Kodlamayan RNA’lar

Yang JX, Rastetter RH, Wilhelm D. Non-coding RNAs: An Introduction. Adv Exp Med Biol. 2016;886:13-32.

Zhao J, Mu L, Wang Z, Fang X, He X, Zhang X, et al. The potential roles of circular RNAs in osteonecrosis of the femoral head (Review). Mol Med Rep. 2020;21(2):533-9.

Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S. Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell. 2003;113(3):383-94.

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921.

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science. 2001;291(5507):1304-51.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, et al. The transcriptional landscape of the mammalian genome. Science. 2005;309(5740):1559-63.

Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007;17(6):746-59.

Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116(2):281-97.

Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009;10(3):155-9.

Taft RJ, Pheasant M, Mattick JS. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays. 2007;29(3):288-99.

Carninci P. Molecular biology: The long and short of RNAs. Nature. 2009;457(7232):974-5.

Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet. 2014;15(1):7-21.

Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 2009;23(13):1494-504.

Zhang K, Shi ZM, Chang YN, Hu ZM, Qi HX, Hong W. The ways of action of long non-coding RNAs in cytoplasm and nucleus. Gene. 2014;547(1):1-9.

Chakraborty A, Uechi T, Kenmochi N. Guarding the 'translation apparatus': defective ribosome biogenesis and the p53 signaling pathway. Wiley Interdiscip Rev RNA. 2011;2(4):507-22.

Warner JR. Twenty years of ribosome assembly and ribosomopathies. RNA. 2015;21(4):758-9.

Yan Q, Zhu C, Guang S, Feng X. The Functions of Non-coding RNAs in rRNA Regulation. Front Genet. 2019;10:290.

Eickbush TH, Eickbush DG. Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics. 2007;175(2):477-85.

Bierhoff H, Postepska-Igielska A, Grummt I. Noisy silence: non-coding RNA and heterochromatin formation at repetitive elements. Epigenetics. 2014;9(1):53-61.

Wilson DN, Doudna Cate JH. The structure and function of the eukaryotic ribosome. Cold Spring Harb Perspect Biol. 2012;4(5).

Henras AK, Plisson-Chastang C, O'Donohue MF, Chakraborty A, Gleizes PE. An overview of pre-ribosomal RNA processing in eukaryotes. Wiley Interdiscip Rev RNA. 2015;6(2):225-42.

Ginisty H, Amalric F, Bouvet P. Nucleolin functions in the first step of ribosomal RNA processing. EMBO J. 1998;17(5):1476-86.

Steitz TA. A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol. 2008;9(3):242-53.

Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999;24(11):437-40.

WATSON JD. Involvement of RNA in the synthesis of proteins. Science. 1963;140(3562):17-26.

Bratkovič T, Božič J, Rogelj B. Functional diversity of small nucleolar RNAs. Nucleic Acids Res. 2020;48(4):1627-51.

Bachellerie JP, Cavaillé J, Hüttenhofer A. The expanding snoRNA world. Biochimie. 2002;84(8):775-90.

Ishizu H, Siomi H, Siomi MC. Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines. Genes Dev. 2012;26(21):2361-73.

Siddiqi S, Matushansky I. Piwis and piwi-interacting RNAs in the epigenetics of cancer. J Cell Biochem. 2012;113(2):373-80.

Matera AG, Terns RM, Terns MP. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol. 2007;8(3):209-20.

Kishore S, Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science. 2006;311(5758):230-2.

Tanaka R, Satoh H, Moriyama M, Satoh K, Morishita Y, Yoshida S, 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. Genes Cells. 2000;5(4):277-87.

Dong XY, Rodriguez C, Guo P, Sun X, Talbot JT, Zhou W, et al. SnoRNA U50 is a candidate tumor-suppressor gene at 6q14.3 with a mutation associated with clinically significant prostate cancer. Hum Mol Genet. 2008;17(7):1031-42.

Martens-Uzunova ES, Hoogstrate Y, Kalsbeek A, Pigmans B, Vredenbregt-van den Berg M, Dits N, et al. C/D-box snoRNA-derived RNA production is associated with malignant transformation and metastatic progression in prostate cancer. Oncotarget. 2015;6(19):17430-44.

Dong XY, Guo P, Boyd J, Sun X, Li Q, Zhou W, et al. Implication of snoRNA U50 in human breast cancer. J Genet Genomics. 2009;36(8):447-54.

Lyons SM, Fay MM, Ivanov P. The role of RNA modifications in the regulation of tRNA cleavage. FEBS Lett. 2018;592(17):2828-44.

Kirchner S, Ignatova Z. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat Rev Genet. 2015;16(2):98-112.

Huang SQ, Sun B, Xiong ZP, Shu Y, Zhou HH, Zhang W, et al. The dysregulation of tRNAs and tRNA derivatives in cancer. J Exp Clin Cancer Res. 2018;37(1):101.

Itoh Y, Sekine S, Suetsugu S, Yokoyama S. Tertiary structure of bacterial selenocysteine tRNA. Nucleic Acids Res. 2013;41(13):6729-38.

Burns EM, Turner C. Pure-tone pitch anomalies. II. Pitch-intensity effects and diplacusis in impaired ears. J Acoust Soc Am. 1986;79(5):1530-40.

Goodenbour JM, Pan T. Diversity of tRNA genes in eukaryotes. Nucleic Acids Res. 2006;34(21):6137-46.

Ibba M, Soll D. Aminoacyl-tRNA synthesis. Annu Rev Biochem. 2000;69:617-50.

Sprinzl M, Cramer F. The -C-C-A end of tRNA and its role in protein biosynthesis. Prog Nucleic Acid Res Mol Biol. 1979;22:1-69.

Green R, Noller HF. Ribosomes and translation. Annu Rev Biochem. 1997;66:679-716.

Rubio Gomez MA, Ibba M. Aminoacyl-tRNA synthetases. RNA. 2020;26(8):910-36.

Smith D, Yarus M. Transfer RNA structure and coding specificity. I. Evidence that a D-arm mutation reduces tRNA dissociation from the ribosome. J Mol Biol. 1989;206(3):489-501.

Crick FH. Codon--anticodon pairing: the wobble hypothesis. J Mol Biol. 1966;19(2):548-55.

Agris PF. Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified-wobble hypothesis. Biochimie. 1991;73(11):1345-9.

Agris PF. Decoding the genome: a modified view. Nucleic Acids Res. 2004;32(1):223-38.

Schmidt RL, Simonović M. Synthesis and decoding of selenocysteine and human health. Croat Med J. 2012;53(6):535-50.

Rédei GP. tRNA (transfer RNA). Encyclopedia of Genetics, Genomics, Proteomics and Informatics. Dordrecht: Springer Netherlands; 2008. p. 2038-.

Pan T. Modifications and functional genomics of human transfer RNA. Cell Res. 2018;28(4):395-404.

Tomikawa C. 7-Methylguanosine Modifications in Transfer RNA (tRNA). Int J Mol Sci. 2018;19(12).

Weinberg RA, Penman S. Small molecular weight monodisperse nuclear RNA. J Mol Biol. 1968;38(3):289-304.

Matera AG, Weiner AM, Schmid CW. Structure and evolution of the U2 small nuclear RNA multigene family in primates: gene amplification under natural selection? Mol Cell Biol. 1990;10(11):5876-82.

Card CO, Morris GF, Brown DT, Marzluff WF. Sea urchin small nuclear RNA genes are organized in distinct tandemly repeating units. Nucleic Acids Res. 1982;10(23):7677-88.

Staley JP, Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell. 1998;92(3):315-26.

Jurica MS, Moore MJ. Pre-mRNA splicing: awash in a sea of proteins. Mol Cell. 2003;12(1):5-14.

Valadkhan S. snRNAs as the catalysts of pre-mRNA splicing. Curr Opin Chem Biol. 2005;9(6):603-8.

Gadgil A, Raczyńska KD. U7 snRNA: A tool for gene therapy. J Gene Med. 2021;23(4):e3321.

Shen X, Corey DR. Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs. Nucleic Acids Res. 2018;46(4):1584-600.

Stephenson ML, Zamecnik PC. Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. Proc Natl Acad Sci U S A. 1978;75(1):285-8.

Ma X, Zhao X, Yu YT. Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism. EMBO J. 2003;22(8):1889-97.

Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75(5):843-54.

Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ. Processing of primary microRNAs by the Microprocessor complex. Nature. 2004;432(7014):231-5.

Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007;27(1):91-105.

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Elbashir SM, Lendeckel W, Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 2001;15(2):188-200.

Saima Shakil Malik and Nosheen Masood and Alice Sherrard and Paul NB. Chapter 7 - Small non-coding RNAs as a tool for personalized therapy in familial cancers. In: Bibekanand M, editor. AGO-Driven Non-Coding RNAs: Academic Press; 2019. p. 179-208.

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Meng S, Zhou H, Feng Z, Xu Z, Tang Y, Li P, et al. CircRNA: functions and properties of a novel potential biomarker for cancer. Mol Cancer. 2017;16(1):94.

Yang JX, Rastetter RH, Wilhelm D. Non-coding RNAs: An Introduction. Adv Exp Med Biol. 2016;886:13-32.

Zhao J, Mu L, Wang Z, Fang X, He X, Zhang X, et al. The potential roles of circular RNAs in osteonecrosis of the femoral head (Review). Mol Med Rep. 2020;21(2):533-9.

Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S. Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell. 2003;113(3):383-94.

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921.

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science. 2001;291(5507):1304-51.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, et al. The transcriptional landscape of the mammalian genome. Science. 2005;309(5740):1559-63.

Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007;17(6):746-59.

Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116(2):281-97.

Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009;10(3):155-9.

Taft RJ, Pheasant M, Mattick JS. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays. 2007;29(3):288-99.

Carninci P. Molecular biology: The long and short of RNAs. Nature. 2009;457(7232):974-5.

Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet. 2014;15(1):7-21.

Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 2009;23(13):1494-504.

Zhang K, Shi ZM, Chang YN, Hu ZM, Qi HX, Hong W. The ways of action of long non-coding RNAs in cytoplasm and nucleus. Gene. 2014;547(1):1-9.

Chakraborty A, Uechi T, Kenmochi N. Guarding the 'translation apparatus': defective ribosome biogenesis and the p53 signaling pathway. Wiley Interdiscip Rev RNA. 2011;2(4):507-22.

Warner JR. Twenty years of ribosome assembly and ribosomopathies. RNA. 2015;21(4):758-9.

Yan Q, Zhu C, Guang S, Feng X. The Functions of Non-coding RNAs in rRNA Regulation. Front Genet. 2019;10:290.

Eickbush TH, Eickbush DG. Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics. 2007;175(2):477-85.

Bierhoff H, Postepska-Igielska A, Grummt I. Noisy silence: non-coding RNA and heterochromatin formation at repetitive elements. Epigenetics. 2014;9(1):53-61.

Wilson DN, Doudna Cate JH. The structure and function of the eukaryotic ribosome. Cold Spring Harb Perspect Biol. 2012;4(5).

Henras AK, Plisson-Chastang C, O'Donohue MF, Chakraborty A, Gleizes PE. An overview of pre-ribosomal RNA processing in eukaryotes. Wiley Interdiscip Rev RNA. 2015;6(2):225-42.

Ginisty H, Amalric F, Bouvet P. Nucleolin functions in the first step of ribosomal RNA processing. EMBO J. 1998;17(5):1476-86.

Steitz TA. A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol. 2008;9(3):242-53.

Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999;24(11):437-40.

WATSON JD. Involvement of RNA in the synthesis of proteins. Science. 1963;140(3562):17-26.

Bratkovič T, Božič J, Rogelj B. Functional diversity of small nucleolar RNAs. Nucleic Acids Res. 2020;48(4):1627-51.

Bachellerie JP, Cavaillé J, Hüttenhofer A. The expanding snoRNA world. Biochimie. 2002;84(8):775-90.

Ishizu H, Siomi H, Siomi MC. Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines. Genes Dev. 2012;26(21):2361-73.

Siddiqi S, Matushansky I. Piwis and piwi-interacting RNAs in the epigenetics of cancer. J Cell Biochem. 2012;113(2):373-80.

Matera AG, Terns RM, Terns MP. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol. 2007;8(3):209-20.

Kishore S, Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science. 2006;311(5758):230-2.

Tanaka R, Satoh H, Moriyama M, Satoh K, Morishita Y, Yoshida S, 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. Genes Cells. 2000;5(4):277-87.

Dong XY, Rodriguez C, Guo P, Sun X, Talbot JT, Zhou W, et al. SnoRNA U50 is a candidate tumor-suppressor gene at 6q14.3 with a mutation associated with clinically significant prostate cancer. Hum Mol Genet. 2008;17(7):1031-42.

Martens-Uzunova ES, Hoogstrate Y, Kalsbeek A, Pigmans B, Vredenbregt-van den Berg M, Dits N, et al. C/D-box snoRNA-derived RNA production is associated with malignant transformation and metastatic progression in prostate cancer. Oncotarget. 2015;6(19):17430-44.

Dong XY, Guo P, Boyd J, Sun X, Li Q, Zhou W, et al. Implication of snoRNA U50 in human breast cancer. J Genet Genomics. 2009;36(8):447-54.

Lyons SM, Fay MM, Ivanov P. The role of RNA modifications in the regulation of tRNA cleavage. FEBS Lett. 2018;592(17):2828-44.

Kirchner S, Ignatova Z. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat Rev Genet. 2015;16(2):98-112.

Huang SQ, Sun B, Xiong ZP, Shu Y, Zhou HH, Zhang W, et al. The dysregulation of tRNAs and tRNA derivatives in cancer. J Exp Clin Cancer Res. 2018;37(1):101.

Itoh Y, Sekine S, Suetsugu S, Yokoyama S. Tertiary structure of bacterial selenocysteine tRNA. Nucleic Acids Res. 2013;41(13):6729-38.

Burns EM, Turner C. Pure-tone pitch anomalies. II. Pitch-intensity effects and diplacusis in impaired ears. J Acoust Soc Am. 1986;79(5):1530-40.

Goodenbour JM, Pan T. Diversity of tRNA genes in eukaryotes. Nucleic Acids Res. 2006;34(21):6137-46.

Ibba M, Soll D. Aminoacyl-tRNA synthesis. Annu Rev Biochem. 2000;69:617-50.

Sprinzl M, Cramer F. The -C-C-A end of tRNA and its role in protein biosynthesis. Prog Nucleic Acid Res Mol Biol. 1979;22:1-69.

Green R, Noller HF. Ribosomes and translation. Annu Rev Biochem. 1997;66:679-716.

Rubio Gomez MA, Ibba M. Aminoacyl-tRNA synthetases. RNA. 2020;26(8):910-36.

Smith D, Yarus M. Transfer RNA structure and coding specificity. I. Evidence that a D-arm mutation reduces tRNA dissociation from the ribosome. J Mol Biol. 1989;206(3):489-501.

Crick FH. Codon--anticodon pairing: the wobble hypothesis. J Mol Biol. 1966;19(2):548-55.

Agris PF. Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified-wobble hypothesis. Biochimie. 1991;73(11):1345-9.

Agris PF. Decoding the genome: a modified view. Nucleic Acids Res. 2004;32(1):223-38.

Schmidt RL, Simonović M. Synthesis and decoding of selenocysteine and human health. Croat Med J. 2012;53(6):535-50.

Rédei GP. tRNA (transfer RNA). Encyclopedia of Genetics, Genomics, Proteomics and Informatics. Dordrecht: Springer Netherlands; 2008. p. 2038-.

Pan T. Modifications and functional genomics of human transfer RNA. Cell Res. 2018;28(4):395-404.

Tomikawa C. 7-Methylguanosine Modifications in Transfer RNA (tRNA). Int J Mol Sci. 2018;19(12).

Weinberg RA, Penman S. Small molecular weight monodisperse nuclear RNA. J Mol Biol. 1968;38(3):289-304.

Matera AG, Weiner AM, Schmid CW. Structure and evolution of the U2 small nuclear RNA multigene family in primates: gene amplification under natural selection? Mol Cell Biol. 1990;10(11):5876-82.

Card CO, Morris GF, Brown DT, Marzluff WF. Sea urchin small nuclear RNA genes are organized in distinct tandemly repeating units. Nucleic Acids Res. 1982;10(23):7677-88.

Staley JP, Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell. 1998;92(3):315-26.

Jurica MS, Moore MJ. Pre-mRNA splicing: awash in a sea of proteins. Mol Cell. 2003;12(1):5-14.

Valadkhan S. snRNAs as the catalysts of pre-mRNA splicing. Curr Opin Chem Biol. 2005;9(6):603-8.

Gadgil A, Raczyńska KD. U7 snRNA: A tool for gene therapy. J Gene Med. 2021;23(4):e3321.

Shen X, Corey DR. Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs. Nucleic Acids Res. 2018;46(4):1584-600.

Stephenson ML, Zamecnik PC. Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. Proc Natl Acad Sci U S A. 1978;75(1):285-8.

Ma X, Zhao X, Yu YT. Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism. EMBO J. 2003;22(8):1889-97.

Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75(5):843-54.

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