Beyond microRNA--novel RNAs derived from small non-coding RNA and their implication in cancer.

[1]  A. Yudelevich.  Specific cleavage of an Escherichia coli leucine transfer RNA following bacteriophage T4 infection. , 1971, Journal of molecular biology.

[2]  K. Kuo,et al.  tRNA breakdown products as markers for cancer , 1979, Cancer.

[3]  E. Ullu,et al.  Human 7SL RNA consists of a 140 nucleotide middle-repetitive sequence inserted in an Alu sequence , 1982, Cell.

[4]  J. Steitz,et al.  Identification of the human U7 snRNP as one of several factors involved in the 3' end maturation of histone premessenger RNA's. , 1987, Science.

[5]  M. Baer,et al.  Structure and transcription of a human gene for H1 RNA, the RNA component of human RNase P , 1990, Nucleic Acids Res..

[6]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[7]  et al.,et al.  The RNA component of human telomerase , 1995, Science.

[8]  C. Ehresmann,et al.  tRNAs as primer of reverse transcriptases. , 1995, Biochimie.

[9]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[10]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[11]  D. Tollervey,et al.  The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. , 1998, Genes & development.

[12]  Jeffrey B. Cheng,et al.  A Box H/ACA Small Nucleolar RNA-Like Domain at the Human Telomerase RNA 3′ End , 1999, Molecular and Cellular Biology.

[13]  D. Ingber,et al.  New role for tRNA and its fragment purified from human urinary bladder carcinoma conditioned medium: Inhibition of endothelial cell growth , 1999, Journal of cellular biochemistry.

[14]  H. Satoh,et al.  Intronic U50 small‐nucleolar‐RNA (snoRNA) host gene of no protein‐coding potential is mapped at the chromosome breakpoint t(3;6)(q27;q15) of human B‐cell lymphoma , 2000, Genes to cells : devoted to molecular & cellular mechanisms.

[15]  A. Pasquinelli,et al.  A Cellular Function for the RNA-Interference Enzyme Dicer in the Maturation of the let-7 Small Temporal RNA , 2001, Science.

[16]  A. Fatica,et al.  Release of U18 snoRNA from its host intron requires interaction of Nop1p with the Rnt1p endonuclease , 2001, The EMBO journal.

[17]  S. Petersen,et al.  Chromosomal imbalances of primary and metastatic lung adenocarcinomas , 2002, The Journal of pathology.

[18]  Ofer Levy,et al.  Therapeutic potential of the , 2002, Expert opinion on investigational drugs.

[19]  A. Hüttenhofer,et al.  The expanding snoRNA world. , 2002, Biochimie.

[20]  W. Filipowicz,et al.  Biogenesis of small nucleolar ribonucleoproteins. , 2002, Current opinion in cell biology.

[21]  A. Marchfelder,et al.  Assigning a function to a conserved group of proteins: the tRNA 3′‐processing enzymes , 2002, The EMBO journal.

[22]  S. Jayasena,et al.  Functional siRNAs and miRNAs Exhibit Strand Bias , 2003, Cell.

[23]  T. Du,et al.  Asymmetry in the Assembly of the RNAi Enzyme Complex , 2003, Cell.

[24]  V. Kim,et al.  The Drosha-DGCR8 complex in primary microRNA processing. , 2004, Genes & development.

[25]  V. Kim,et al.  MicroRNA precursors in motion: exportin-5 mediates their nuclear export. , 2004, Trends in cell biology.

[26]  Jiunn-Liang Chen,et al.  Telomerase RNA structure and function: implications for dyskeratosis congenita. , 2004, Trends in biochemical sciences.

[27]  K. Morris,et al.  Small Interfering RNA-Induced Transcriptional Gene Silencing in Human Cells , 2004, Science.

[28]  Christophe Dez,et al.  RNA structure and function in C/D and H/ACA s(no)RNPs. , 2004, Current opinion in structural biology.

[29]  K. Collins,et al.  Starvation-induced Cleavage of the tRNA Anticodon Loop in Tetrahymena thermophila* , 2005, Journal of Biological Chemistry.

[30]  N. Sonenberg,et al.  Translational control in stress and apoptosis , 2005, Nature Reviews Molecular Cell Biology.

[31]  W. Berger,et al.  Cellular functions of vaults and their involvement in multidrug resistance. , 2006, Current drug targets.

[32]  D. Baker,et al.  Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita. , 2006, Molecular cell.

[33]  S. Stamm,et al.  The snoRNA HBII-52 Regulates Alternative Splicing of the Serotonin Receptor 2C , 2006, Science.

[34]  V. Kim,et al.  Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes. , 2006, Genes & development.

[35]  T. Krude,et al.  Functional Requirement of Noncoding Y RNAs for Human Chromosomal DNA Replication , 2006, Molecular and Cellular Biology.

[36]  John J Rossi,et al.  Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells , 2006, Nature Structural &Molecular Biology.

[37]  R. Place,et al.  Small dsRNAs induce transcriptional activation in human cells , 2006, Proceedings of the National Academy of Sciences.

[38]  D. Engelke,et al.  Ribonuclease P: The Evolution of an Ancient RNA Enzyme , 2006, Critical reviews in biochemistry and molecular biology.

[39]  M. Brunori,et al.  The structure of the endoribonuclease XendoU: From small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication , 2006, Proceedings of the National Academy of Sciences.

[40]  F. Boisvert,et al.  The multifunctional nucleolus , 2007, Nature Reviews Molecular Cell Biology.

[41]  J. Kelso,et al.  A splice variant of the human CCA-adding enzyme with modified activity. , 2007, Journal of molecular biology.

[42]  G. van Ommen,et al.  Antisense-mediated exon skipping: a versatile tool with therapeutic and research applications. , 2007, RNA.

[43]  D. Haber,et al.  Dual Role for Argonautes in MicroRNA Processing and Posttranscriptional Regulation of MicroRNA Expression , 2007, Cell.

[44]  A. Sandelin,et al.  Hidden layers of human small RNAs , 2008, BMC Genomics.

[45]  Oliver H. Tam,et al.  Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes , 2008, Nature.

[46]  P. Sætrom,et al.  MicroRNA-directed transcriptional gene silencing in mammalian cells , 2008, Proceedings of the National Academy of Sciences.

[47]  David L. Spector,et al.  3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA , 2008, Cell.

[48]  N. Rajewsky,et al.  A human snoRNA with microRNA-like functions. , 2008, Molecular cell.

[49]  B. Horsthemke,et al.  Mechanisms of imprinting of the Prader–Willi/Angelman region , 2008, American journal of medical genetics. Part A.

[50]  Rino Ragno,et al.  The Tumor Marker Human Placental Protein 11 Is an Endoribonuclease* , 2008, Journal of Biological Chemistry.

[51]  Bo Zhang,et al.  Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells , 2009, BMC Molecular Biology.

[52]  Ashesh A. Saraiya,et al.  snoRNA, a Novel Precursor of microRNA in Giardia lamblia , 2008, PLoS pathogens.

[53]  M. Westergaard,et al.  A RNA antagonist of hypoxia-inducible factor-1α, EZN-2968, inhibits tumor cell growth , 2008, Molecular Cancer Therapeutics.

[54]  Eric C. Lai,et al.  Endogenous small interfering RNAs in animals , 2008, Nature Reviews Molecular Cell Biology.

[55]  Pamela J Green,et al.  tRNA cleavage is a conserved response to oxidative stress in eukaryotes. , 2008, RNA.

[56]  D. Pisano,et al.  Mechanistic principles of chromatin remodeling guided by siRNAs and miRNAs , 2008, Cell cycle.

[57]  Daniel B. Martin,et al.  Circulating microRNAs as stable blood-based markers for cancer detection , 2008, Proceedings of the National Academy of Sciences.

[58]  K. Calvin,et al.  RNA-splicing endonuclease structure and function , 2008, Cellular and Molecular Life Sciences.

[59]  Y. Sakaki,et al.  Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes , 2008, Nature.

[60]  A. Kibel,et al.  SnoRNA U50 is a candidate tumor-suppressor gene at 6q14.3 with a mutation associated with clinically significant prostate cancer. , 2007, Human molecular genetics.

[61]  Robert Blelloch,et al.  Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. , 2008, Genes & development.

[62]  Valery Shepelev,et al.  snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. , 2008, Gene.

[63]  Hui Zhou,et al.  Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia , 2008, Nucleic acids research.

[64]  R. Place,et al.  MicroRNA-373 induces expression of genes with complementary promoter sequences , 2008, Proceedings of the National Academy of Sciences.

[65]  Peter F. Stadler,et al.  Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis , 2008, Nucleic acids research.

[66]  Paul F Agris,et al.  tRNA's modifications bring order to gene expression. , 2008, Current opinion in microbiology.

[67]  M. Mourtada-Maarabouni,et al.  GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer , 2009, Oncogene.

[68]  Finn Verner Jensen,et al.  Bayesian networks , 1998, Data Mining and Knowledge Discovery Handbook.

[69]  A. Riggs,et al.  CRM1 mediates nuclear-cytoplasmic shuttling of mature microRNAs , 2009, Proceedings of the National Academy of Sciences.

[70]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[71]  T. Eggermann.  Silver-Russell and Beckwith-Wiedemann Syndromes: Opposite (Epi)Mutations in 11p15 Result in Opposite Clinical Pictures , 2009, Hormone Research in Paediatrics.

[72]  Yi Tie,et al.  Stress induces tRNA cleavage by angiogenin in mammalian cells , 2009, FEBS letters.

[73]  D. Moazed.  Small RNAs in transcriptional gene silencing and genome defence , 2009, Nature.

[74]  R. Parker,et al.  Eukaryotic stress granules: the ins and outs of translation. , 2009, Molecular cell.

[75]  Petra Schwille,et al.  Importin 8 Is a Gene Silencing Factor that Targets Argonaute Proteins to Distinct mRNAs , 2009, Cell.

[76]  Piotr J. Balwierz,et al.  Expression and Processing of a Small Nucleolar RNA from the Epstein-Barr Virus Genome , 2009, PLoS Pathogens.

[77]  S. Yamasaki,et al.  Angiogenin cleaves tRNA and promotes stress-induced translational repression , 2009, The Journal of cell biology.

[78]  Robert D. Finn,et al.  Rfam: updates to the RNA families database , 2008, Nucleic Acids Res..

[79]  S. Le,et al.  Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid , 2009, Nucleic acids research.

[80]  J. Mattick,et al.  Small RNAs derived from snoRNAs. , 2009, RNA.

[81]  G. Barton,et al.  Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. , 2009, RNA.

[82]  A. Malhotra,et al.  A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). , 2009, Genes & development.

[83]  V. Kim,et al.  Biogenesis of small RNAs in animals , 2009, Nature Reviews Molecular Cell Biology.

[84]  B. Montanini,et al.  Eukaryotic snoRNAs: a paradigm for gene expression flexibility. , 2009, Genomics.

[85]  Manuel de la Mata,et al.  Control of alternative splicing through siRNA-mediated transcriptional gene silencing , 2009, Nature Structural &Molecular Biology.

[86]  Geoffrey J. Barton,et al.  Human miRNA Precursors with Box H/ACA snoRNA Features , 2009, PLoS Comput. Biol..

[87]  R. Parker,et al.  Stressing Out over tRNA Cleavage , 2009, Cell.

[88]  Wei Zhou,et al.  Implication of snoRNA U50 in human breast cancer. , 2009, Journal of genetics and genomics = Yi chuan xue bao.

[89]  Z. Weng,et al.  Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. , 2010, RNA.

[90]  Pavel Ivanov,et al.  Angiogenin-induced tRNA-derived Stress-induced RNAs Promote Stress-induced Stress Granule Assembly* , 2010, The Journal of Biological Chemistry.

[91]  Jing Xia,et al.  Identification of Novel MicroRNA-Like Molecules Generated from Herpesvirus and Host tRNA Transcripts , 2010, Journal of Virology.

[92]  A. S. Krasilnikov,et al.  Of proteins and RNA: the RNase P/MRP family. , 2010, RNA.

[93]  Zhenqiu Liu,et al.  Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer , 2010, Molecular Cancer.

[94]  D. Haussecker,et al.  Human tRNA-derived small RNAs in the global regulation of RNA silencing. , 2010, RNA.

[95]  A. Hopper,et al.  Cellular dynamics of tRNAs and their genes , 2010, FEBS letters.

[96]  G. Hannon,et al.  A dicer-independent miRNA biogenesis pathway that requires Ago catalysis , 2010, Nature.

[97]  E. Lai,et al.  Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis , 2010, Proceedings of the National Academy of Sciences.

[98]  R. Sachidanandam,et al.  A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo. , 2010, Genes & development.

[99]  B. Cullen,et al.  A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs. , 2010, Molecular cell.

[100]  R. V. van Nues,et al.  The Spatial-Functional Coupling of Box C/D and C′/D′ RNPs Is an Evolutionarily Conserved Feature of the Eukaryotic Box C/D snoRNP Nucleotide Modification Complex , 2010, Molecular and Cellular Biology.

[101]  A. Hopper,et al.  tRNA biology charges to the front. , 2010, Genes & development.

[102]  Francesca Tuorto,et al.  RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. , 2010, Genes & development.

[103]  Michelle S. Scott,et al.  Analysis of Human Small Nucleolar RNAs (snoRNA) and the Development of snoRNA Modulator of Gene Expression Vectors , 2010, Molecular biology of the cell.

[104]  Alon Herschhorn,et al.  Retroviral reverse transcriptases , 2010, Cellular and Molecular Life Sciences.

[105]  Mihaela Zavolan,et al.  The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. , 2010, Human molecular genetics.

[106]  M. Helm,et al.  tRNA stabilization by modified nucleotides. , 2010, Biochemistry.

[107]  David W. Taylor,et al.  A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity , 2010, Science.

[108]  S. Goldenberg,et al.  A population of tRNA-derived small RNAs is actively produced in Trypanosoma cruzi and recruited to specific cytoplasmic granules. , 2010, Molecular and biochemical parasitology.

[109]  J. Yong,et al.  tRNA binds to cytochrome c and inhibits caspase activation. , 2010, Molecular cell.

[110]  S. Stamm,et al.  Regulation of alternative splicing by short non-coding nuclear RNAs , 2010, RNA biology.

[111]  S. Kauppinen,et al.  Therapeutic Silencing of MicroRNA-122 in Primates with Chronic Hepatitis C Virus Infection , 2010, Science.

[112]  L. V. van Dyk,et al.  Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters. , 2010, RNA.

[113]  Hui Zhou,et al.  deepBase: a database for deeply annotating and mining deep sequencing data , 2009, Nucleic Acids Res..

[114]  Michelle S. Scott,et al.  Identification of human miRNA precursors that resemble box C/D snoRNAs , 2011, Nucleic acids research.

[115]  J. Mattick,et al.  SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. , 2011, RNA.

[116]  Caroline Paulus,et al.  Misfolded human tRNA isodecoder binds and neutralizes a 3′ UTR-embedded Alu element , 2011, Proceedings of the National Academy of Sciences.

[117]  Michelle S. Scott,et al.  From snoRNA to miRNA: Dual function regulatory non-coding RNAs , 2011, Biochimie.

[118]  G. Hutvagner,et al.  Transfer RNA‐derived fragments: origins, processing, and functions , 2011, Wiley interdisciplinary reviews. RNA.

[119]  R. Place,et al.  Small RNA and transcriptional upregulation , 2011, Wiley interdisciplinary reviews. RNA.

[120]  E. Ullian,et al.  A role for noncanonical microRNAs in the mammalian brain revealed by phenotypic differences in Dgcr8 versus Dicer1 knockouts and small RNA sequencing. , 2011, RNA.

[121]  Hongyu Zhao,et al.  Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans. , 2011, RNA.

[122]  Ana Kozomara,et al.  miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..

[123]  Manolis Kellis,et al.  New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. , 2011, Genome research.

[124]  J. Ragoussis,et al.  The small-nucleolar RNAs commonly used for microRNA normalisation correlate with tumour pathology and prognosis , 2011, British Journal of Cancer.

[125]  Markus Brameier,et al.  Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs , 2010, Nucleic Acids Res..

[126]  Yoshihide Hayashizaki,et al.  Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin , 2011, RNA biology.

[127]  M. Behlke,et al.  Small nucleolar RNAs U32a, U33, and U35a are critical mediators of metabolic stress. , 2011, Cell metabolism.

[128]  M. Mathews,et al.  The evolution and expression of the snaR family of small non-coding RNAs , 2010, Nucleic acids research.

[129]  Michael Q. Zhang,et al.  Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression , 2011, Nucleic acids research.

[130]  Wei Li,et al.  Gene Regulation in Giardia lambia Involves a Putative MicroRNA Derived from a Small Nucleolar RNA , 2011, PLoS neglected tropical diseases.

[131]  Michelle S. Scott,et al.  Human box C/D snoRNA processing conservation across multiple cell types , 2011, Nucleic acids research.

[132]  P. Brousset,et al.  Specific small nucleolar RNA expression profiles in acute leukemia , 2012, Leukemia.

[133]  G. Zardo,et al.  Transcriptional targeting by microRNA-Polycomb complexes , 2012, Cell cycle.

[134]  J. Mendell,et al.  MicroRNAs in Stress Signaling and Human Disease , 2012, Cell.

[135]  D. Duelli,et al.  Supplemental Materials and Methods: Linker Ligation , 2022 .

[136]  Michal Linial,et al.  Conservation of the relative tRNA composition in healthy and cancerous tissues. , 2012, RNA.

[137]  B. Peterlin,et al.  7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription , 2012, Wiley interdisciplinary reviews. RNA.

[138]  S. Kauppinen,et al.  LNA-mediated anti-miR-155 silencing in low-grade B-cell lymphomas. , 2012, Blood.

[139]  R. Place,et al.  Upregulation of Cyclin B1 by miRNA and its implications in cancer , 2011, Nucleic acids research.

[140]  F. Jiang,et al.  Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis , 2011, Oncogene.

[141]  A. Chakraborty,et al.  Loss of ribosomal RNA modification causes developmental defects in zebrafish , 2011, Nucleic acids research.

[142]  D. J. Driscoll,et al.  Prader-Willi syndrome. , 1984, Current problems in pediatrics.

[143]  D. Corey,et al.  Argonaute and the nuclear RNAs: new pathways for RNA-mediated control of gene expression. , 2012, Nucleic acid therapeutics.

[144]  Yuan Chang,et al.  Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs , 2012, Nucleic acids research.

[145]  Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation , 2012, Nucleic acids research.

[146]  M. Bohnsack,et al.  The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA , 2012, Wiley interdisciplinary reviews. RNA.

[147]  Holger Heyn,et al.  CpG island hypermethylation-associated silencing of small nucleolar RNAs in human cancer , 2012, RNA biology.

[148]  C. Croce,et al.  MicroRNA dysregulation in cancer: diagnostics, monitoring and therapeutics. A comprehensive review , 2012, EMBO molecular medicine.

[149]  T. Visakorpi,et al.  Diagnostic and prognostic signatures from the small non-coding RNA transcriptome in prostate cancer , 2012, Oncogene.

[150]  J. Cavaille,et al.  The SNORD115 (H/MBII-52) and SNORD116 (H/MBII-85) gene clusters at the imprinted Prader–Willi locus generate canonical box C/D snoRNAs , 2012, Nucleic acids research.

[151]  T. Kiss,et al.  Human intron-encoded Alu RNAs are processed and packaged into Wdr79-associated nucleoplasmic box H/ACA RNPs. , 2012, Genes & development.

[152]  A. Dejean,et al.  Senescence is an endogenous trigger for microRNA-directed transcriptional gene silencing in human cells , 2012, Nature Cell Biology.

[153]  Long-Cheng Li,et al.  miRNA goes nuclear , 2012, RNA biology.

[154]  A. Schleiffer,et al.  Diversity and roles of (t)RNA ligases , 2012, Cellular and Molecular Life Sciences.

[155]  C. Andersen,et al.  Circulating U2 small nuclear RNA fragments as a novel diagnostic biomarker for pancreatic and colorectal adenocarcinoma , 2013, International journal of cancer.