A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis

References

• Kung JTY, Colognori D, Lee JT. Long noncoding RNAs: Past, present, and future. Genetics. 2013;193(3):651−669. doi:10.1534/genetics.112.146704
   Web of Science ®Google Scholar
• Engreitz JM, Ollikainen N, Guttman M. Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol. 2016;17(12):756−770. doi:10.1038/nrm.2016.126
   PubMed Web of Science ®Google Scholar
• Liu X, Hao L, Li D, et al. Long Non-coding RNAs and Their Biological Roles in Plants. Genomics Proteomics Bioinformatics. 2015;13(3):137−147. doi:10.1016/j.gpb.2015.02.003
   Web of Science ®Google Scholar
• Swiezewski S, Liu F, Magusin A, et al. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature. 2009;462(7274):799−802. doi:10.1038/nature08618
   PubMed Web of Science ®Google Scholar
• Heo JB, Sung S. Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA. Science (80-). 2011;331(6013):76−79. doi:10.1126/science.1197349
   Web of Science ®Google Scholar
• Ariel F, Jegu T, Latrasse D, et al. Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop. Mol Cell. 2014;55(3):383−396. doi:10.1016/j.molcel.2014.06.011
   Web of Science ®Google Scholar
• Ben Amor B, Wirth S, Merchan F, et al. Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res. 2009;19(1):57−69. doi:10.1101/gr.080275.108
   PubMed Web of Science ®Google Scholar
• Wierzbicki AT, Haag JR, Pikaard CS. Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes. Cell. 2008;135(4):635−648. doi:10.1016/j.cell.2008.09.035
   Web of Science ®Google Scholar
• Franco-Zorrilla JM, Valli A, Todesco M, et al. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet. 2007;39(8):1033−1037. doi:10.1038/ng2079
   Web of Science ®Google Scholar
• Wang Y, Fan X, Lin F, et al. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc Natl Acad Sci. 2014;111(28):10359−10364. doi:10.1073/pnas.1409457111
   Web of Science ®Google Scholar
• Ding J, Lu Q, Ouyang Y, et al. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci U S A. 2012;109(7):2654−2659. doi:10.1073/pnas.1121374109
   Web of Science ®Google Scholar
• Campalans A, Kondorosi A, Crespi M. Enod40, a Short Open Reading Frame-Containing mRNA, Induces Cytoplasmic Localization of a Nuclear RNA Binding Protein in Medicago truncatula. Plant Cell. 2004;16(4):1047−1059. doi:10.1105/tpc.019406
   Web of Science ®Google Scholar
• Bardou F, Ariel F, Simpson CG, et al. Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis. Dev Cell. 2014;30(2):166−176. doi:10.1016/j.devcel.2014.06.017
   Web of Science ®Google Scholar
• Seo JS, Sun H-X, Park BS, et al. ELF18-INDUCED LONG-NONCODING RNA Associates with Mediator to Enhance Expression of Innate Immune Response Genes in Arabidopsis. Plant Cell. 2017;29(5):1024−1038. doi:10.1105/tpc.16.00886
   PubMed Web of Science ®Google Scholar
• Taylor CB, Green PJ. Identification and characterization of genes with unstable transcripts (GUTs) in tobacco. Plant Mol Biol. 1995;28(1):27−38.
   PubMed Web of Science ®Google Scholar
• Ambro van Hoof, James P, Kastenmayer CBT and PJG. GUT15 cDNAs from Tobacco (Accession No. U84972) and Arabidopsis (Accession No. U84973) Correspond to Transcripts with Unusual Metabolism and a Short Conserved ORF. Plant Physiol. 1997;113:1004.
   Google Scholar
• Söll D, RajBhandary U. TRNA: Structure, Biosynthesis, and Function. ASM Press; 1995.
   Google Scholar
• Lamesch P, Berardini TZ, Li D, et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 2012;40(Database issue):D1202−10. doi:10.1093/nar/gkr1090
   PubMedGoogle Scholar
• Thompson A, Zielezinski A, Plewka P, et al. tRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana. Plant Cell Physiol. 2018;59(1):e1−e1. doi:10.1093/pcp/pcx173
   Web of Science ®Google Scholar
• Kmieciak M, Simpson CG, Lewandowska D, et al. Cloning and characterization of two subunits of Arabidopsis thaliana nuclear cap-binding complex. Gene. 2002;283(1):171−183. doi:10.1016/S0378-1119(01)00859-9
   Web of Science ®Google Scholar
• Ylstra B, McCormick S. Analysis of mRNA stabilities during pollen development and in BY2 cells. Plant J. 1999;20(1):101−108. doi:10.1046/j.1365-313X.1999.00580.x
   Web of Science ®Google Scholar
• Teramoto H, Toyama T, Takeba G, et al. Noncoding RNA for CR20, a cytokinin-repressed gene of cucumber. Plant Mol Biol. 1996;32(5):797−808. doi: doi.org/10.1007/BF00020478
   PubMed Web of Science ®Google Scholar
• MacIntosh GC, Wilkerson C, Green PJ. Identification and Analysis of Arabidopsis Expressed Sequence Tags Characteristic of Non-Coding RNAs. Plant Physiol. 2001;127(November):765−776. doi:10.1104/pp.010501.cient
   Google Scholar
• Liu J, Jung C, Xu J, et al. Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis. Plant Cell. 2012;24(11):4333−4345. doi:10.1105/tpc.112.102855
   Web of Science ®Google Scholar
• Cheng Lu, Gustavo MacIntosh PG. Two Non-coding RNAs, AtGUT15 and AtCR20, modulate the ABA response at high temperature in Arabidopsis. 501707136
   Google Scholar
• Vörtler S, Mörl M. tRNA-nucleotidyltransferases: Highly unusual RNA polymerases with vital functions. FEBS Lett. 2010;584(2):297−302. doi:10.1016/j.febslet.2009.10.078
   PubMed Web of Science ®Google Scholar
• Shi PY, Weiner AM, Maizels N. A top-half tDNA minihelix is a good substrate for the eubacterial CCA-adding enzyme. RNA. 1998;4(3):276−284.
   Web of Science ®Google Scholar
• Li Z, Sun Y, Thurlow DL. RNA minihelices as model substrates for ATP/CTP:tRNA nucleotidyltransferase. Biochem J. 1997;327(Pt 3):847−851.
   Google Scholar
• Dreher TW. Role of tRNA-like structures in controlling plant virus replication. Virus Res. 2009;139(2):217−229. doi:10.1016/j.virusres.2008.06.010
   Web of Science ®Google Scholar
• Keiler KC, Waller PRH, Sauer RT. Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA. Science (80- ). 1996;271(5251):990−993. doi:10.1126/science.271.5251.990
   Web of Science ®Google Scholar
• Wilusz JE, Freier SM, Spector DL. 3′ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell .2008;135(5):919−932. doi:10.1016/j.cell.2008.10.012
   Web of Science ®Google Scholar
• Sunwoo H, Dinger ME, Wilusz JE, et al. MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 2009;19(3):347−359. doi:10.1101/gr.087775.108
   Web of Science ®Google Scholar
• Zhang B, Mao YS, Diermeier SD, et al. Identification and Characterization of a Class of MALAT1 -like Genomic Loci. Cell Rep. 2017;19(8):1723−1738. doi:10.1016/j.celrep.2017.05.006
   PubMed Web of Science ®Google Scholar
• Aeby E, Ullu E, Yepiskoposyan H, et al. tRNASec is transcribed by RNA polymerase II in Trypanosoma brucei but not in humans. Nucleic Acids Res. 2010;38(17):5833−5843. doi:10.1093/nar/gkq345
   Web of Science ®Google Scholar
• Hsu PY, Calviello L, Wu H-YL, et al. Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proc Natl Acad Sci. 2016;113(45):E7126−E7135. doi:10.1073/pnas.1614788113
   PubMed Web of Science ®Google Scholar
• Rohrig H, Schmidt J, Miklashevichs E, et al. Soybean ENOD40 encodes two peptides that bind to sucrose synthase. Proc Natl Acad Sci U S A. 2002;99(4):1915−1920. doi:10.1073/pnas.022664799
   Web of Science ®Google Scholar
• Carlevaro-Fita J, Rahim A, Guigó R, et al. Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells. RNA .2016;22(6):867–882. doi:10.1261/rna.053561.115
   PubMed Web of Science ®Google Scholar
• Zhang W, Thieme CJ, Kollwig G, et al. tRNA-Related Sequences Trigger Systemic mRNA Transport in Plants. Plant Cell. 2016;28(6):1237−1249. doi:10.1105/tpc.15.01056
   Web of Science ®Google Scholar
• Thieme CJ, Rojas-Triana M, Stecyk E, et al. Endogenous Arabidopsis messenger RNAs transported to distant tissues. Nat Plants. 2015;1(4):15025. doi:10.1038/nplants.2015.25
   PubMed Web of Science ®Google Scholar
• Knop K, Stepien A, Barciszewska-Pacak M, et al. Active 5′ splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes. Nucleic Acids Res. 2016;323(5):gkw895. doi:10.1093/nar/gkw895
   Google Scholar
• Curtis MD, Grossniklaus U. A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol. 2003;133(2):462−469. doi:10.1104/pp.103.027979
   Web of Science ®Google Scholar
• Simpson CG, Clark G, Davidson D, et al. Mutation of putative branchpoint consensus sequences in plant introns reduces splicing efficiency. Plant J. 1996;9(3):369−380. doi:10.1046/j.1365-313X.1996.09030369.x
   Web of Science ®Google Scholar
• Lewandowska D, Simpson CG, Clark GP, et al. Determinants of plant U12-dependent intron splicing efficiency. Plant Cell. 2004;16(5):1340−1352. doi:10.1105/tpc.020743
   Web of Science ®Google Scholar
• Bielewicz D, Kalak M, Kalyna M, et al. Introns of plant pri-miRNAs enhance miRNA biogenesis. EMBO Rep. 2013;14(7):622−628. doi:10.1038/embor.2013.62
   Web of Science ®Google Scholar
• Chomczynski P, Sacchi N. The single-step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction: twenty-something years on. Nat Protoc. 2006;1(2):581−585. doi:10.1038/nprot.2006.83
   Web of Science ®Google Scholar
• Kruszka K, Pacak A, Swida-Barteczka A, et al. Developmentally regulated expression and complex processing of barley pri-microRNAs. BMC Genomics. 2013;14(1):34. doi:10.1186/1471-2164-14-34
   PubMedGoogle Scholar
• Varkonyi-Gasic E, Wu R, Wood M, et al. Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods. 2007;3:12. doi:10.1186/1746-4811-3-12
   PubMed Web of Science ®Google Scholar
• Gaston KW, Rubio MAT, Alfonzo JD. OXOPAP assay: For selective amplification of aminoacylated tRNAs from total cellular fractions. Methods. 2008;44(2):170−175. doi:10.1016/j.ymeth.2007.10.003
   Web of Science ®Google Scholar
• Crooks G, Hon G, Chandonia J, et al. NCBI GenBank FTP Site\nWebLogo: a sequence logo generator. Genome Res. 2004;14:1188−1190. doi:10.1101/gr.849004.1
   Google Scholar
• Pall GS, Hamilton AJ. Improved northern blot method for enhanced detection of small RNA. Nat Protoc. 2008;3(6):1077−1084. doi:10.1038/nprot.2008.67
   Web of Science ®Google Scholar
• Raczynska KD, Ruepp M-D, Brzek A, et al. FUS/TLS contributes to replication-dependent histone gene expression by interaction with U7 snRNPs and histone-specific transcription factors. Nucleic Acids Res. 2015;43(20):9711−9728. doi:10.1093/nar/gkv794
   Web of Science ®Google Scholar