Mapping rRNA 2’-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants

References

• Decatur WA, Fournier MJ. rRNA modifications and ribosome function. Trends Biochem Sci. 2002;27(7):344–351.
   PubMed Web of Science ®Google Scholar
• Polikanov YS, Melnikov SV, Soll D, et al. Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat Struct Mol Biol. 2015;22(4):342–344.
   PubMed Web of Science ®Google Scholar
• Sharma S, Lafontaine DL. ‘View from a bridge’: a new perspective on eukaryotic rrna base modification. Trends Biochem Sci. 2015;40(10):560–575.
   PubMed Web of Science ®Google Scholar
• Sloan KE, Warda AS, Sharma S, et al. Tuning the ribosome: the influence of rRNA modification on eukaryotic ribosome biogenesis and function. RNA Biol. 2017;14(9):1138–1152.
   PubMed Web of Science ®Google Scholar
• Blanchard SC, Puglisi JD. Solution structure of the A loop of 23S ribosomal RNA. Proc Natl Acad Sci USA. 2001;98:3720–3725.
   Google Scholar
• Liang XH, Liu Q, Fournier MJ. Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing. RNA. 2009;15:1716–1728.
   Google Scholar
• Erales J, Marchand V, Panthu B, et al. Evidence for rRNA 2ʹ-O-methylation plasticity: control of intrinsic translational capabilities of human ribosomes. Proc Natl Acad Sci U S A. 2017;114(49):12934–12939.
   PubMed Web of Science ®Google Scholar
• Marcel V, Ghayad SE, Belin S, et al. p53 acts as a safeguard of translational control by regulating fibrillarin and rRNA methylation in cancer. Cancer Cell. 2013;24(3):318–330. .
   PubMed Web of Science ®Google Scholar
• Monaco PL, Marcel V, Diaz JJ, et al. 2ʹ-O-Methylation of Ribosomal RNA: towards an Epitranscriptomic control of translation? Biomolecules. 2018;8(4):1–13.
   Web of Science ®Google Scholar
• Ayadi L, Galvanin A, Pichot F, et al. RNA ribose methylation (2ʹ-O-methylation): occurrence, biosynthesis and biological functions. Biochim Biophys Acta Gene Regul Mech. 2019;1862(3):253–269.
   PubMed Web of Science ®Google Scholar
• Massenet S, Bertrand E, Verheggen C. Assembly and trafficking of box C/D and H/ACA snoRNPs. RNA Biol. 2017;14(6):680–692.
   PubMed Web of Science ®Google Scholar
• Watkins NJ, Bohnsack MT. The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. Wiley Interdiscip Rev RNA. 2012;3(3):397–414.
   PubMed Web of Science ®Google Scholar
• Yu G, Zhao Y, Li H. The multistructural forms of box C/D ribonucleoprotein particles. RNA. 2018;24(12):1625–1633.
   PubMed Web of Science ®Google Scholar
• Brown JW, Clark GP, Leader DJ, et al. Multiple snoRNA gene clusters from Arabidopsis. RNA. 2001;7(12):1817–1832.
   PubMed Web of Science ®Google Scholar
• Qu LH, Meng Q, Zhou H, et al. Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana. Nucleic Acids Res. 2001;29(7):1623–1630.
   PubMed Web of Science ®Google Scholar
• Brown JW, Echeverria M, Qu LH. Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci. 2003;8(1):42–49.
   PubMed Web of Science ®Google Scholar
• Chen HM, Wu SH. Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis. Nucleic Acids Res. 2009;37(9):e69.
   PubMed Web of Science ®Google Scholar
• Kim SH, Spensley M, Choi SK, et al. Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli. Nucleic Acids Res. 2010;38(9):3054–3067.
   PubMed Web of Science ®Google Scholar
• Chen CL, Liang D, Zhou H, et al. The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa. Nucleic Acids Res. 2003;31(10):2601–2613.
   PubMed Web of Science ®Google Scholar
• Liu TT, Zhu D, Chen W, et al. A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa. Mol Plant. 2013;6(3):830–846.
   PubMed Web of Science ®Google Scholar
• Patra Bhattacharya D, Canzler S, Kehr S, et al. Phylogenetic distribution of plant snoRNA families. BMC Genomics. 2016;17(1):1–12.
   PubMedGoogle Scholar
• Zhu P, Wang Y, Qin N, et al. Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesi. Proc Natl Acad Sci U S A. 2016;113(42):11967–11972.
   PubMed Web of Science ®Google Scholar
• Rodor J, Jobet E, Bizarro J, et al. AtNUFIP, an essential protein for plant development, reveals the impact of snoRNA gene organisation on the assembly of snoRNPs and rRNA methylation in Arabidopsis thaliana. Plant J. 2011;65(5):807–819.
   PubMed Web of Science ®Google Scholar
• Piekna-Przybylska D, Decatur WA, Fournier MJ. The 3D rRNA modification maps database: with interactive tools for ribosome analysis. Nucleic Acids Res. 2008;36: D178–D183.
   PubMed Web of Science ®Google Scholar
• Barneche F, Gaspin C, Guyot R, et al. Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2ʹ-O-methylation sites. J Mol Biol. 2001;311(1):57–73.
   PubMed Web of Science ®Google Scholar
• Marchand V, Blanloeil-Oillo F, Helm M, et al. Illumina-based RiboMethSeq approach for mapping of 2ʹ-O-Me residues in RNA. Nucleic Acids Res. 2016;44(16):e135.
   PubMed Web of Science ®Google Scholar
• Gruendler P, Unfried I, Pointner R, et al. Nucleotide sequence of the 25S-18S ribosomal gene spacer from Arabidopsis thaliana. Nucleic Acids Res. 1989;17(15):6395–6396.
   PubMed Web of Science ®Google Scholar
• Unfried I, Gruendler P. Nucleotide sequence of the 5.8S and 25S rRNA genes and of the internal transcribed spacers from Arabidopsis thaliana. Nucleic Acids Res. 1990;18(13):4011.
   PubMed Web of Science ®Google Scholar
• Unfried I, Stocker U, Gruendler P. Nucleotide sequence of the 18S rRNA gene from Arabidopsis thaliana Co10. Nucleic Acids Res. 1989;17(18):7513.
   PubMed Web of Science ®Google Scholar
• Pichot F, Marchand V, Ayadi L, et al. Holistic optimization of bioinformatic analysis pipeline for detection and quantification of 2ʹ-O-Methylations in RNA by RiboMethSeq. Front Genet. 2020;11:38.
   PubMed Web of Science ®Google Scholar
• Incarnato D, Anselmi F, Morandi E, et al. High-throughput single-base resolution mapping of RNA 2΄-O-methylated residues. Nucleic Acids Res. 2017;45(3):1433–1441.
   PubMed Web of Science ®Google Scholar
• Montacie C, Durut N, Opsomer A, et al. Nucleolar proteome analysis and proteasomal activity assays reveal a link between nucleolus and 26S Proteasome in A. thaliana. Front Plant Sci. 2017;8:1–13.
   PubMed Web of Science ®Google Scholar
• Pontvianne F, Carpentier MC, Durut N, et al. Identification of nucleolus-associated chromatin domains reveals a role for the nucleolus in 3d organization of the a. thaliana genome. Cell Rep. 2016;16(6):1574–1587. .
   PubMed Web of Science ®Google Scholar
• Yoshihama M, Nakao A, Kenmochi N. snOPY: a small nucleolar RNA orthological gene database. BMC Res Notes. 2013;6:6.
   PubMedGoogle Scholar
• Krishnakumar V, Hanlon MR, Contrino S, et al. Araport: the Arabidopsis information portal. Nucleic Acids Res. 2015;43(D1):D1003–1009.
   PubMed Web of Science ®Google Scholar
• Berardini TZ, Reiser L, Li D, et al. The Arabidopsis information resource: making and mining the “gold standard” annotated reference plant genome. Genesis. 2015;53:474–485.
   PubMed Web of Science ®Google Scholar
• Qu G, Kruszka K, Plewka P, et al. Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana. BMC Genomics. 2015;16(1):1–15.
   PubMedGoogle Scholar
• Tajrishi MM, Tuteja R, Tuteja N. Nucleolin: the most abundant multifunctional phosphoprotein of nucleolus. Commun Integr Biol. 2011;4(3):267–275.
   PubMedGoogle Scholar
• Ugrinova I, Petrova M, Chalabi-Dchar M, et al. Multifaceted nucleolin protein and its molecular partners in oncogenesis. Adv Protein Chem Struct Biol. 2018;111:133–164.
   PubMed Web of Science ®Google Scholar
• Kojima H, Suzuki T, Kato T, et al. Sugar-inducible expression of the nucleolin-1 gene of Arabidopsis thaliana and its role in ribosome synthesis, growth and development. Plant J. 2007;49(6):1053–1063. .
   PubMed Web of Science ®Google Scholar
• Petricka JJ, Nelson TM. Arabidopsis nucleolin affects plant development and patterning. Plant Physiol. 2007;144(1):173–186.
   PubMed Web of Science ®Google Scholar
• Pontvianne F, Matia I, Douet J, et al. Characterization of AtNUC l1 reveals a central role of nucleolin in nucleolus organization and silencing of AtNUC L2 gene in Arabidopsis. Mol Biol Cell. 2007;18(2):369–379.
   PubMed Web of Science ®Google Scholar
• Tang Y, Wu Y, Xu R, et al. Identification and exploration of 2ʹ-O-methylation sites in rRNA and mRNA with a novel RNase based platform. bioRxiv. 2020;2020(2003):2027.011759.
   Google Scholar
• Dupuis-Sandoval F, Poirier M, Scott M. The emerging landscape of small nucleolar RNAs in cell biology. WIREs RNA. 2015;6(4):381–397.
   Google Scholar
• Decatur WA, Liang X-H, Piekna-Przybylska D, et al. Identifying effects of snorna-guided modifications on the synthesis and function of the yeast Ribosome. Methods Enzymol. 2007;425:283–316.
   PubMed Web of Science ®Google Scholar
• Wu CC, Zinshteyn B, Wehner KA, et al. High-resolution ribosome profiling defines discrete ribosome elongation states and translational regulation during cellular stress. Mol Cell. 2019;73(959–970):e955.
   Google Scholar
• Camiolo S, Farina L, Porceddu A. The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana. Genetics. 2012;192(2):641–649.
   PubMed Web of Science ®Google Scholar
• Kiss-Laszlo Z, Henry Y, Bachellerie JP, et al. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell. 1996;85(7):1077–1088.
   PubMed Web of Science ®Google Scholar
• Lestrade L, Weber MJ. snoRNA-LBME-db, a comprensive database of human H/ACA and C/D box snoRNA. Nucleic Acid Research. 2006;34(90001):158–162.
   Google Scholar
• Sergeeva OV, Bogdanov AA, Sergiev PV. What do we know about ribosomal RNA methylation in Escherichia coli. Biochimie. 2015;117:110–118.
   PubMed Web of Science ®Google Scholar
• Pintard L, Lecointe F, Bijnicki JM, et al. Trm7p catalyses the formation of two 2ʹ-O-methylriboses in yeast tRNA anticodin loop. Embo J. 2002;21(7):1811–1820.
   PubMed Web of Science ®Google Scholar
• Bachellerie JP, Cavaille J, Huttenhofer A. The expanding snoRNA world. Biochimie. 2002;84(8):775–790.
   PubMed Web of Science ®Google Scholar
• Decatur WA, Fournier MJ. RNA-guided nucleotide modification of ribosomal and other rNAs. J Biol Chem. 2003;278(2):695–698.
   PubMed Web of Science ®Google Scholar
• Sharma S, Yang J, van Nues R, et al. Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation. PLoS Genet. 2017;13(5):e1006804.
   PubMed Web of Science ®Google Scholar
• Beltrame M, Tollervey D. Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. Embo J. 1995;14(17):4350–4356.
   PubMed Web of Science ®Google Scholar
• Borovjagin AV, Gerbi SA. U3 small nucleolar RNA is essential for cleavage at sites 1, 2 and 3 in pre-rRNA and determines which rRNA processing pathway is taken in Xenopus oocytes. J Mol Biol. 1999;286(5):1347–1363.
   PubMed Web of Science ®Google Scholar
• Saez-Vasquez J, Caparros-Ruiz D, Barneche F, et al. A plant snoRNP complex containing snoRNAs, fibrillarin, and nucleolin-like proteins is competent for both rRNA gene binding and pre-rRNA processing in vitro. Mol Cell Biol. 2004;24(16):7284–7297.
   PubMed Web of Science ®Google Scholar
• Consortium TR. RNAcentral: a hub of information for non-coding RNA sequences. NAR. 2019;47(D1):D221–D229.
   PubMed Web of Science ®Google Scholar
• Streit D, Shanmugam T, Garbelyanski A, et al. The existence and localization of nuclear snoRNAs in Arabidopsis thaliana revisited. Plants (Basel). 2020;9(8):9.
   Google Scholar
• Wang Y, Li H, Sun Q, et al. Characterization of small rnas derived from trnas, rrnas and snornas and their response to heat stress in wheat seedlings. PLoS One. 2016;11(3):e0150933.
   PubMed Web of Science ®Google Scholar
• Zheng J, Zeng E, Du Y, et al. Temporal small rna expression profiling under drought reveals a potential regulatory role of small nucleolar rnas in the drought responses of maize. Plant Genome. 2019;12(1):1–15. .
   PubMed Web of Science ®Google Scholar
• Falaleeva M, Welden JR, Duncan MJ, et al. C/D-box snoRNAs form methylating and non-methylating ribonucleoprotein complexes: old dogs show new tricks. Bioessays. 2017;39(6):1–10.
   Web of Science ®Google Scholar
• Stepanov GA, Filippova JA, Komissarov AB, et al. Regulatory role of small nucleolar RNAs in human diseases. Biomed Res Int. 2015;2015:206849.
   PubMed Web of Science ®Google Scholar
• McKeegan KS, Debieux CM, Boulon S, et al. A dynamic scaffold of pre-snoRNP factors facilitates human box C/D snoRNP assembly. Mol Cell Biol. 2007;27(19):6782–6793.
   PubMed Web of Science ®Google Scholar
• Dimitrova DG, Teysset L, Carre C. RNA 2ʹ-O-Methylation (nm) modification in human diseases. Genes (Basel). 2019;10(2):1–23.
   Web of Science ®Google Scholar
• Bizarro J, Charron C, Boulon S, et al. Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control. J Cell Biol. 2014;7:1–18.
   Google Scholar
• Rothe B, Manival X, Rolland N, et al. Implication of the box C/D snoRNP assembly factor Rsa1p in U3 snoRNP assembly. Nucleic Acids Res. 2017;45(12):7455–7473.
   PubMed Web of Science ®Google Scholar
• Soeno Y, Taya Y, Stasyk T, et al. Identification of novel ribonucleo-protein complexes from the brain-specific snoRNA MBII-52. RNA. 2010;16(7):1293–1300.
   PubMed Web of Science ®Google Scholar
• Verheggen C, Lafontaine DL, Samarsky D, et al. Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments. Embo J. 2002;21(11):2736–2745.
   PubMed Web of Science ®Google Scholar
• Pontvianne F, Abou-Ellail M, Douet J, et al. Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana. PLoS Genet. 2010;6(11):1–13. .
   Web of Science ®Google Scholar
• Dsouza M, Larsen N, Overbeek R. Searching for patterns in genomic data. Trends Genet. 1997;13(12):497–498.
   PubMed Web of Science ®Google Scholar
• Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10–12.
   Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359.
   PubMed Web of Science ®Google Scholar
• Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol 2001;29:24–26.
   Google Scholar