References
- Dever TE, Green R. The elongation, termination, and recycling phases of translation in eukaryotes. Cold Spring Harb Perspect Biol. 2012;4:1–16.
- Geiduschek EP, Kassavetis GA. The RNA polymerase III transcription apparatus. J Mol Biol. 2001;310:1–26.
- Paule MR, White RJ. Survey and summary: transcription by RNA polymerases I and III. Nucleic Acids Res. Internet] 2000; 28:1283–1298. Available from: http://www.ncbi.nlm.nih.gov/pubmed/10684922%5Cnhttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC111039.
- Krokowski D, Han J, Saikia M, et al. A self-defeating anabolic program leads to ??-cell apoptosis in endoplasmic reticulum stress-induced diabetes via regulation of amino acid flux. J Biol Chem. 2013;288:17202–17213.
- Girstmair H, Saffert P, Rode S, et al. Depletion of cognate charged transfer RNA causes translational frameshifting within the expanded CAG stretch in huntingtin. Cell Rep Internet] 2013; 3:148–159. DOI: 10.1016/j.celrep.2012.12.019
- Grewal SS. Why should cancer biologists care about tRNAs? TRNA synthesis, mRNA translation and the control of growth. Biochim Biophys Acta - Gene Regul Mech Internet] 2014; 1849:898–907.
- Pavon-Eternod M, Gomes S, Geslain R, et al. tRNA over-expression in breast cancer and functional consequences. Nucleic Acids Res. 2009;37:7268–7280.
- Truitt ML, Ruggero D. New frontiers in translational control of the cancer genome. Nat Rev Cancer. Internet] 2016; 16:288–304. Available from: http://www.ncbi.nlm.nih.gov/pubmed/27112207.
- Zhou Y, Goodenbour JM, Godley LA, et al. High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma. Biochem Biophys Res Commun Internet] 2009; 385:160–164.
- Goodarzi H, Nguyen HCB, Zhang S, et al. Modulated expression of specific tRNAs drives gene expression and cancer progression. Cell Internet] 2016; 165:1416–1427. Available from. ;:.
- Weinstein JN, Collisson EA, Mills GB, et al., The Cancer Genome Atlas Research Network. The cancer genome atlas pan-cancer analysis project. Nat Genet. Internet] 2013; 45:1113–1120. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24071849
- Hu Q, Ye Y, Chan L-C, et al. Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression. Nat Immunol. 2019;20:835–851.
- Xiang Y, Ye Y, Lou Y, et al. Comprehensive characterization of alternative polyadenylation in human cancer. J Natl Cancer Inst. 2018;110:379–389.
- Ye Y, Xiang Y, Ozguc FM, et al. The genomic landscape and pharmacogenomic interactions of clock genes in cancer chronotherapy. Cell Syst. 2018;6:314–328.e2.
- Xiang Y, Ye Y, Zhang Z, et al. Maximizing the utility of cancer transcriptomic data. Trends Cancer. 2018;4:823–837.
- Ye Y, Hu Q, Chen H, et al. Characterization of hypoxia-associated molecular features to aid hypoxia-targeted therapy. Nat Metab. 2019;1:431–444.
- Gao J, Aksoy BA, Dogrusoz U, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6(269).
- Cerami E, Gao J, Dogrusoz U, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data: figure 1. Cancer Discov. 2012;2:401–404.
- Li J, Lu Y, Akbani R, et al. TCPA: A resource for cancer functional proteomics data. Nat Methods. 2013;10:1046–1047.
- Gong J, Mei S, Liu C, et al. PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types. Nucleic Acids Res Internet] 2017; Available from: https://academic.oup.com/nar/article/46/D1/D971/4210944
- Ewing B, Green P. Analysis of expressed sequence tags indicates 35,000 human genes. Nat Genet. Internet] 2000; 25:232–234. Available from: http://www.ncbi.nlm.nih.gov/pubmed/10835644.
- Gong J, Li Y, Liu C-J, et al. A pan-cancer analysis of the expression and clinical relevance of small nucleolar RNAs in human cancer. CellReports. Internet] 2017; 21:1968–1981. Available from: https://www.cell.com/cell-reports/fulltext/S2211-1247(17)31533-4.
- Cozen AE, Quartley E, Holmes AD, et al. ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat Methods. 2015;12:879–884.
- Guo Y, Xiong Y, Sheng Q, et al. A micro-RNA expression signature for human NAFLD progression. J Gastroenterol. 2016;51:1022–1030.
- Pundhir S, Gorodkin J. Differential and coherent processing patterns from small RNAs. Sci Rep. Internet] 2015; 5:12062. Available from: https://www.nature.com/articles/srep12062.
- Pang YLJ, Abo R, Levine SS, et al. Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number. Nucleic Acids Res. 2014;42(22).
- Krishnan P, Ghosh S, Wang B, et al. Genome-wide profiling of transfer RNAs and their role as novel prognostic markers for breast cancer. Nat Publ Gr Internet] 2016;:1–12. Available from. ;. DOI:10.1038/srep32843.
- Danielson KM, Rubio R, Abderazzaq F, et al. High throughput sequencing of extracellular RNA from human plasma. PLoS One. 2017;12:1–18.
- Beck D, Ayers S, Wen J, et al. Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes. BMC Med Genomics. Internet] 2011; 4:19.Available from: https://bmcmedgenomics.biomedcentral.com/articles/10.1186/1755-8794-4-19.
- Sheng Q, Vickers K, Zhao S, et al. Multi-perspective quality control of Illumina RNA sequencing data analysis. Brief Funct Genomics. Internet] 2016; 16:elw035. Available from: https://academic.oup.com/bfg/article-lookup/doi/10.1093/bfgp/elw035.
- Zhong J, Xiao C, Gu W, et al. Transfer RNAs mediate the rapid adaptation of escherichia coli to oxidative stress. PLoS Genet. 2015;11:1–24.
- Guo Y, Bosompem A, Mohan S, et al. Transfer RNA detection by small RNA deep sequencing and disease association with myelodysplastic syndromes. BMC Genomics. Internet] 2015; 16:727. Available from: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1929-y.
- Zhang Z, Ye Y, Gong J, et al. Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers. Commun Biol. 2018;1(234).
- Robinson M, Oshlack A, Halsall JA, et al. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. Internet] 2010; 11:R25.Available from: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-3-r25.
- Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009;26:139–140.