminoacyl-tRNA synthetases: Structure, function, and drug discovery. Int J Biol Macromol. 2018; 111:400-414. DOI: 10.1016/j.ijbiomac.2017.12.157. View

18.

Geslain R, Pan T . Functional analysis of human tRNA isodecoders. J Mol Biol. 2009; 396(3):821-31. PMC: 2822071. DOI: 10.1016/j.jmb.2009.12.018. View

19.

Richly E, Leister D . NUMTs in sequenced eukaryotic genomes. Mol Biol Evol. 2004; 21(6):1081-4. DOI: 10.1093/molbev/msh110. View

20.

Chamberlain S, Szocs E . taxize: taxonomic search and retrieval in R. F1000Res. 2014; 2:191. PMC: 3901538. DOI: 10.12688/f1000research.2-191.v2. View