Abdelhamid,, R. F., Plessy,, C., Yamauchi,, Y., Taoka,, M., de Hoon,, M., Gingeras,, T. R., … Carninci,, P. (2014). Multiplicity of 5′ cap structures present on short RNAs. PLoS One, 9(7), e102895. https://doi.org/10.1371/journal.pone.0102895
Andersen,, E. S., Rosenblad,, M. A., Larsen,, N., Westergaard,, J. C., Burks,, J., Wower,, I. K., … Zwieb,, C. (2006). The tmRDB and SRPDB resources. Nucleic Acids Research, 34, D163–D168. https://doi.org/10.1093/nar/gkj142
Anderson,, P., & Ivanov,, P. (2014). tRNA fragments in human health and disease. FEBS Letters, 588(23), 4297–4304. https://doi.org/10.1016/j.febslet.2014.09.001
Ares,, M., Jr., & Weiser,, B. (1995). Rearrangement of snRNA structure during assembly and function of the spliceosome. Progress in Nucleic Acid Research and Molecular Biology, 50, 131–159.
Bachellerie,, J. P., Cavaille,, J., & Huttenhofer,, A. (2002). The expanding snoRNA world. Biochimie, 84(8), 775–790.
Beggs,, J. D. (2005). Lsm proteins and RNA processing. Biochemical Society Transactions, 33(Pt. 3), 433–438. https://doi.org/10.1042/BST0330433
Belostotsky,, R., Frishberg,, Y., & Entelis,, N. (2012). Human mitochondrial tRNA quality control in health and disease: A channelling mechanism? RNA Biology, 9(1), 33–39. https://doi.org/10.4161/rna.9.1.18009
Bermudez‐Santana,, C., Attolini,, C. S., Kirsten,, T., Engelhardt,, J., Prohaska,, S. J., Steigele,, S., & Stadler,, P. F. (2010). Genomic organization of eukaryotic tRNAs. BMC Genomics, 11, 270. https://doi.org/10.1186/1471-2164-11-270
Bohnsack,, M. T., & Sloan,, K. E. (2018). Modifications in small nuclear RNAs and their roles in spliceosome assembly and function. Biological Chemistry, 399(11), 1265–1276. https://doi.org/10.1515/hsz-2018-0205
Boivin,, V., Deschamps‐Francoeur,, G., Couture,, S., Nottingham,, R. M., Bouchard‐Bourelle,, P., Lambowitz,, A. M., … Abou‐Elela,, S. (2018). Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes. RNA, 24(7), 950–965. https://doi.org/10.1261/rna.064493.117
Boivin,, V., Deschamps‐Francoeur,, G., & Scott,, M. S. (2018). Protein coding genes as hosts for noncoding RNA expression. Seminars in Cell %26 Developmental Biology, 75, 3–12. https://doi.org/10.1016/j.semcdb.2017.08.016
Bortolin‐Cavaille,, M. L., & Cavaille,, J. (2012). The SNORD115 (H/MBII‐52) and SNORD116 (H/MBII‐85) gene clusters at the imprinted Prader‐Willi locus generate canonical box C/D snoRNAs. Nucleic Acids Research, 40(14), 6800–6807. https://doi.org/10.1093/nar/gks321
Brosnan,, C. A., & Voinnet,, O. (2009). The long and the short of noncoding RNAs. Current Opinion in Cell Biology, 21(3), 416–425. https://doi.org/10.1016/j.ceb.2009.04.001
Brow,, D. A., & Guthrie,, C. (1988). Spliceosomal RNA U6 is remarkably conserved from yeast to mammals. Nature, 334(6179), 213–218. https://doi.org/10.1038/334213a0
Brow,, D. A., & Guthrie,, C. (1990). Transcription of a yeast U6 snRNA gene requires a polymerase III promoter element in a novel position. Genes and Development, 4(8), 1345–1356.
Brown,, J. W. (1999). The ribonuclease P database. Nucleic Acids Research, 27(1), 314.
Brown,, J. W., Marshall,, D. F., & Echeverria,, M. (2008). Intronic noncoding RNAs and splicing. Trends in Plant Science, 13(7), 335–342. https://doi.org/10.1016/j.tplants.2008.04.010
Brown,, Y., Abraham,, M., Pearl,, S., Kabaha,, M. M., Elboher,, E., & Tzfati,, Y. (2007). A critical three‐way junction is conserved in budding yeast and vertebrate telomerase RNAs. Nucleic Acids Research, 35(18), 6280–6289. https://doi.org/10.1093/nar/gkm713
Buratti,, E., & Baralle,, D. (2010). Novel roles of U1 snRNP in alternative splicing regulation. RNA Biology, 7(4), 412–419.
Bush,, S. J., Chen,, L., Tovar‐Corona,, J. M., & Urrutia,, A. O. (2017). Alternative splicing and the evolution of phenotypic novelty. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 372(1713), 20150474. https://doi.org/10.1098/rstb.2015.0474
Canella,, D., Praz,, V., Reina,, J. H., Cousin,, P., & Hernandez,, N. (2010). Defining the RNA polymerase III transcriptome: Genome‐wide localization of the RNA polymerase III transcription machinery in human cells. Genome Research, 20(6), 710–721. https://doi.org/10.1101/gr.101337.109
Caputa,, G., & Schaffer,, J. E. (2016). RNA regulation of lipotoxicity and metabolic stress. Diabetes, 65(7), 1816–1823. https://doi.org/10.2337/db16-0147
Cavaille,, J., Buiting,, K., Kiefmann,, M., Lalande,, M., Brannan,, C. I., Horsthemke,, B., … Huttenhofer,, A. (2000). Identification of brain‐specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proceedings of the National Academy of Sciences of the United States of America, 97(26), 14311–14316. https://doi.org/10.1073/pnas.250426397
Cazzola,, M., Rossi,, M., Malcovati,, L., & Associazione Italiana per la Ricerca sul Cancro Gruppo Italiano Malattie Mieloproliferative Investigators. (2013). Biologic and clinical significance of somatic mutations of SF3B1 in myeloid and lymphoid neoplasms. Blood, 121(2), 260–269. https://doi.org/10.1182/blood-2012-09-399725
Chan,, P. P., & Lowe,, T. M. (2016). GtRNAdb 2.0: An expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Research, 44(D1), D184–D189. https://doi.org/10.1093/nar/gkv1309
Chatterjee,, K., Nostramo,, R. T., Wan,, Y., & Hopper,, A. K. (2018). tRNA dynamics between the nucleus, cytoplasm and mitochondrial surface: Location, location, location. Biochimica et Biophysica Acta, Gene Regulatory Mechanisms, 1861(4), 373–386. https://doi.org/10.1016/j.bbagrm.2017.11.007
Chen,, J. L., & Greider,, C. W. (2004). Telomerase RNA structure and function: Implications for dyskeratosis congenita. Trends in Biochemical Sciences, 29(4), 183–192. https://doi.org/10.1016/j.tibs.2004.02.003
Cheng,, Y., Dong,, L., Zhang,, J., Zhao,, Y., & Li,, Z. (2018). Recent advances in microRNA detection. Analyst, 143(8), 1758–1774. https://doi.org/10.1039/C7AN02001E
Chu,, L., Su,, M. Y., Maggi,, L. B., Jr., Lu,, L., Mullins,, C., Crosby,, S., … Tomasson,, M. H. (2012). Multiple myeloma‐associated chromosomal translocation activates orphan snoRNA ACA11 to suppress oxidative stress. Journal of Clinical Investigation, 122(8), 2793–2806. https://doi.org/10.1172/JCI63051
Cole,, C., Sobala,, A., Lu,, C., Thatcher,, S. R., Bowman,, A., Brown,, J. W., … Hutvagner,, G. (2009). Filtering of deep sequencing data reveals the existence of abundant dicer‐dependent small RNAs derived from tRNAs. RNA, 15(12), 2147–2160. https://doi.org/10.1261/rna.1738409
Cordin,, O., Hahn,, D., & Beggs,, J. D. (2012). Structure, function and regulation of spliceosomal RNA helicases. Current Opinion in Cell Biology, 24(3), 431–438. https://doi.org/10.1016/j.ceb.2012.03.004
Crick,, F. H. (1968). The origin of the genetic code. Journal of Molecular Biology, 38(3), 367–379.
Cui,, L., Nakano,, K., Obchoei,, S., Setoguchi,, K., Matsumoto,, M., Yamamoto,, T., … Hiraoka,, N. (2017). Small nucleolar noncoding RNA SNORA23, up‐regulated in human pancreatic ductal adenocarcinoma, regulates expression of spectrin repeat‐containing nuclear envelope 2 to promote growth and metastasis of xenograft tumors in mice. Gastroenterology, 153(1), 292–306.e2. https://doi.org/10.1053/j.gastro.2017.03.050
Davis,, M. P., Carrieri,, C., Saini,, H. K., van Dongen,, S., Leonardi,, T., Bussotti,, G., … Enright,, A. J. (2017). Transposon‐driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution. EMBO Reports, 18(7), 1231–1247. https://doi.org/10.15252/embr.201744059
Decatur,, W. A., Liang,, X. H., Piekna‐Przybylska,, D., & Fournier,, M. J. (2007). Identifying effects of snoRNA‐guided modifications on the synthesis and function of the yeast ribosome. Methods in Enzymology, 425, 283–316. https://doi.org/10.1016/S0076-6879(07)25013-X
Decker,, C. J., Teixeira,, D., & Parker,, R. (2007). Edc3p and a glutamine/asparagine‐rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae. Journal of Cell Biology, 179(3), 437–449. https://doi.org/10.1083/jcb.200704147
Deschamps‐Francoeur,, G., Garneau,, D., Dupuis‐Sandoval,, F., Roy,, A., Frappier,, M., Catala,, M., … Scott,, M. S. (2014). Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency. Nucleic Acids Research, 42(15), 10073–10085. https://doi.org/10.1093/nar/gku664
Dhanoa,, J. K., Sethi,, R. S., Verma,, R., Arora,, J. S., & Mukhopadhyay,, C. S. (2018). Long non‐coding RNA: Its evolutionary relics and biological implications in mammals: A review. Journal of Animal Science and Technology, 60, 25. https://doi.org/10.1186/s40781-018-0183-7
Didychuk,, A. L., Butcher,, S. E., & Brow,, D. A. (2018). The life of U6 small nuclear RNA, from cradle to grave. RNA, 24(4), 437–460. https://doi.org/10.1261/rna.065136.117
Diebel,, K. W., Zhou,, K., Clarke,, A. B., & Bemis,, L. T. (2016). Beyond the ribosome: Extra‐translational functions of tRNA fragments. Biomarker Insights, 11(Suppl. 1), 1–8. https://doi.org/10.4137/BMI.S35904
Dieci,, G., Fiorino,, G., Castelnuovo,, M., Teichmann,, M., & Pagano,, A. (2007). The expanding RNA polymerase III transcriptome. Trends in Genetics, 23(12), 614–622. https://doi.org/10.1016/j.tig.2007.09.001
Dieci,, G., Preti,, M., & Montanini,, B. (2009). Eukaryotic snoRNAs: A paradigm for gene expression flexibility. Genomics, 94(2), 83–88. https://doi.org/10.1016/j.ygeno.2009.05.002
Dong,, X. Y., Guo,, P., Boyd,, J., Sun,, X., Li,, Q., Zhou,, W., & Dong,, J. T. (2009). Implication of snoRNA U50 in human breast cancer. Journal of Genetics and Genomics, 36(8), 447–454. https://doi.org/10.1016/S1673-8527(08)60134-4
Doucet,, A. J., Droc,, G., Siol,, O., Audoux,, J., & Gilbert,, N. (2015). U6 snRNA pseudogenes: Markers of retrotransposition dynamics in mammals. Molecular Biology and Evolution, 32(7), 1815–1832. https://doi.org/10.1093/molbev/msv062
Dupuis‐Sandoval,, F., Poirier,, M., & Scott,, M. S. (2015). The emerging landscape of small nucleolar RNAs in cell biology. WIREs RNA, 6(4), 381–397. https://doi.org/10.1002/wrna.1284
El Yacoubi,, B., Bailly,, M., & de Crecy‐Lagard,, V. (2012). Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Annual Review of Genetics, 46, 69–95. https://doi.org/10.1146/annurev-genet-110711-155641
Esakova,, O., & Krasilnikov,, A. S. (2010). Of proteins and RNA: The RNase P/MRP family. RNA, 16(9), 1725–1747. https://doi.org/10.1261/rna.2214510
Falaleeva,, M., Pages,, A., Matuszek,, Z., Hidmi,, S., Agranat‐Tamir,, L., Korotkov,, K., … Stamm,, S. (2016). Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre‐mRNA splicing. Proceedings of the National Academy of Sciences of the United States of America, 113(12), E1625–E1634. https://doi.org/10.1073/pnas.1519292113
Falaleeva,, M., & Stamm,, S. (2013). Processing of snoRNAs as a new source of regulatory non‐coding RNAs: snoRNA fragments form a new class of functional RNAs. BioEssays, 35(1), 46–54. https://doi.org/10.1002/bies.201200117
Falaleeva,, M., Welden,, J. R., Duncan,, M. J., & Stamm,, S. (2017). C/D‐box snoRNAs form methylating and non‐methylating ribonucleoprotein complexes: Old dogs show new tricks. BioEssays, 39(6), 1–28. https://doi.org/10.1002/bies.201600264
Fang,, P., & Guo,, M. (2017). Structural characterization of human aminoacyl‐tRNA synthetases for translational and nontranslational functions. Methods, 113, 83–90. https://doi.org/10.1016/j.ymeth.2016.11.014
Filipowicz,, W., Pelczar,, P., Pogacic,, V., & Dragon,, F. (1999). Structure and biogenesis of small nucleolar RNAs acting as guides for ribosomal RNA modification. Acta Biochimica Polonica, 46(2), 377–389.
Frankish,, A., Uszczynska,, B., Ritchie,, G. R., Gonzalez,, J. M., Pervouchine,, D., Petryszak,, R., … Harrow,, J. (2015). Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. BMC Genomics, 16(Suppl. 8), S2. https://doi.org/10.1186/1471-2164-16-S8-S2
Frendewey,, D., Barta,, I., Gillespie,, M., & Potashkin,, J. (1990). Schizosaccharomyces U6 genes have a sequence within their introns that matches the B box consensus of tRNA internal promoters. Nucleic Acids Research, 18(8), 2025–2032.
Giege,, R., Juhling,, F., Putz,, J., Stadler,, P., Sauter,, C., & Florentz,, C. (2012). Structure of transfer RNAs: Similarity and variability. WIREs RNA, 3(1), 37–61. https://doi.org/10.1002/wrna.103
Gogakos,, T., Brown,, M., Garzia,, A., Meyer,, C., Hafner,, M., & Tuschl,, T. (2017). Characterizing expression and processing of precursor and mature human tRNAs by hydro‐tRNAseq and PAR‐CLIP. Cell Reports, 20(6), 1463–1475. https://doi.org/10.1016/j.celrep.2017.07.029
Goodarzi,, H., Nguyen,, H. C. B., Zhang,, S., Dill,, B. D., Molina,, H., & Tavazoie,, S. F. (2016). Modulated expression of specific tRNAs drives gene expression and cancer progression. Cell, 165(6), 1416–1427. https://doi.org/10.1016/j.cell.2016.05.046
Gorodkin,, J., Knudsen,, B., Zwieb,, C., & Samuelsson,, T. (2001). SRPDB (signal recognition particle database). Nucleic Acids Research, 29(1), 169–170.
Gossringer,, M., Lechner,, M., Brillante,, N., Weber,, C., Rossmanith,, W., & Hartmann,, R. K. (2017). Protein‐only RNase P function in Escherichia coli: Viability, processing defects and differences between PRORP isoenzymes. Nucleic Acids Research, 45(12), 7441–7454. https://doi.org/10.1093/nar/gkx405
Grummt,, I. (2003). Life on a planet of its own: Regulation of RNA polymerase I transcription in the nucleolus. Genes %26 Development, 17(14), 1691–1702.
Grutzmann,, K., Szafranski,, K., Pohl,, M., Voigt,, K., Petzold,, A., & Schuster,, S. (2014). Fungal alternative splicing is associated with multicellular complexity and virulence: A genome‐wide multi‐species study. DNA Research, 21(1), 27–39. https://doi.org/10.1093/dnares/dst038
Guerrier‐Takada,, C., Gardiner,, K., Marsh,, T., Pace,, N., & Altman,, S. (1983). The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35(3, Pt. 2), 849–857.
Guiro,, J., & Murphy,, S. (2017). Regulation of expression of human RNA polymerase II‐transcribed snRNA genes. Open Biology, 7(6), 1–9. https://doi.org/10.1098/rsob.170073
Haeusler,, R. A., & Engelke,, D. R. (2006). Spatial organization of transcription by RNA polymerase III. Nucleic Acids Research, 34(17), 4826–4836. https://doi.org/10.1093/nar/gkl656
Hall,, A. E., Turnbull,, C., & Dalmay,, T. (2013). Y RNAs: Recent developments. Biomolecular Concepts, 4(2), 103–110. https://doi.org/10.1515/bmc-2012-0050
Harbour,, J. W. (2013). Genomic, prognostic, and cell‐signaling advances in uveal melanoma. American Society of Clinical Oncology Educational Book, 388–391. https://doi.org/10.1200/EdBook_AM.2013.33.388
Harrow,, J., Frankish,, A., Gonzalez,, J. M., Tapanari,, E., Diekhans,, M., Kokocinski,, F., & Hubbard,, T. J. (2012). GENCODE: The reference human genome annotation for the ENCODE project. Genome Research, 22(9), 1760–1774. https://doi.org/10.1101/gr.135350.111
Hesselberth,, J. R. (2013). Lives that introns lead after splicing. WIREs RNA, 4(6), 677–691. https://doi.org/10.1002/wrna.1187
Hinegardner,, R. T., & Engelberg,, J. (1963). Rationale for a universal genetic code. Science, 142(3595), 1083–1085.
Hirose,, T., & Steitz,, J. A. (2001). Position within the host intron is critical for efficient processing of box C/D snoRNAs in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America, 98(23), 12914–12919. https://doi.org/10.1073/pnas.231490998
Hoeppner,, M. P., Denisenko,, E., Gardner,, P. P., Schmeier,, S., & Poole,, A. M. (2018). An evaluation of function of multicopy noncoding RNAs in mammals using ENCODE/FANTOM data and comparative genomics. Molecular Biology and Evolution, 35(6), 1451–1462. https://doi.org/10.1093/molbev/msy046
Hoeppner,, M. P., & Poole,, A. M. (2012). Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. BMC Evolutionary Biology, 12, 183. https://doi.org/10.1186/1471-2148-12-183
Holzmann,, J., Frank,, P., Loffler,, E., Bennett,, K. L., Gerner,, C., & Rossmanith,, W. (2008). RNase P without RNA: Identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell, 135(3), 462–474. https://doi.org/10.1016/j.cell.2008.09.013
Huang,, C., Shi,, J., Guo,, Y., Huang,, W., Huang,, S., Ming,, S., … Yao,, C. (2017). A snoRNA modulates mRNA 3′ end processing and regulates the expression of a subset of mRNAs. Nucleic Acids Research, 45(15), 8647–8660. https://doi.org/10.1093/nar/gkx651
Hudson,, A. J., Moore,, A. N., Elniski,, D., Joseph,, J., Yee,, J., & Russell,, A. G. (2012). Evolutionarily divergent spliceosomal snRNAs and a conserved non‐coding RNA processing motif in Giardia lamblia. Nucleic Acids Research, 40(21), 10995–11008. https://doi.org/10.1093/nar/gks887
Iben,, J. R., & Maraia,, R. J. (2014). tRNA gene copy number variation in humans. Gene, 536(2), 376–384. https://doi.org/10.1016/j.gene.2013.11.049
Irimia,, M., & Roy,, S. W. (2014). Origin of spliceosomal introns and alternative splicing. Cold Spring Harbor Perspectives in Biology, 6(6), a016071. https://doi.org/10.1101/cshperspect.a016071
Itzkovitz,, S., & Alon,, U. (2007). The genetic code is nearly optimal for allowing additional information within protein‐coding sequences. Genome Research, 17(4), 405–412. https://doi.org/10.1101/gr.5987307
Jady,, B. E., Ketele,, A., & Kiss,, T. (2012). Human intron‐encoded Alu RNAs are processed and packaged into Wdr79‐associated nucleoplasmic box H/ACA RNPs. Genes %26 Development, 26(17), 1897–1910. https://doi.org/10.1101/gad.197467.112
Jarrous,, N., & Gopalan,, V. (2010). Archaeal/eukaryal RNase P: Subunits, functions and RNA diversification. Nucleic Acids Research, 38(22), 7885–7894. https://doi.org/10.1093/nar/gkq701
Jawdekar,, G. W., & Henry,, R. W. (2008). Transcriptional regulation of human small nuclear RNA genes. Biochimica et Biophysica Acta, 1779(5), 295–305. https://doi.org/10.1016/j.bbagrm.2008.04.001
Jorjani,, H., Kehr,, S., Jedlinski,, D. J., Gumienny,, R., Hertel,, J., Stadler,, P. F., … Gruber,, A. R. (2016). An updated human snoRNAome. Nucleic Acids Research, 44(11), 5068–5082. https://doi.org/10.1093/nar/gkw386
Juhling,, F., Morl,, M., Hartmann,, R. K., Sprinzl,, M., Stadler,, P. F., & Putz,, J. (2009). tRNAdb 2009: Compilation of tRNA sequences and tRNA genes. Nucleic Acids Research, 37, D159–D162. https://doi.org/10.1093/nar/gkn772
Katz,, A., Elgamal,, S., Rajkovic,, A., & Ibba,, M. (2016). Non‐canonical roles of tRNAs and tRNA mimics in bacterial cell biology. Molecular Microbiology, 101(4), 545–558. https://doi.org/10.1111/mmi.13419
Keam,, S. P., & Hutvagner,, G. (2015). tRNA‐derived fragments (tRFs): Emerging new roles for an ancient RNA in the regulation of gene expression. Life, 5(4), 1638–1651. https://doi.org/10.3390/life5041638
Kedersha,, N. L., Miquel,, M. C., Bittner,, D., & Rome,, L. H. (1990). Vaults. II. Ribonucleoprotein structures are highly conserved among higher and lower eukaryotes. Journal of Cell Biology, 110(4), 895–901.
Kelemen,, O., Convertini,, P., Zhang,, Z., Wen,, Y., Shen,, M., Falaleeva,, M., & Stamm,, S. (2013). Function of alternative splicing. Gene, 514(1), 1–30. https://doi.org/10.1016/j.gene.2012.07.083
Ketele,, A., Kiss,, T., & Jady,, B. E. (2016). Human intron‐encoded AluACA RNAs and telomerase RNA share a common element promoting RNA accumulation. RNA Biology, 13(12), 1274–1285. https://doi.org/10.1080/15476286.2016.1239689
Kikovska,, E., Svard,, S. G., & Kirsebom,, L. A. (2007). Eukaryotic RNase P RNA mediates cleavage in the absence of protein. Proceedings of the National Academy of Sciences of the United States of America, 104(7), 2062–2067. https://doi.org/10.1073/pnas.0607326104
Kishore,, S., Gruber,, A. R., Jedlinski,, D. J., Syed,, A. P., Jorjani,, H., & Zavolan,, M. (2013). Insights into snoRNA biogenesis and processing from PAR‐CLIP of snoRNA core proteins and small RNA sequencing. Genome Biology, 14(5), R45. https://doi.org/10.1186/gb-2013-14-5-r45
Kishore,, S., Khanna,, A., Zhang,, Z., Hui,, J., Balwierz,, P. J., Stefan,, M., … Stamm,, S. (2010). The snoRNA MBII‐52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Human Molecular Genetics, 19(7), 1153–1164. https://doi.org/10.1093/hmg/ddp585
Kishore,, S., & Stamm,, S. (2006). The snoRNA HBII‐52 regulates alternative splicing of the serotonin receptor 2C. Science, 311(5758), 230–232.
Kiss,, T. (2004). Biogenesis of small nuclear RNPs. Journal of Cell Science, 117(Pt. 25), 5949–5951. https://doi.org/10.1242/jcs.01487
Kiss,, T., Fayet,, E., Jady,, B. E., Richard,, P., & Weber,, M. (2006). Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. Cold Spring Harbor Symposia on Quantitative Biology, 71, 407–417.
Kitagawa,, T., Taniuchi,, K., Tsuboi,, M., Sakaguchi,, M., Kohsaki,, T., Okabayashi,, T., & Saibara,, T. (2019). Circulating pancreatic cancer exosomal RNAs for detection of pancreatic cancer. Molecular Oncology, 13(2), 212–227. https://doi.org/10.1002/1878-0261.12398
Klimenko,, O. V. (2017). Small non‐coding RNAs as regulators of structural evolution and carcinogenesis. Noncoding RNA Research, 2(2), 88–92. https://doi.org/10.1016/j.ncrna.2017.06.002
Kolb,, S. J., Battle,, D. J., & Dreyfuss,, G. (2007). Molecular functions of the SMN complex. Journal of Child Neurology, 22(8), 990–994. https://doi.org/10.1177/0883073807305666
Koonin,, E. V., & Novozhilov,, A. S. (2009). Origin and evolution of the genetic code: The universal enigma. IUBMB Life, 61(2), 99–111. https://doi.org/10.1002/iub.146
Kriegs,, J. O., Churakov,, G., Jurka,, J., Brosius,, J., & Schmitz,, J. (2007). Evolutionary history of 7SL RNA‐derived SINEs in supraprimates. Trends in Genetics, 23(4), 158–161. https://doi.org/10.1016/j.tig.2007.02.002
Lafontaine,, D. L., & Tollervey,, D. (1998). Birth of the snoRNPs: The evolution of the modification‐guide snoRNAs. Trends in Biochemical Sciences, 23(10), 383–388.
Langhendries,, J. L., Nicolas,, E., Doumont,, G., Goldman,, S., & Lafontaine,, D. L. (2016). The human box C/D snoRNAs U3 and U8 are required for pre‐rRNA processing and tumorigenesis. Oncotarget, 7(37), 59519–59534. https://doi.org/10.18632/oncotarget.11148
Le Thomas,, A., Toth,, K. F., & Aravin,, A. A. (2014). To be or not to be a piRNA: Genomic origin and processing of piRNAs. Genome Biology, 15(1), 204. https://doi.org/10.1186/gb4154
Lee,, Y., & Rio,, D. C. (2015). Mechanisms and regulation of alternative pre‐mRNA splicing. Annual Review of Biochemistry, 84, 291–323. https://doi.org/10.1146/annurev-biochem-060614-034316
Lestrade,, L., & Weber,, M. J. (2006). snoRNA‐LBME‐db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Research, 34, D158–D162. https://doi.org/10.1093/nar/gkj002
Leung,, E., & Brown,, J. D. (2010). Biogenesis of the signal recognition particle. Biochemical Society Transactions, 38(4), 1093–1098. https://doi.org/10.1042/BST0381093
Leung,, Y. Y., Kuksa,, P. P., Amlie‐Wolf,, A., Valladares,, O., Ungar,, L. H., Kannan,, S., … Wang,, L. S. (2016). DASHR: Database of small human noncoding RNAs. Nucleic Acids Research, 44(D1), D216–D222. https://doi.org/10.1093/nar/gkv1188
Li,, S., Duan,, J., Li,, D., Ma,, S., & Ye,, K. (2011). Structure of the Shq1‐Cbf5‐Nop10‐Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita. EMBO Journal, 30(24), 5010–5020. https://doi.org/10.1038/emboj.2011.427
Liao,, J., Yu,, L., Mei,, Y., Guarnera,, M., Shen,, J., Li,, R., … Jiang,, F. (2010). Small nucleolar RNA signatures as biomarkers for non‐small‐cell lung cancer. Molecular Cancer, 9, 198. https://doi.org/10.1186/1476-4598-9-198
Lorenz,, C., Lunse,, C. E., & Morl,, M. (2017). tRNA modifications: Impact on structure and thermal adaptation. Biomolecules, 7(2), E35. https://doi.org/10.3390/biom7020035
Lorkovic,, Z. J., Lehner,, R., Forstner,, C., & Barta,, A. (2005). Evolutionary conservation of minor U12‐type spliceosome between plants and humans. RNA, 11(7), 1095–1107. https://doi.org/10.1261/rna.2440305
Lu,, Z., & Matera,, A. G. (2014). Developmental analysis of spliceosomal snRNA isoform expression. G3 (Bethesda), 5(1), 103–110. https://doi.org/10.1534/g3.114.015735
Lui,, L., & Lowe,, T. (2013). Small nucleolar RNAs and RNA‐guided post‐transcriptional modification. Essays in Biochemistry, 54, 53–77. https://doi.org/10.1042/bse0540053
Mannoor,, K., Shen,, J., Liao,, J., Liu,, Z., & Jiang,, F. (2014). Small nucleolar RNA signatures of lung tumor‐initiating cells. Molecular Cancer, 13, 104. https://doi.org/10.1186/1476-4598-13-104
Marquez,, S. M., Chen,, J. L., Evans,, D., & Pace,, N. R. (2006). Structure and function of eukaryotic ribonuclease P RNA. Molecular Cell, 24(3), 445–456. https://doi.org/10.1016/j.molcel.2006.09.011
Martens‐Uzunova,, E. S., Hoogstrate,, Y., Kalsbeek,, A., Pigmans,, B., Vredenbregt‐van den Berg,, M., Dits,, N., … Jenster,, G. (2015). C/D‐box snoRNA‐derived RNA production is associated with malignant transformation and metastatic progression in prostate cancer. Oncotarget, 6(19), 17430–17444. https://doi.org/10.18632/oncotarget.4172
Marz,, M., Donath,, A., Verstraete,, N., Nguyen,, V. T., Stadler,, P. F., & Bensaude,, O. (2009). Evolution of 7SK RNA and its protein partners in metazoa. Molecular Biology and Evolution, 26(12), 2821–2830. https://doi.org/10.1093/molbev/msp198
Marz,, M., Kirsten,, T., & Stadler,, P. F. (2008). Evolution of spliceosomal snRNA genes in metazoan animals. Journal of Molecular Evolution, 67(6), 594–607. https://doi.org/10.1007/s00239-008-9149-6
Massenet,, S., Bertrand,, E., & Verheggen,, C. (2017). Assembly and trafficking of box C/D and H/ACA snoRNPs. RNA Biology, 14(6), 680–692. https://doi.org/10.1080/15476286.2016.1243646
McQuillen,, K., Roberts,, R. B., & Britten,, R. J. (1959). Synthesis of nascent protein by ribosomes in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 45(9), 1437–1447.
Mei,, Y. P., Liao,, J. P., Shen,, J., Yu,, L., Liu,, B. L., Liu,, L., … Jiang,, F. (2012). Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis. Oncogene, 31(22), 2794–2804. https://doi.org/10.1038/onc.2011.449
Michaud,, M., Cognat,, V., Duchene,, A. M., & Marechal‐Drouard,, L. (2011). A global picture of tRNA genes in plant genomes. The Plant Journal, 66(1), 80–93. https://doi.org/10.1111/j.1365-313X.2011.04490.x
Michel,, C. I., Holley,, C. L., Scruggs,, B. S., Sidhu,, R., Brookheart,, R. T., Listenberger,, L. L., … Schaffer,, J. E. (2011). Small nucleolar RNAs U32a, U33, and U35a are critical mediators of metabolic stress. Cell Metabolism, 14(1), 33–44. https://doi.org/10.1016/j.cmet.2011.04.009
Moreno Diaz de la Espina,, S., Alverca,, E., Cuadrado,, A., & Franca,, S. (2005). Organization of the genome and gene expression in a nuclear environment lacking histones and nucleosomes: The amazing dinoflagellates. European Journal of Cell Biology, 84(2–3), 137–149.
Mosig,, A., Guofeng,, M., Stadler,, B. M., & Stadler,, P. F. (2007). Evolution of the vertebrate Y RNA cluster. Theory in Biosciences, 126(1), 9–14. https://doi.org/10.1007/s12064-007-0003-y
Mroczek,, S., & Dziembowski,, A. (2013). U6 RNA biogenesis and disease association. WIREs RNA, 4(5), 581–592. https://doi.org/10.1002/wrna.1181
Nachtergaele,, S., & He,, C. (2017). The emerging biology of RNA post‐transcriptional modifications. RNA Biology, 14(2), 156–163. https://doi.org/10.1080/15476286.2016.1267096
Nickel,, A. I., Waber,, N. B., Gossringer,, M., Lechner,, M., Linne,, U., Toth,, U., … Hartmann,, R. K. (2017). Minimal and RNA‐free RNase P in Aquifex aeolicus. Proceedings of the National Academy of Sciences of the United States of America, 114(42), 11121–11126. https://doi.org/10.1073/pnas.1707862114
Ogami,, K., Chen,, Y., & Manley,, J. L. (2018). RNA surveillance by the nuclear RNA exosome: Mechanisms and significance. Noncoding RNA, 4(1), 1–21. https://doi.org/10.3390/ncrna4010008
Oh,, J. M., Di,, C., Venters,, C. C., Guo,, J., Arai,, C., So,, B. R., … Dreyfuss,, G. (2017). U1 snRNP telescripting regulates a size‐function‐stratified human genome. Nature Structural %26 Molecular Biology, 24(11), 993–999. https://doi.org/10.1038/nsmb.3473
O`Leary,, N. A., Wright,, M. W., Brister,, J. R., Ciufo,, S., Haddad,, D., McVeigh,, R., … Pruitt,, K. D. (2016). Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation. Nucleic Acids Research, 44(D1), D733–D745. https://doi.org/10.1093/nar/gkv1189
Ono,, M., Yamada,, K., Avolio,, F., Scott,, M. S., van Koningsbruggen,, S., Barton,, G. J., & Lamond,, A. I. (2010). Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. Molecular Biology of the Cell, 21(9), 1569–1584. https://doi.org/10.1091/mbc.E10-01-0078
Ooi,, S. L., Samarsky,, D. A., Fournier,, M. J., & Boeke,, J. D. (1998). Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat‐debranching enzyme: Intron length effects and activity of a precursor snoRNA. RNA, 4(9), 1096–1110.
O`Reilly,, D., Dienstbier,, M., Cowley,, S. A., Vazquez,, P., Drozdz,, M., Taylor,, S., … Murphy,, S. (2013). Differentially expressed, variant U1 snRNAs regulate gene expression in human cells. Genome Research, 23(2), 281–291. https://doi.org/10.1101/gr.142968.112
Orioli,, A. (2017). tRNA biology in the omics era: Stress signalling dynamics and cancer progression. BioEssays, 39(3). https://doi.org/10.1002/bies.201600158
Palazzo,, A. F., & Lee,, E. S. (2015). Non‐coding RNA: What is functional and what is junk? Frontiers in Genetics, 6, 2. https://doi.org/10.3389/fgene.2015.00002
Pechmann,, S., & Frydman,, J. (2013). Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nature Structural %26 Molecular Biology, 20(2), 237–243. https://doi.org/10.1038/nsmb.2466
Perumal,, K., & Reddy,, R. (2002). The 3′ end formation in small RNAs. Gene Expression, 10(1–2), 59–78.
Peterlin,, B. M., Brogie,, J. E., & Price,, D. H. (2012). 7SK snRNA: A noncoding RNA that plays a major role in regulating eukaryotic transcription. WIREs RNA, 3(1), 92–103. https://doi.org/10.1002/wrna.106
Petfalski,, E., Dandekar,, T., Henry,, Y., & Tollervey,, D. (1998). Processing of the precursors to small nucleolar RNAs and rRNAs requires common components. Molecular and Cellular Biology, 18(3), 1181–1189.
Piekna‐Przybylska,, D., Liu,, B., & Fournier,, M. J. (2007). The U1 snRNA hairpin II as a RNA affinity tag for selecting snoRNP complexes. Methods in Enzymology, 425, 317–353. https://doi.org/10.1016/S0076-6879(07)25014-1
Podlevsky,, J. D., & Chen,, J. J. (2016). Evolutionary perspectives of telomerase RNA structure and function. RNA Biology, 13(8), 720–732. https://doi.org/10.1080/15476286.2016.1205768
Qi,, X., Li,, Y., Honda,, S., Hoffmann,, S., Marz,, M., Mosig,, A., … Chen,, J. J. (2013). The common ancestral core of vertebrate and fungal telomerase RNAs. Nucleic Acids Research, 41(1), 450–462. https://doi.org/10.1093/nar/gks980
Quek,, X. C., Thomson,, D. W., Maag,, J. L., Bartonicek,, N., Signal,, B., Clark,, M. B., … Dinger,, M. E. (2015). lncRNAdb v2.0: Expanding the reference database for functional long noncoding RNAs. Nucleic Acids Research, 43, D168–D173. https://doi.org/10.1093/nar/gku988
Quinn,, J. J., & Chang,, H. Y. (2016). Unique features of long non‐coding RNA biogenesis and function. Nature Reviews. Genetics, 17(1), 47–62. https://doi.org/10.1038/nrg.2015.10
Rashid,, R., Liang,, B., Baker,, D. L., Youssef,, O. A., He,, Y., Phipps,, K., … Li,, H. (2006). Crystal structure of a Cbf5‐Nop10‐Gar1 complex and implications in RNA‐guided pseudouridylation and dyskeratosis congenita. Molecular Cell, 21(2), 249–260. https://doi.org/10.1016/j.molcel.2005.11.017
Reiner,, R., Ben‐Asouli,, Y., Krilovetzky,, I., & Jarrous,, N. (2006). A role for the catalytic ribonucleoprotein RNase P in RNA polymerase III transcription. Genes %26 Development, 20(12), 1621–1635. https://doi.org/10.1101/gad.386706
Reynolds,, N. M., Vargas‐Rodriguez,, O., Soll,, D., & Crnkovic,, A. (2017). The central role of tRNA in genetic code expansion. Biochimica et Biophysica Acta ‐ General Subjects, 1861(11, Pt. B), 3001–3008. https://doi.org/10.1016/j.bbagen.2017.03.012
Rich,, A., & RajBhandary,, U. L. (1976). Transfer RNA: Molecular structure, sequence, and properties. Annual Review of Biochemistry, 45, 805–860. https://doi.org/10.1146/annurev.bi.45.070176.004105
RNAcentral. (2017). RNAcentral: A comprehensive database of non‐coding RNA sequences. Nucleic Acids Research, 45(D1), D128–D134. https://doi.org/10.1093/nar/gkw1008
Rogozin,, I. B., Carmel,, L., Csuros,, M., & Koonin,, E. V. (2012). Origin and evolution of spliceosomal introns. Biology Direct, 7, 11. https://doi.org/10.1186/1745-6150-7-11
Romero,, D. P., & Blackburn,, E. H. (1991). A conserved secondary structure for telomerase RNA. Cell, 67(2), 343–353.
Rosenblad,, M. A., Gorodkin,, J., Knudsen,, B., Zwieb,, C., & Samuelsson,, T. (2003). SRPDB: Signal recognition particle database. Nucleic Acids Research, 31(1), 363–364.
Rosenblad,, M. A., Larsen,, N., Samuelsson,, T., & Zwieb,, C. (2009). Kinship in the SRP RNA family. RNA Biology, 6(5), 508–516.
Rothe,, B., Back,, R., Quinternet,, M., Bizarro,, J., Robert,, M. C., Blaud,, M., … Branlant,, C. (2014). Characterization of the interaction between protein Snu13p/15.5K and the Rsa1p/NUFIP factor and demonstration of its functional importance for snoRNP assembly. Nucleic Acids Research, 42(3), 2015–2036. https://doi.org/10.1093/nar/gkt1091
Russell,, A. G., Charette,, J. M., Spencer,, D. F., & Gray,, M. W. (2006). An early evolutionary origin for the minor spliceosome. Nature, 443(7113), 863–866. https://doi.org/10.1038/nature05228
Russell,, J., & Zomerdijk,, J. C. (2005). RNA‐polymerase‐I‐directed rDNA transcription, life and works. Trends in Biochemical Sciences, 30(2), 87–96. https://doi.org/10.1016/j.tibs.2004.12.008
Sagi,, D., Rak,, R., Gingold,, H., Adir,, I., Maayan,, G., Dahan,, O., … Rechavi,, O. (2016). Tissue‐ and time‐specific expression of otherwise identical tRNA genes. PLoS Genetics, 12(8), e1006264. https://doi.org/10.1371/journal.pgen.1006264
Sbisa,, E., Pesole,, G., Tullo,, A., & Saccone,, C. (1996). The evolution of the RNase P‐ and RNase MRP‐associated RNAs: Phylogenetic analysis and nucleotide substitution rate. Journal of Molecular Evolution, 43(1), 46–57.
Schmidt,, K., & Butler,, J. S. (2013). Nuclear RNA surveillance: Role of TRAMP in controlling exosome specificity. WIREs RNA, 4(2), 217–231. https://doi.org/10.1002/wrna.1155
Schmitt,, M. E., & Clayton,, D. A. (1993). Nuclear RNase MRP is required for correct processing of pre‐5.8S rRNA in Saccharomyces cerevisiae. Molecular and Cellular Biology, 13(12), 7935–7941.
Schumperli,, D., & Pillai,, R. S. (2004). The special Sm core structure of the U7 snRNP: Far‐reaching significance of a small nuclear ribonucleoprotein. Cellular and Molecular Life Sciences, 61(19–20), 2560–2570. https://doi.org/10.1007/s00018-004-4190-0
Scott,, L. M., & Rebel,, V. I. (2013). Acquired mutations that affect pre‐mRNA splicing in hematologic malignancies and solid tumors. Journal of the National Cancer Institute, 105(20), 1540–1549. https://doi.org/10.1093/jnci/djt257
Scott,, M. S., & Ono,, M. (2011). From snoRNA to miRNA: Dual function regulatory non‐coding RNAs. Biochimie, 93(11), 1987–1992. https://doi.org/10.1016/j.biochi.2011.05.026
Scott,, M. S., Ono,, M., Yamada,, K., Endo,, A., Barton,, G. J., & Lamond,, A. I. (2012). Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Research, 40(8), 3676–3688. https://doi.org/10.1093/nar/gkr1233
Sergeeva,, O. V., Bogdanov,, A. A., & Sergiev,, P. V. (2015). What do we know about ribosomal RNA methylation in Escherichia coli? Biochimie, 117, 110–118. https://doi.org/10.1016/j.biochi.2014.11.019
Shen,, Y., Yu,, X., Zhu,, L., Li,, T., Yan,, Z., & Guo,, J. (2018). Transfer RNA‐derived fragments and tRNA halves: Biogenesis, biological functions and their roles in diseases. Journal of Molecular Medicine, 96(11), 1167–1176. https://doi.org/10.1007/s00109-018-1693-y
Shi,, J., Huang,, C., Huang,, S., & Yao,, C. (2018). snoRNAs associate with mRNA 3′ processing complex: New wine in old bottles. RNA Biology, 15(2), 194–197. https://doi.org/10.1080/15476286.2017.1416278
Soares,, A. R., & Santos,, M. (2017). Discovery and function of transfer RNA‐derived fragments and their role in disease. WIREs RNA, 8(5). https://doi.org/10.1002/wrna.1423
Soeno,, Y., Taya,, Y., Stasyk,, T., Huber,, L. A., Aoba,, T., & Huttenhofer,, A. (2010). Identification of novel ribonucleo‐protein complexes from the brain‐specific snoRNA MBII‐52. RNA, 16(7), 1293–1300. https://doi.org/10.1261/rna.2109710
Spiller,, M. P., Boon,, K. L., Reijns,, M. A., & Beggs,, J. D. (2007). The Lsm2‐8 complex determines nuclear localization of the spliceosomal U6 snRNA. Nucleic Acids Research, 35(3), 923–929. https://doi.org/10.1093/nar/gkl1130
Stadler,, P. F., Chen,, J. J., Hackermuller,, J., Hoffmann,, S., Horn,, F., Khaitovich,, P., … Ullmann,, K. (2009). Evolution of vault RNAs. Molecular Biology and Evolution, 26(9), 1975–1991. https://doi.org/10.1093/molbev/msp112
Su,, J., Liao,, J., Gao,, L., Shen,, J., Guarnera,, M. A., Zhan,, M., … Jiang,, F. (2016). Analysis of small nucleolar RNAs in sputum for lung cancer diagnosis. Oncotarget, 7(5), 5131–5142. https://doi.org/10.18632/oncotarget.4219
Sun,, C., Fu,, Z., Wang,, S., Li,, J., Li,, Y., Zhang,, Y., … Yin,, Y. (2018). Roles of tRNA‐derived fragments in human cancers. Cancer Letters, 414, 16–25. https://doi.org/10.1016/j.canlet.2017.10.031
Szymanski,, M., Barciszewska,, M. Z., Zywicki,, M., & Barciszewski,, J. (2003). Noncoding RNA transcripts. Journal of Applied Genetics, 44(1), 1–19.
Taft,, R. J., Glazov,, E. A., Lassmann,, T., Hayashizaki,, Y., Carninci,, P., & Mattick,, J. S. (2009). Small RNAs derived from snoRNAs. RNA, 15(7), 1233–1240. https://doi.org/10.1261/rna.1528909
Terns,, M. P., & Terns,, R. M. (2002). Small nucleolar RNAs: Versatile trans‐acting molecules of ancient evolutionary origin. Gene Expression, 10(1–2), 17–39.
Torres,, A. G., Batlle,, E., & Ribas de Pouplana,, L. (2014). Role of tRNA modifications in human diseases. Trends in Molecular Medicine, 20(6), 306–314. https://doi.org/10.1016/j.molmed.2014.01.008
Tuorto,, F., & Lyko,, F. (2016). Genome recoding by tRNA modifications. Open Biology, 6(12). https://doi.org/10.1098/rsob.160287
Turunen,, J. J., Niemela,, E. H., Verma,, B., & Frilander,, M. J. (2013). The significant other: Splicing by the minor spliceosome. WIREs RNA, 4(1), 61–76. https://doi.org/10.1002/wrna.1141
Valadkhan,, S., & Gunawardane,, L. S. (2013). Role of small nuclear RNAs in eukaryotic gene expression. Essays in Biochemistry, 54, 79–90. https://doi.org/10.1042/bse0540079
van Zon,, A., Mossink,, M. H., Scheper,, R. J., Sonneveld,, P., & Wiemer,, E. A. (2003). The vault complex. Cellular and Molecular Life Sciences, 60(9), 1828–1837. https://doi.org/10.1007/s00018-003-3030-y
Vanacova,, S., Yan,, W., Carlton,, J. M., & Johnson,, P. J. (2005). Spliceosomal introns in the deep‐branching eukaryote Trichomonas vaginalis. Proceedings of the National Academy of Sciences of the United States of America, 102(12), 4430–4435. https://doi.org/10.1073/pnas.0407500102
Verdone,, L., Galardi,, S., Page,, D., & Beggs,, J. D. (2004). Lsm proteins promote regeneration of pre‐mRNA splicing activity. Current Biology, 14(16), 1487–1491. https://doi.org/10.1016/j.cub.2004.08.032
Villa,, T., Pleiss,, J. A., & Guthrie,, C. (2002). Spliceosomal snRNAs: Mg(2+)‐dependent chemistry at the catalytic core? Cell, 109(2), 149–152.
Vincenti,, S., De Chiara,, V., Bozzoni,, I., & Presutti,, C. (2007). The position of yeast snoRNA‐coding regions within host introns is essential for their biosynthesis and for efficient splicing of the host pre‐mRNA. RNA, 13(1), 138–150. https://doi.org/10.1261/rna.251907
Visconte,, V., Makishima,, H., Maciejewski,, J. P., & Tiu,, R. V. (2012). Emerging roles of the spliceosomal machinery in myelodysplastic syndromes and other hematological disorders. Leukemia, 26(12), 2447–2454. https://doi.org/10.1038/leu.2012.130
Wan,, Y., & Wu,, C. J. (2013). SF3B1 mutations in chronic lymphocytic leukemia. Blood, 121(23), 4627–4634. https://doi.org/10.1182/blood-2013-02-427641
Watkins,, N. J., Gottschalk,, A., Neubauer,, G., Kastner,, B., Fabrizio,, P., Mann,, M., & Luhrmann,, R. (1998). Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA‐binding protein, are present together with Gar1p in all H BOX/ACA‐motif snoRNPs and constitute a common bipartite structure. RNA, 4(12), 1549–1568.
Weber,, M. J. (2006). Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genetics, 2(12), e205.
Weiss,, M. C., Sousa,, F. L., Mrnjavac,, N., Neukirchen,, S., Roettger,, M., Nelson‐Sathi,, S., & Martin,, W. F. (2016). The physiology and habitat of the last universal common ancestor. Nature Microbiology, 1(9), 16116. https://doi.org/10.1038/nmicrobiol.2016.116
Wichtowska,, D., Turowski,, T. W., & Boguta,, M. (2013). An interplay between transcription, processing, and degradation determines tRNA levels in yeast. WIREs RNA, 4(6), 709–722. https://doi.org/10.1002/wrna.1190
Wong,, W. M., Abrahamson,, J. L., & Nazar,, R. N. (1984). Are DNA spacers relics of gene amplification events? Proceedings of the National Academy of Sciences of the United States of America, 81(6), 1768–1770.
Woolford,, J. L., Jr., & Baserga,, S. J. (2013). Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics, 195(3), 643–681. https://doi.org/10.1534/genetics.113.153197
Xing,, Y. H., & Chen,, L. L. (2018). Processing and roles of snoRNA‐ended long noncoding RNAs. Critical Reviews in Biochemistry and Molecular Biology, 53, 1–11. https://doi.org/10.1080/10409238.2018.1508411
Yang,, Y., Wen,, L., & Zhu,, H. (2015). Unveiling the hidden function of long non‐coding RNA by identifying its major partner‐protein. Cell %26 Bioscience, 5, 59. https://doi.org/10.1186/s13578-015-0050-x
Yoshihama,, M., Nakao,, A., & Kenmochi,, N. (2013). snOPY: A small nucleolar RNA orthological gene database. BMC Research Notes, 6, 426. https://doi.org/10.1186/1756-0500-6-426
Younis,, I., Dittmar,, K., Wang,, W., Foley,, S. W., Berg,, M. G., Hu,, K. Y., … Dreyfuss,, G. (2013). Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA. eLife, 2, e00780. https://doi.org/10.7554/eLife.00780
Youssef,, O. A., Safran,, S. A., Nakamura,, T., Nix,, D. A., Hotamisligil,, G. S., & Bass,, B. L. (2015). Potential role for snoRNAs in PKR activation during metabolic stress. Proceedings of the National Academy of Sciences of the United States of America, 112(16), 5023–5028. https://doi.org/10.1073/pnas.1424044112
Zampetaki,, A., Albrecht,, A., & Steinhofel,, K. (2018). Long non‐coding RNA structure and function: Is there a link? Frontiers in Physiology, 9, 1201. https://doi.org/10.3389/fphys.2018.01201
Zent,, C. S., & Burack,, W. R. (2014). Mutations in chronic lymphocytic leukemia and how they affect therapy choice: Focus on NOTCH1, SF3B1, and TP53. Hematology/The Education Program of the American Society of Hematology, 2014(1), 119–124. https://doi.org/10.1182/asheducation-2014.1.119
Zhao,, Y., Li,, H., Fang,, S., Kang,, Y., Wu,, W., Hao,, Y., … Chen,, R. (2016). NONCODE 2016: An informative and valuable data source of long non‐coding RNAs. Nucleic Acids Research, 44(D1), D203–D208. https://doi.org/10.1093/nar/gkv1252