Abstract
Key message
The manuscript by Alves et al. entitled “Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants” describes the identification and characterization of tRNAderived sRNA fragments in plants. By combining bioinformatic analysis and genetic and molecular approaches, we show that tRF biogenesis does not rely on canonical microRNA/siRNA processing machinery (i.e., independent of DICER-LIKE proteins). Moreover, we provide evidences that the Arabidopsis S-like Ribonuclease 1 (RNS1) might be involved in the biogenesis of tRFs. Detailed analyses showed that plant tRFs are sorted into different types of ARGONAUTE proteins and that they have potential target candidate genes. Our work advances the understanding of the tRF biology in plants by providing evidences that plant and animal tRFs shared common features and raising the hypothesis that an interplay between tRFs and other sRNAs might be important to fine-tune gene expression and protein biosynthesis in plant cells.
Abstract
Small RNA (sRNA) fragments derived from tRNAs (3′-loop, 5′-loop, anti-codon loop), named tRFs, have been reported in several organisms, including humans and plants. Although they may interfere with gene expression, their biogenesis and biological functions in plants remain poorly understood. Here, we capitalized on small RNA sequencing data from distinct species such as Arabidopsis thaliana, Oryza sativa, and Physcomitrella patens to examine the diversity of plant tRFs and provide insight into their properties. In silico analyzes of 19 to 25-nt tRFs derived from 5′ (tRF-5s) and 3′CCA (tRF-3s) tRNA loops in these three evolutionary distant species showed that they are conserved and their abundance did not correlate with the number of genomic copies of the parental tRNAs. Moreover, tRF-5 is the most abundant variant in all three species. In silico and in vivo expression analyses unraveled differential accumulation of tRFs in Arabidopsis tissues/organs, suggesting that they are not byproducts of tRNA degradation. We also verified that the biogenesis of most Arabidopsis 19–25 nt tRF-5s and tRF-3s is not primarily dependent on DICER-LIKE proteins, though they seem to be associated with ARGONAUTE proteins and have few potential targets. Finally, we provide evidence that Arabidopsis ribonuclease RNS1 might be involved in the processing and/or degradation of tRFs. Our data support the notion that an interplay between tRFs and other sRNAs might be important to fine tune gene expression and protein biosynthesis in plant cells.
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References
Asha S, Soniya EV (2016) Transfer RNA derived small RNAs targeting defense responsive genes are induced during Phytophthora capsici infection in Black Pepper (Piper nigrum L.). Front Plant Sci 7:1–16. doi:10.3389/fpls.2016.00767
Asman A, Vetukuri RR, Jahan SN, Fogelqvist J, Corcoran P, Avrova AO, Whisson SC, Dixelius C (2014) Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection. BMC Microbiol 14:308. doi:10.1186/s12866-014-0308-1
Bariola PA, Howard CJ, Taylor CB, Verburg MT, Jaglan VD, Green PJ (1994) The Arabidopsis ribonuclease gene RNS1 is tightly controlled in response to phosphate limitation. Plant J 6:673–685. doi:10.1046/j.1365-313X.1994.6050673.x
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A (2013) NCBI GEO: archive for functional genomics data sets—Update. Nucleic Acids Res 41:991–995. doi:10.1093/nar/gks1193
Begcy K, Mariano ED, Mattiello L, Nunes AV, Mazzafera P, Maia IG, Menossi M (2011) An Arabidopsis mitochondrial uncoupling protein confers tolerance to drought and salt stress in transgenic tobacco plants. PLoS One 6:e23776. doi:10.1371/journal.pone.0023776
Buhler M, Spies N, Bartel DP, Moazed D (2008) TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol 15:1015–1023. doi:10.1038/nsmb.1481
Cai P, Piao X, Hao L, Liu S, Hou N, Wang H, Chen Q (2013) A deep analysis of the small non-coding RNA population in Schistosoma japonicum eggs. PLoS One. doi:10.1371/journal.pone.0064003
Chan PP, Lowe TM (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37:93–97. doi:10.1093/nar/gkn787
Chen C-J, Liu Q, Zhang Y-C, Qu L-H, Chen Y-Q, Gautheret D (2011) Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus. RNA Biol 8:538–547. doi:10.4161/rna.8.3.15199
Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JWS, Green PJ, Barton GJ, Hutvagner G (2009) Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 15:2147–2160. doi:10.1261/rna.1738409
Dai X, Zhao PX (2011) PsRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:155–159. doi:10.1093/nar/gkr319
Dong Z, Han M-H, Fedoroff N (2008) The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc Natl Acad Sci USA 105:9970–9975. doi:10.1073/pnas.0803356105
Duarte GT, Matiolli CC, Pant BD, Schlereth A, Scheible WR, Stitt M, Vicentini R, Vincentz M (2013) Involvement of microRNA-related regulatory pathways in the glucose-mediated control of Arabidopsis early seedling development. J Exp Bot 64:4301–4312. doi:10.1093/jxb/ert239
Emara MM, Ivanov P, Hickman T, Dawra N, Tisdale S, Kedersha N, Hu GF, Anderson P (2010) Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J Biol Chem 285:10959–10968. doi:10.1074/jbc.M109.077560
Farazi T a, Juranek S a, Tuschl T (2008) The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135:1201–1214. doi:10.1242/dev.005629
Fu Y, Lee I, Lee YS, Bao X (2015) Small non-coding transfer RNA-Derived RNA fragments (tRFs): their biogenesis, function and implication in human diseases. Genomics Inform 13:94. doi:10.5808/GI.2015.13.4.94
Gebetsberger J, Polacek N (2013) Slicing tRNAs to boost functional ncRNA diversity. RNA Biol 10:1798–1806. doi:10.4161/rna.27177
Gebetsberger J, Zywicki M, Künzi A, Polacek N (2012) tRNA-derived fragments target the ribosome and function as regulatory non-coding RNA in Haloferax volcanii. Archaea 2012:1–11. doi:10.1155/2012/260909
German MA, Pillay M, Jeong D-H, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26:941–946. doi:10.1038/nbt1417
Hackenberg M, Huang P-J, Huang C-Y, Shi B-J, Gustafson P, Langridge P (2012) A comprehensive expression profile of MicroRNAs and other classes of non-coding small RNAs in barley under phosphorous-deficient and -sufficient conditions. DNA Res 1–17. doi:10.1093/dnares/dss037
Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA (2010) Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16:673–695. doi:10.1261/rna.2000810
Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, Jacobsen SE (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet 38:721–725. doi:10.1038/ng1804
Hillwig MS, LeBrasseur ND, Green PJ, MacIntosh GC (2008) Impact of transcriptional, ABA-dependent, and ABA-independent pathways on wounding regulation of RNS1 expression. Mol Genet Genomics 280:249–261. doi:10.1007/s00438-008-0360-3
Honda S, Shigematsu M, Morichika K, Telonis AG, Kirino Y (2015) Four-leaf clover qRT-PCR: a convenient method for selective quantification of mature tRNA. RNA Biol 12:501–508. doi:10.1080/15476286.2015.1031951
Hopper AK, Shaheen HH (2008) A decade of surprises for tRNA nuclear-cytoplasmic dynamics. Trends Cell Biol 18:98–104. doi:10.1016/j.tcb.2008.01.001
Hsieh L-C, Lin S-I, Shih AC-C, Chen J-W, Lin W-Y, Tseng C-Y, Li W-H, Chiou T-J (2009) Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol 151:2120–2132. doi:10.1104/pp.109.147280
Hurto RL (2011) Unexpected functions of tRNA and tRNA processing enzymes. In: Collins LJ (ed) RNA infrastructure and networks. Landes Bioscience and Springer Science, pp 137–155
Ivanov P, Emara MM, Villen J, Gygi SP, Anderson P (2011) Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell 43:613–623. doi:10.1016/j.molcel.2011.06.022
Kellner S, Burhenne J, Helm M (2010) Detection of RNA modifications. RNA Biol 7(2):237–247
Kenrick P, Crane PR (1997) The origin and early evolution of plants on land. Nature 389:33–39. doi:10.1038/37918
Kim S, Choi K, Park C, Hwang HJ, Lee I (2006) SUPPRESSOR OF FRIGIDA4, encoding a C2H2-Type zinc finger protein, represses flowering by transcriptional activation of Arabidopsis FLOWERING LOCUS C. Plant Cell 18(11):2985-2998
Kumar P, Anaya J, Mudunuri SB, Dutta A (2014) 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 12:1–14
Lai Z, Schluttenhofer CM, Bhide K, Shreve J, Thimmapuram J, Lee SY, Yun D-J, Mengiste T (2014) MED18 interaction with distinct transcription factors regulates multiple plant functions. Nat Commun 5:3064. doi:10.1038/ncomms4064
Lee YS, Shibata Y, Malhotra A, Dutta A (2009) A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23:2639–2649. doi:10.1101/gad.1837609
Li CF, Henderson IR, Song L, Fedoroff N, Lagrange T, Jacobsen SE (2008) Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana. PLoS Genet 4(2):e27. doi:10.1371/journal.pgen.0040027
Li Z, Ender C, Meister G, Moore PS, Chang Y, John B (2012) Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res 40:6787–6799. doi:10.1093/nar/gks307
Li Q, Hu B, Hu G, Chen C, Niu X, Liu J, Zhou S, Zhang C, Wang Y, Deng Z-F (2016) tRNA-derived small non-coding RNAs in response to Ischemia Inhibit Angiogenesis. Sci Rep 6:20850. doi:10.1038/srep20850
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(−∆∆C(T)) Method. Methods 25:402–408. doi:10.1006/meth.2001.1262
Loss-Morais G, Waterhouse PM, Margis R (2013) Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets. Biol Direct 8:6. doi:10.1186/1745-6150-8-6
MacIntosh GC, Hillwig MS, Meyer A, Flagel L (2010) RNase T2 genes from rice and the evolution of secretory ribonucleases in plants. Mol Genet Genomics 283:381–396. doi:10.1007/s00438-010-0524-9
Megel C, Cognat V, Morelle GR, Ubrig E, Molinier J, Duchêne AM, Drouard L (2015) Arabidopsis tRNA-derived RNA Fragments as a new source of small noncoding RNAs. Poster session presented at: the 26th International Conference on Arabidopsis Research; July 5–9; Paris, France
Mei Y, Yong J, Liu H, Shi Y, Meinkoth J, Dreyfuss G, Yang X (2010) tRNA binds to cytochrome c and inhibits caspase activation. Mol Cell 37:668–678. doi:10.1016/j.molcel.2010.01.023
Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y (2008) Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 5 0 terminal nucleotide. Cell 116–127. doi:10.1016/j.cell.2008.02.034
Moore B, Zhou L, Rolland F, Hall Q, Cheng W-H, Liu Y-X, Hwang I, Jones T, Sheen J (2003) Role of the Arabidopsis glucose sensor HXK1 in nutrient, light, and hormonal signaling. Science 300:332–336. doi:10.1126/science.1080585
Nogueira FTS, Sarkar AK, Chitwood DH, Timmermans MCP (2006) Organ polarity in plants Is specified through the opposing activity of two distinct small regulatory RNAs. Cold Spring Harb Symp Quant Biol 71:157–164. doi:10.1101/sqb.2006.71.045
Olovnikov I, Chan K, Sachidanandam R, Newman D, Aravin A (2013) Bacterial Argonaute samples the Transcriptome to identify Foreign DNA. Mol Cell 51:594–605. doi:10.1016/j.molcel.2013.08.014
Olvedy M, Scaravilli M, Hoogstrate Y, Visakorpi T, Jenster G, Martens-Uzunova ES (2016) A comprehensive repertoire of tRNA-derived fragments in prostate cancer. Oncotarget. 7(17):24766–24777. doi:10.18632/oncotarget.8293.
Ortiz-Morea FA, Vicentini R, Silva GFF, Silva EM, Carrer H, Rodrigues AP, Nogueira FTS (2013) Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth. J Exp Bot 64:2307–2320. doi:10.1093/jxb/ert089
Parisien M, Wang X, Pan T (2013) Diversity of human tRNA genes from the 1000-genomes project. RNA Biol 10:1853–1867. doi:10.4161/rna.27361
Phizicky EM, Hopper AK (2010) tRNA biology charges to the front. Genes Dev 24:1832–1860
Prigge MJ, Bezanilla M (2010) Evolutionary crossroads in developmental biology: Physcomitrella patens. Development137(21):3535-3543
Raina M, Ibba M (2014) tRNAs as regulators of biological processes. Front Genet 5:171. doi:10.3389/fgene.2014.00171
Rook F, Hadingham SA, Li Y, Bevan MW (2006) Sugar and ABA response pathways and the control of gene expression. Plant Cell Environ 29:426–434. doi:10.1111/j.1365-3040.2005.01477.x
Rose NR, Klose RJ (2014) Understanding the relationship between DNA methylation and histone lysine methylation. Biochim Biophys Acta—Gene Regul Mech 1839:1362–1372.
Smeets K, Opdenakker K, Remans T, Van Sanden S, Van Belleghem F, Semane B, Horemans N, Guisez Y, Vangronsveld J, Cuypers A (2009) Oxidative stress-related responses at transcriptional and enzymatic levels after exposure to Cd or Cu in a multipollution context. J Plant Physiol 166:1982–1992. doi:10.1016/j.jplph.2009.06.014
Soares AR, Fernandes N, Reverendo M, Araújo HR, Oliveira JL, Moura GM, Santos MA (2015) Conserved and highly expressed tRNA derived fragments in zebrafish. BMC Mol Biol 16:22. doi:10.1186/s12867-015-0050-8
Sobala A, Hutvagner G (2013) Small RNAs derived from the 5′ end of tRNA can inhibit protein translation in human cells. RNA Biol 10:553–563. doi:10.4161/rna.24285
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121
Thompson DM, Lu C, Green PJ, Parker R (2008) tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14:2095–2103. doi:10.1261/rna.1232808
Tuck AC, Tollervey D (2011) RNA in pieces. Trends Genet 27:422–432. doi:10.1016/j.tig.2011.06.001
Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 3:12
Vazquez F, Gasciolli V, Crété P, Vaucheret H (2004) The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr Biol 14:346–351. doi:10.1016/j.cub.2004.01.035
Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2:E104. doi:10.1371/journal.pbio.0020104
Xie Z, Allen E, Wilken A, Carrington JC (2005) DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci USA 102:12984–12989. doi:10.1073/pnas.0506426102
Xiong Y, Steitz TA (2006) A story with a good ending: tRNA 3′-end maturation by CCA-adding enzymes. Curr Opin Struct Biol 16:12–17. doi:10.1016/j.sbi.2005.12.001
Yamasaki S, Ivanov P, Hu G-F, Anderson P (2009) Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol 185:35–42. doi:10.1083/jcb.200811106
Ye R, Chen Z, Lian B, Rowley MJ, Xia N, Chai J, Li Y, He X-J, Wierzbicki AT, Qi Y (2015) A dicer-independent route for biogenesis of siRNAs that direct DNA Methylation in Arabidopsis. Mol Cell 61:1–14. doi:10.1016/j.molcel.2015.11.015
Yeung ML, Bennasser Y, Watashi K, Le SY, Houzet L, Jeang KT (2009) 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 37:6575–6586. doi:10.1093/nar/gkp707
Zhang J-F, Yuan L-J, Shao Y, Du W, Yan D-W, Lu Y-T (2008) The disturbance of small RNA pathways enhanced abscisic acid response and multiple stress responses in Arabidopsis. Plant Cell Environ 31:562–574. doi:10.1111/j.1365-3040.2008.01786.x
Acknowledgments
We thank Dr. Nogueira’s lab members for helpful discussions. This work was supported by the State of Sao Paulo Research Foundation, FAPESP, and National Council of Technological and Scientific Development (CNPq), Brazil (Grants No. 480628/2012-2 and 07/58289-5). CSA was a recipient of a fellowship (No. 2011/19512-6) from the State of Sao Paulo Research Foundation, FAPESP, Brazil.
Author contributions
CSA, GTD, and VFP carried out the molecular biology studies and analyzed the data; RV and CSA carried out the bioinformatic analyzes and MV helped to analyze data; FTSN designed and coordinated the study, and FTSN and CSA wrote the manuscript. All authors read and approved the final manuscript.
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11103_2016_545_MOESM3_ESM.tif
Online Resource 3: Supplemental Figure 1: Distribution and accumulation of 19-25 nt tRF-5s and tRF-3s in evolutionary distant species. (a) Percentage of tRFs discriminated by size (19 to 15 nucleotides) in Arabidopsis, rice and moss. (b) Read counts for tRFs discriminated by size (19 to 15 nucleotides) in Arabidopsis, rice and moss. All read counts were retrieved from publicly available data (see Online Resource 1). RPM, reads per million. At, Arabidopsis thaliana; Os, Oryza sativa; Pp, Physcomitrella patens. (TIF 2646 KB)
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Online Resource 4: Supplemental Figure 2: Conservation of tRF generating sites in plant precursor tRNAs in Arabidopsis (A. thaliana), rice (O.sativa) and moss (P. patens). The logos were done by using the available tool on WebLogo (http://weblogo.berkeley.edu/logo.cgi) (Crooks et al. 2004). (JPG 1496 KB)
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Online Resource 5: Supplemental Figure 3: Validation of tRF-5s and tRF-3s in Arabidopsis. (a) Dissociation curves of real-time PCR amplification of primers of tRF-5s ArgTCG and ArgCCT, as well as tRF-3s SerGGA and TyrGTA. (b) Stem-loop reverse transcription polymerase chain reaction (PCR). The sizes of the PCR products were approximately 60 nt. “M” indicates low molecular weight DNA ladder (NEB). (c) Sequence alignments of cloned tRFs. Arrows indicate vector sequence. (JPG 3236 KB)
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Online Resource 8: Supplemental Figure4: Accumulation patterns of specific tRFs in Col-0 (WT), dcl2, dcl3, and dcl4 seedlings. Expression values in WT were set to one. Values are mean ± SD of at least three biological replicates. Changes in transcript accumulation marked with an asterisk were considered significant with p ≤ 0.05 according to Student’s t-test (two tailed). Actin2 was used as an endogenous control. R.E, relative expression. (TIF 1517 KB)
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Online Resource 9: Supplemental Figure 5: Accumulation patterns of specific tRF-5s in rice (WT) as well as dcl1 and dcl3 mutants. Read counts for tRF-5s ArgCCT (black) and ArgTCG (white) in rice dcl1 and dcl3 mutants comparing with WT. Read counts were retrieved from publicly available data (see Online Resource 1). RPM, reads per million. (TIF 443 KB)
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Online Resource 10: Supplemental Figure 6: Sequence analyses of RNS1-like proteins. (a) Alignment of Arabidopsis RNS1 (AtRNS1) and RNS1-like proteins (b) Unrooted phylogenetic three was construted by using protein sequences given in (a). Alignments and phylogenetic three were done by using MEGA version 5.05 program (Tamura et al. 2011). Accession numbers: Arabidopsis thaliana RNS1 (AtRNS1), AAM63798.1; Brassica rapa RNS1-like (BrRNS1), XP_009129105.1; Camelina sativa RNS1-like (CsRNS1-like), XP_010502310.1; Jatropha curcas RNS1-like (JcRNS1-like), XP_012067650.1; Malus domestica RNS LE-like (MdRNS LE), XP_008339897.1; Eucalyptus grandis RNS1-like (EgRNS1-like), XP_010066907.1; Theobroma cacao RNS1 (TcRNS1), XP_007046081.1; Oryza sativa Japonica Group RNS-LE (OsRNS-LE), XP_015650871.1; Physcomitrella patens RNS predicted (PpRNS predicted), XP_001763141.1; Homo sapiens Angiogenin (HsANGIOGENIN), AAA51678.1. (JPG 1143 KB)
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Online Resource 11: Supplemental Figure 7: Genotyping of rns1-1 mutant plants. Top panel: Schematic representation of the T-DNA insertion in the promoter region of RNS1 locus (At2g02990). Arrows on top of the RNS1 locus represent primers used in the PCR genotyping. Gray bars represent promoter, 5’-UTR and 3’-UTR regions. Black bars represent exons. White arrows indicate the direction of the transcription. Bottom panel: agarose gel showing genomic PCR products for WT and rns1-1 homozygous leaf tissue samples. (JPG 629 KB)
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Online Resource 12: Supplemental Figure 8: Accumulation patterns of representative microRNAs (miR156, miR160, miR166, and miR172) in distinct Arabidopsis AGOs. Read counts were retrieved from publicly available data (see Online Resource 1). RPM, reads per million. (TIF 405 KB)
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Online Resource 13: Supplemental Figure 9: Potential targets for Arabidopsis tRFs. (a) Most abundant AGO1-associated tRFs and their potential target genes as well as known AGO1-associated microRNAs and their well-established target genes. Targets were identified by psRNATarget (Dai and Zhao 2011). Underlined bold nucleotides indicated potential (for tRFs) and experimentally confirmed (for miRNAs) cleavage sites based on degradome analysis. (b) Schematic representation of the potential complementary site for 24-nt tRF-3 LeuCAA on SUF4 locus. (JPG 1763 KB)
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Alves, C.S., Vicentini, R., Duarte, G.T. et al. Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants. Plant Mol Biol 93, 35–48 (2017). https://doi.org/10.1007/s11103-016-0545-9
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DOI: https://doi.org/10.1007/s11103-016-0545-9