Generic placeholder image

Current Pharmaceutical Biotechnology

Editor-in-Chief

ISSN (Print): 1389-2010
ISSN (Online): 1873-4316

Review Article

Noncoding RNAs: A New Layer of Functional RNAs

Author(s): Dilek Cansu Gurer and Bünyamin Akgül*

Volume 24, Issue 7, 2023

Published on: 20 August, 2022

Page: [856 - 871] Pages: 16

DOI: 10.2174/1389201023666220602102133

Price: $65

Abstract

The conventional central dogma of molecular biology dictates that the genetic information contained within deoxyribonucleic acid (DNA) is passed onto messenger ribonucleic acids (mRNAs), which are then used as templates to synthesize proteins. Although these types of proteincoding genes have been historically prioritized in typical phenotype-genotype studies with a parallel disregard to the rest of the genome, the completion of genome projects has unveiled a surprising layer of genetic information that can play critical roles in cellular processes without coding for proteins. These types of genes are called noncoding genes as they do not code for proteins. Noncoding genes come in different sizes and shapes, and they are just as versatile in carrying out cellular biochemical processes as proteins. In this review, we cover a comprehensive review of housekeeping and regulatory noncoding genes and their mode of action.

Keywords: Noncoding RNA, miRNA, siRNA, piRNA, lncRNA, circRNA.

Graphical Abstract
[1]
Jarroux, J.; Morillon, A.; Pinskaya, M. Long non coding RNA biology - History. Adv. Exp. Med. Biol., 2017, 1008.
[http://dx.doi.org/10.1007/978-981-10-5203-3]
[2]
Costa, F.F. Non-coding RNAs: lost in translation? Gene, 2007, 386(1-2), 1-10.
[http://dx.doi.org/10.1016/j.gene.2006.09.028] [PMID: 17113247]
[3]
Larochelle, M.; Robert, M.A.; Hébert, J.N.; Liu, X.; Matteau, D.; Rodrigue, S.; Tian, B.; Jacques, P.É.; Bachand, F. Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast. Nat. Commun., 2018, 9(1), 4364.
[http://dx.doi.org/10.1038/s41467-018-06546-x] [PMID: 30341288]
[4]
Djebali, S.; Davis, C.A.; Merkel, A.; Dobin, A.; Lassmann, T.; Mortazavi, A.; Tanzer, A.; Lagarde, J.; Lin, W.; Schlesinger, F.; Xue, C.; Marinov, G.K.; Khatun, J.; Williams, B.A.; Zaleski, C.; Rozowsky, J.; Röder, M.; Kokocinski, F.; Abdelhamid, R.F.; Alioto, T.; Antoshechkin, I.; Baer, M.T.; Bar, N.S.; Batut, P.; Bell, K.; Bell, I.; Chakrabortty, S.; Chen, X.; Chrast, J.; Curado, J.; Derrien, T.; Drenkow, J.; Dumais, E.; Dumais, J.; Duttagupta, R.; Falconnet, E.; Fastuca, M.; Fejes-Toth, K.; Ferreira, P.; Foissac, S.; Fullwood, M.J.; Gao, H.; Gonzalez, D.; Gordon, A.; Gunawardena, H.; Howald, C.; Jha, S.; Johnson, R.; Kapranov, P.; King, B.; Kingswood, C.; Luo, O.J.; Park, E.; Persaud, K.; Preall, J.B.; Ribeca, P.; Risk, B.; Robyr, D.; Sammeth, M.; Schaffer, L.; See, L.H.; Shahab, A.; Skancke, J.; Suzuki, A.M.; Takahashi, H.; Tilgner, H.; Trout, D.; Walters, N.; Wang, H.; Wrobel, J.; Yu, Y.; Ruan, X.; Hayashizaki, Y.; Harrow, J.; Gerstein, M.; Hubbard, T.; Reymond, A.; Antonarakis, S.E.; Hannon, G.; Giddings, M.C.; Ruan, Y.; Wold, B.; Carninci, P.; Guigó, R.; Gingeras, T.R. Landscape of transcription in human cells. Nature, 2012, 489(7414), 101-108.
[http://dx.doi.org/10.1038/nature11233] [PMID: 22955620]
[5]
Yu, L.; Xia, K.; Cen, X.; Huang, X.; Sun, W.; Zhao, Z.; Liu, J. DNA methylation of noncoding RNAs: New insights into osteogenesis and common bone diseases. Stem Cell Res. Ther., 2020, 11(1), 109.
[http://dx.doi.org/10.1186/s13287-020-01625-7] [PMID: 32143708]
[6]
Lujambio, A.; Portela, A.; Liz, J.; Melo, S.A.; Rossi, S.; Spizzo, R.; Croce, C.M.; Calin, G.A.; Esteller, M. CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer. Oncogene, 2010, 29(48), 6390-6401.
[http://dx.doi.org/10.1038/onc.2010.361] [PMID: 20802525]
[7]
Brannan, C.I.; Dees, E.C.; Ingram, R.S.; Tilghman, S.M. The product of the H19 gene may function as an RNA. Mol. Cell. Biol., 1990, 10(1), 28-36.
[http://dx.doi.org/10.1128/MCB.10.1.28] [PMID: 1688465]
[8]
Marchese, F.P.; Huarte, M. Long non-coding RNAs and chromatin modifiers: Their place in the epigenetic code. Epigenetics, 2014, 9(1), 21-26.
[http://dx.doi.org/10.4161/epi.27472] [PMID: 24335342]
[9]
Pratt, H.; Weng, Z. Decoding the non-coding genome: Opportunities and challenges of genomic and epigenomic consortium data. Curr. Opin. Syst. Biol., 2018, 11, 82-90.
[http://dx.doi.org/10.1016/j.coisb.2018.09.002]
[10]
Harrow, J.; Denoeud, F.; Frankish, A.; Reymond, A.; Chen, C.K.; Chrast, J.; Lagarde, J.; Gilbert, J.G.R.; Storey, R.; Swarbreck, D. GENCODE: Producing a reference annotation for ENCODE. Genome Biol., 2006, 7(1), 1-9.
[http://dx.doi.org/10.1186/gb-2006-7-s1-s4]
[11]
Zhang, Z.; Carriero, N.; Gerstein, M. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet., 2004, 20(2), 62-67.
[http://dx.doi.org/10.1016/j.tig.2003.12.005] [PMID: 14746985]
[12]
Hunt, S.E.; McLaren, W.; Gil, L.; Thormann, A.; Schuilenburg, H.; Sheppard, D.; Parton, A.; Armean, I.M.; Trevanion, S.J.; Flicek, P.; Cunningham, F. Ensembl variation resources. Database, 2018, 2018(8), 1-12.
[http://dx.doi.org/10.1093/database/bay119] [PMID: 30576484]
[13]
Hombach, S.; Kretz, M. Non-Coding RNAs: Classification; Biology and Functioning. Non-Coding RNAs in Colorectal Cancer. 2016, 3-17.
[http://dx.doi.org/10.1007/978-3-319-42059-2]
[14]
Yang, S.; Sun, Z.; Zhou, Q.; Wang, W.; Wang, G.; Song, J.; Li, Z.; Zhang, Z.; Chang, Y.; Xia, K.; Liu, J.; Yuan, W. MicroRNAs, long noncoding RNAs, and circular RNAs: Potential tumor biomarkers and targets for colorectal cancer. Cancer Manag. Res., 2018, 10, 2249-2257.
[http://dx.doi.org/10.2147/CMAR.S166308] [PMID: 30100756]
[15]
Tüncel, Ö.; Kara, M.; Yaylak, B. Erdoğan, İ Akgül, B. Noncoding RNAs in apoptosis: Identification and function. Turk. J. Biol., 2022.
[http://dx.doi.org/10.3906/biy-2109-35]
[16]
Aronson, A.I. McCARTHY, B.J. Studies of E. coli ribosomal RNA and its degradation products. Biophys. J., 1961, 1(3), 215-226.
[http://dx.doi.org/10.1016/S0006-3495(61)86885-9] [PMID: 14448379]
[17]
Dahlberg, A.E. The functional role of ribosomal RNA in protein synthesis. Cell, 1989, 57(4), 525-529.
[http://dx.doi.org/10.1016/0092-8674(89)90122-0] [PMID: 2655923]
[18]
Saw, P.E.; Xu, X.; Chen, J.; Song, E.W. Non-Coding RNAs: The new central dogma of cancer biology. Sci. China Life Sci., 2020, 64(1), 22-50.
[http://dx.doi.org/10.1007/s11427-020-1700-9] [PMID: 32930921]
[19]
Scheitl, C.P.M.; Ghaem Maghami, M.; Lenz, A.K.; Höbartner, C. Site-specific RNA methylation by a methyltransferase ribozyme. Nature, 2020, 587(7835), 663-667.
[http://dx.doi.org/10.1038/s41586-020-2854-z] [PMID: 33116304]
[20]
Valadkhan, S.; Manley, J.L. Characterization of the catalytic activity of U2 and U6 snRNAs. RNA, 2003, 9(7), 892-904.
[http://dx.doi.org/10.1261/rna.5440303] [PMID: 12810922]
[21]
Robertson, M.P.; Joyce, G.F. The origins of the RNA world. Cold Spring Harb. Perspect. Biol., 2012, 4(5), 1.
[http://dx.doi.org/10.1101/cshperspect.a003608] [PMID: 20739415]
[22]
Woese, C.R. The Genetic Code: The Molecular Basis for Genetic Expression; 1967.
[23]
Crick, F.H. The origin of the genetic code. J. Mol. Biol., 1968, 38(3), 367-379.
[http://dx.doi.org/10.1016/0022-2836(68)90392-6] [PMID: 4887876]
[24]
Orgel, L.E. Evolution of the genetic apparatus. J. Mol. Biol., 1968, 38(3), 381-393.
[http://dx.doi.org/10.1016/0022-2836(68)90393-8] [PMID: 5718557]
[25]
Sidney, A.; Thomas, R.C. NobelPrize.org; The Nobel Prize in Chemistry, 1989. www.nobelprize.org/prizes/chemistry/1989/summary/
[26]
Matera, A.G.; Terns, R.M.; Terns, M.P. Non-coding RNAs: Lessons from the small nuclear and small nucleolar RNAs. Nat. Rev. Mol. Cell Biol., 2007, 8(3), 209-220.
[http://dx.doi.org/10.1038/nrm2124] [PMID: 17318225]
[27]
Wassarman, K.M.; Zhang, A.; Storz, G. Small RNAs in Escherichia coli. Trends Microbiol., 1999, 7(1), 37-45.
[http://dx.doi.org/10.1016/S0966-842X(98)01379-1] [PMID: 10068996]
[28]
Aravin, A.A.; Naumova, N.M.; Tulin, A.V.; Vagin, V.V.; Rozovsky, Y.M.; Gvozdev, V.A. Double-Stranded RNA-Mediated silencing of genomic tandem repeats and transposable elements in the shown to induce a potent sequence-specific inhibition of gene function in the maintenance of male fertility in Drosophila melanogaster. Curr. Biol., 2001, 11(13), 1017-1027.
[http://dx.doi.org/10.1016/S0960-9822(01)00299-8] [PMID: 11470406]
[29]
Seto, A.G.; Kingston, R.E.; Lau, N.C. The coming of age for Piwi proteins. Mol. Cell, 2007, 26(5), 603-609.
[http://dx.doi.org/10.1016/j.molcel.2007.05.021] [PMID: 17560367]
[30]
Bartel, D.P. Metazoan MicroRNAs. Cell, 2018, 173(1), 20-51.
[http://dx.doi.org/10.1016/j.cell.2018.03.006] [PMID: 29570994]
[31]
Akgül, B. Erdoğan, İ Intracytoplasmic Re-localization of miRISC complexes. Front. Genet., 2018, 9(SEP), 403.
[http://dx.doi.org/10.3389/fgene.2018.00403] [PMID: 30298086]
[32]
Erdoğan, İ.; Coşacak, M.İ.; Nalbant, A.; Akgül, B. Deep sequencing reveals two Jurkat subpopulations with distinct miRNA profiles during camptothecin-induced apoptosis. Turk. J. Biol., 2018, 42(2), 113-122.
[http://dx.doi.org/10.3906/biy-1710-62] [PMID: 30814873]
[33]
Cosacak, M.I.; Erdogan, I.; Nalbant, A.; Akgul, B. Small RNA data set that includes tRNA-derived fragments from Jurkat cells treated with camptothecin. Data Brief, 2018, 17(2), 397-400.
[http://dx.doi.org/10.1016/j.dib.2018.01.050] [PMID: 29876408]
[34]
Ivey, K.N.; Srivastava, D. microRNAs as developmental regulators. Cold Spring Harb. Perspect. Biol., 2015, 7(7)a008144
[http://dx.doi.org/10.1101/cshperspect.a008144] [PMID: 26134312]
[35]
Goodall, G.J.; Wickramasinghe, V.O. RNA in Cancer. Nat. Rev. Cancer, 2021, 21(1), 22-36.
[http://dx.doi.org/10.1038/s41568-020-00306-0] [PMID: 33082563]
[36]
Meola, N.; Gennarino, V.A.; Banfi, S. microRNAs and genetic diseases. PathoGenetics, 2009, 2(1), 7.
[http://dx.doi.org/10.1186/1755-8417-2-7] [PMID: 19889204]
[37]
Hombach, S.; Kretz, M. Non-coding RNAs in colorectal cancer. Adv. Exp. Med. Biol., 2016, 937.
[http://dx.doi.org/10.1007/978-3-319-42059-2]
[38]
Lee, R.C.; Feinbaum, R.L.; Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 1993, 75(5), 843-854.
[http://dx.doi.org/10.1016/0092-8674(93)90529-Y] [PMID: 8252621]
[39]
Griffiths-Jones, S.; Grocock, R.J.; van Dongen, S.; Bateman, A.; Enright, A.J. miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 2006, 34(Suppl. 1), D140-D144.
[http://dx.doi.org/10.1093/nar/gkj112] [PMID: 16381832]
[40]
Lee, Y.; Kim, M.; Han, J.; Yeom, K.H.; Lee, S.; Baek, S.H.; Kim, V.N. MicroRNA genes are transcribed by RNA polymerase II. EMBO J., 2004, 23(20), 4051-4060.
[http://dx.doi.org/10.1038/sj.emboj.7600385] [PMID: 15372072]
[41]
O’Brien, J.; Hayder, H.; Zayed, Y.; Peng, C. Overview of MicroRNA biogenesis, mechanisms of actions, and circulation. Front. Endocrinol., 2018, 9(8), 402.
[http://dx.doi.org/10.3389/fendo.2018.00402] [PMID: 30123182]
[42]
Lee, Y.; Ahn, C.; Han, J.; Choi, H.; Kim, J.; Yim, J.; Lee, J.; Provost, P.; Rådmark, O.; Kim, S.; Kim, V.N. The nuclear RNase III Drosha initiates microRNA processing. Nature, 2003, 425(6956), 415-419.
[http://dx.doi.org/10.1038/nature01957] [PMID: 14508493]
[43]
Lund, E.; Güttinger, S.; Calado, A.; Dahlberg, J.E.; Kutay, U. Nuclear export of MicroRNA precursors. Science, 2004, 303(5654), 95-98.
[http://dx.doi.org/10.1126/science.1090599]
[44]
Chendrimada, T.P.; Gregory, R.I.; Kumaraswamy, E.; Norman, J.; Cooch, N.; Nishikura, K.; Shiekhattar, R. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature, 2005, 436(7051), 740-744.
[http://dx.doi.org/10.1038/nature03868] [PMID: 15973356]
[45]
Iwasaki, S.; Kobayashi, M.; Yoda, M.; Sakaguchi, Y.; Katsuma, S.; Suzuki, T.; Tomari, Y. Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes. Mol. Cell, 2010, 39(2), 292-299.
[http://dx.doi.org/10.1016/j.molcel.2010.05.015] [PMID: 20605501]
[46]
Yoda, M.; Kawamata, T.; Paroo, Z.; Ye, X.; Iwasaki, S.; Liu, Q.; Tomari, Y. ATP-dependent human RISC assembly pathways. Nat. Struct. Mol. Biol., 2010, 17(1), 17-23.
[http://dx.doi.org/10.1038/nsmb.1733] [PMID: 19966796]
[47]
Ha, M.; Kim, V.N. Regulation of microRNA biogenesis. Nat. Rev. Mol. Cell Biol., 2014, 15(8), 509-524.
[http://dx.doi.org/10.1038/nrm3838] [PMID: 25027649]
[48]
Yang, J.S.; Lai, E.C. Alternative miRNA biogenesis pathways and the interpretation of core miRNA pathway mutants. Mol. Cell, 2011, 43(6), 892-903.
[http://dx.doi.org/10.1016/j.molcel.2011.07.024] [PMID: 21925378]
[49]
Ruby, J.G.; Jan, C.H.; Bartel, D.P. Intronic microRNA precursors that bypass Drosha processing. Nature, 2007, 448(7149), 83-86.
[http://dx.doi.org/10.1038/nature05983] [PMID: 17589500]
[50]
Huntzinger, E.; Izaurralde, E. Gene silencing by microRNAs: Contributions of translational repression and mRNA decay. Nat. Rev. Genet., 2011, 12(2), 99-110.
[http://dx.doi.org/10.1038/nrg2936] [PMID: 21245828]
[51]
Xu, W.; San Lucas, A.; Wang, Z.; Liu, Y. Identifying microRNA targets in different gene regions. BMC Bioinformatics, 2014, 15(S7)(Suppl. 7), S4.
[http://dx.doi.org/10.1186/1471-2105-15-S7-S4] [PMID: 25077573]
[52]
Dharap, A.; Pokrzywa, C.; Murali, S.; Pandi, G.; Vemuganti, R. MicroRNA miR-324-3p induces promoter-mediated expression of RelA gene. PLoS One, 2013, 8(11)e79467
[http://dx.doi.org/10.1371/journal.pone.0079467] [PMID: 24265774]
[53]
He, L.; Hannon, G.J. MicroRNAs: Small RNAs with a big role in gene regulation. Nat. Rev. Genet., 2004, 5(7), 522-531.
[http://dx.doi.org/10.1038/nrg1379] [PMID: 15211354]
[54]
Olsen, P.H.; Ambros, V. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol., 1999, 216(2), 671-680.
[http://dx.doi.org/10.1006/dbio.1999.9523] [PMID: 10642801]
[55]
Jo, M.H.; Shin, S.; Jung, S.R.; Kim, E.; Song, J.J.; Hohng, S. Human argonaute 2 has diverse reaction pathways on target RNAs. Mol. Cell, 2015, 59(1), 117-124.
[http://dx.doi.org/10.1016/j.molcel.2015.04.027] [PMID: 26140367]
[56]
Filipowicz, W.; Bhattacharyya, S.N.; Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: Are the answers in sight? Nat. Rev. Genet., 2008, 9(2), 102-114.
[http://dx.doi.org/10.1038/nrg2290] [PMID: 18197166]
[57]
Yekta, S.; Shih, I.H.; Bartel, D.P. MicroRNA-Directed cleavage of HOXB8 MRNA. Science, 2004, 304(5670), 594-596.
[http://dx.doi.org/10.1126/science.1097434]
[58]
Jonas, S.; Izaurralde, E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat. Rev. Genet., 2015, 16(7), 421-433.
[http://dx.doi.org/10.1038/nrg3965] [PMID: 26077373]
[59]
Catalanotto, C.; Cogoni, C.; Zardo, G. MicroRNA in control of gene expression: An overview of nuclear functions. Int. J. Mol. Sci., 2016, 17(10)E1712
[http://dx.doi.org/10.3390/ijms17101712] [PMID: 27754357]
[60]
Fukao, A.; Mishima, Y.; Takizawa, N.; Oka, S.; Imataka, H.; Pelletier, J.; Sonenberg, N.; Thoma, C.; Fujiwara, T. MicroRNAs trigger dissociation of eIF4AI and eIF4AII from target mRNAs in humans. Mol. Cell, 2014, 56(1), 79-89.
[http://dx.doi.org/10.1016/j.molcel.2014.09.005] [PMID: 25280105]
[61]
Fukaya, T.; Iwakawa, H.O.; Tomari, Y. MicroRNAs block assembly of eIF4F translation initiation complex in Drosophila. Mol. Cell, 2014, 56(1), 67-78.
[http://dx.doi.org/10.1016/j.molcel.2014.09.004] [PMID: 25280104]
[62]
Zhang, L.; Ding, L.; Cheung, T.H.; Dong, M.Q.; Chen, J.; Sewell, A.K.; Liu, X.; Yates, J.R., III; Han, M. Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol. Cell, 2007, 28(4), 598-613.
[http://dx.doi.org/10.1016/j.molcel.2007.09.014] [PMID: 18042455]
[63]
Krol, J.; Loedige, I.; Filipowicz, W. The widespread regulation of microRNA biogenesis, function and decay. Nat. Rev. Genet., 2010, 11(9), 597-610.
[http://dx.doi.org/10.1038/nrg2843] [PMID: 20661255]
[64]
Vasudevan, S.; Steitz, J.A. AU-rich-element-mediated upregulation of translation by FXR1 and argonaute 2. Cell, 2007, 6, 1105-1118.
[http://dx.doi.org/10.1016/j.cell.2007.01.038]
[65]
Truesdell, S.S.; Mortensen, R.D.; Seo, M.; Schroeder, J.C.; Lee, J.H.; Letonqueze, O.; Vasudevan, S.V. MicroRNA-mediated MRNA translation activation in quiescent cells and oocytes involves recruitment of a nuclear MicroRNP. Sci. Rep, 2012, 2, 0-11.
[http://dx.doi.org/10.1038/srep00842]
[66]
Nishi, K.; Nishi, A.; Nagasawa, T.; Ui-Tei, K. Human TNRC6A is an Argonaute-navigator protein for microRNA-mediated gene silencing in the nucleus. RNA, 2013, 19(1), 17-35.
[http://dx.doi.org/10.1261/rna.034769.112] [PMID: 23150874]
[67]
Benhamed, M.; Herbig, U.; Ye, T.; Dejean, A.; Bischof, O. Senescence is an endogenous trigger for microRNA-directed transcriptional gene silencing in human cells. Nat. Cell Biol., 2012, 14(3), 266-275.
[http://dx.doi.org/10.1038/ncb2443] [PMID: 22366686]
[68]
Mello, C.C.; Conte, D. Jr Revealing the world of RNA interference. Nature, 2004, 431(7006), 338-342.
[http://dx.doi.org/10.1038/nature02872] [PMID: 15372040]
[69]
Lippman, Z.; Martienssen, R. The role of RNA interference in heterochromatic silencing. Nature, 2004, 431(7006), 364-370.
[http://dx.doi.org/10.1038/nature02875] [PMID: 15372044]
[70]
Vazquez, F.; Vaucheret, H.; Rajagopalan, R.; Lepers, C.; Gasciolli, V.; Mallory, A.C.; Hilbert, J.L.; Bartel, D.P.; Crété, P. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell, 2004, 16(1), 69-79.
[http://dx.doi.org/10.1016/j.molcel.2004.09.028] [PMID: 15469823]
[71]
Nilsen, T.W. Endo-siRNAs: Yet another layer of complexity in RNA silencing. Nat. Struct. Mol. Biol., 2008, 15(6), 546-548.
[http://dx.doi.org/10.1038/nsmb0608-546] [PMID: 18523465]
[72]
Huang, Y.; Ji, L.; Huang, Q.; Vassylyev, D.G.; Chen, X.; Ma, J.B. Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature, 2009, 461(7265), 823-827.
[http://dx.doi.org/10.1038/nature08433] [PMID: 19812675]
[73]
MacRae, I.J.; Ma, E.; Zhou, M.; Robinson, C.V.; Doudna, J.A. In vitro reconstitution of the human RISC-loading complex. Proc. Natl. Acad. Sci. USA, 2008, 105(2), 512-517.
[http://dx.doi.org/10.1073/pnas.0710869105] [PMID: 18178619]
[74]
Tomari, Y.; Du, T.; Zamore, P.D. Sorting of Drosophila small silencing RNAs. Cell, 2007, 130(2), 299-308.
[http://dx.doi.org/10.1016/j.cell.2007.05.057] [PMID: 17662944]
[75]
Piatek, M.J.; Werner, A. Endogenous siRNAs: Regulators of internal affairs. Biochem. Soc. Trans., 2014, 42(4), 1174-1179.
[http://dx.doi.org/10.1042/BST20140068] [PMID: 25110021]
[76]
Sugiyama, T.; Cam, H.; Verdel, A.; Moazed, D.; Grewal, S.I.S. RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production. Proc. Natl. Acad. Sci. USA, 2005, 102(1), 152-157.
[http://dx.doi.org/10.1073/pnas.0407641102] [PMID: 15615848]
[77]
Chen, L.; Dahlstrom, J.E.; Lee, S.H.; Rangasamy, D. Naturally occurring endo-siRNA silences LINE-1 retrotransposons in human cells through DNA methylation. Epigenetics, 2012, 7(7), 758-771.
[http://dx.doi.org/10.4161/epi.20706] [PMID: 22647391]
[78]
Chen, L.; Dahlstrom, J.E.; Chandra, A.; Board, P.; Rangasamy, D. Prognostic value of LINE-1 retrotransposon expression and its subcellular localization in breast cancer. Breast Cancer Res. Treat., 2012, 136(1), 129-142.
[http://dx.doi.org/10.1007/s10549-012-2246-7] [PMID: 23053642]
[79]
Ameyar-Zazoua, M.; Rachez, C.; Souidi, M.; Robin, P.; Fritsch, L.; Young, R.; Morozova, N.; Fenouil, R.; Descostes, N.; Andrau, J.C.; Mathieu, J.; Hamiche, A.; Ait-Si-Ali, S.; Muchardt, C.; Batsché, E.; Harel-Bellan, A. Argonaute proteins couple chromatin silencing to alternative splicing. Nat. Struct. Mol. Biol., 2012, 19(10), 998-1004.
[http://dx.doi.org/10.1038/nsmb.2373] [PMID: 22961379]
[80]
Wu, X.; Pan, Y.; Fang, Y.; Zhang, J.; Xie, M.; Yang, F.; Yu, T.; Ma, P.; Li, W.; Shu, Y. The biogenesis and functions of piRNAs in human diseases. Mol. Ther. Nucleic Acids, 2020, 21(9), 108-120.
[http://dx.doi.org/10.1016/j.omtn.2020.05.023] [PMID: 32516734]
[81]
Girard, A.; Sachidanandam, R.; Hannon, G.J.; Carmell, M.A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature, 2006, 442(7099), 199-202.
[http://dx.doi.org/10.1038/nature04917] [PMID: 16751776]
[82]
Lin, H.; Spradling, A.C. A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary. Development, 1997, 124(12), 2463-2476.
[http://dx.doi.org/10.1242/dev.124.12.2463] [PMID: 9199372]
[83]
Grimson, A.; Srivastava, M.; Fahey, B.; Woodcroft, B.J.; Chiang, H.R.; King, N.; Degnan, B.M.; Rokhsar, D.S.; Bartel, D.P. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature, 2008, 455(7217), 1193-1197.
[http://dx.doi.org/10.1038/nature07415] [PMID: 18830242]
[84]
Brennecke, J.; Aravin, A.A.; Stark, A.; Dus, M.; Kellis, M.; Sachidanandam, R.; Hannon, G.J. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell, 2007, 128(6), 1089-1103.
[http://dx.doi.org/10.1016/j.cell.2007.01.043] [PMID: 17346786]
[85]
Goriaux, C.; Desset, S.; Renaud, Y.; Vaury, C.; Brasset, E. Transcriptional properties and splicing of the flamenco piRNA cluster. EMBO Rep., 2014, 15(4), 411-418.
[http://dx.doi.org/10.1002/embr.201337898] [PMID: 24562610]
[86]
Siomi, M.C.; Sato, K.; Pezic, D.; Aravin, A.A. PIWI-interacting small RNAs: The vanguard of genome defence. Nat. Rev. Mol. Cell Biol., 2011, 12(4), 246-258.
[http://dx.doi.org/10.1038/nrm3089] [PMID: 21427766]
[87]
Nishimasu, H.; Ishizu, H.; Saito, K.; Fukuhara, S.; Kamatani, M.K.; Bonnefond, L.; Matsumoto, N.; Nishizawa, T.; Nakanaga, K.; Aoki, J.; Ishitani, R.; Siomi, H.; Siomi, M.C.; Nureki, O. Structure and function of Zucchini endoribonuclease in piRNA biogenesis. Nature, 2012, 491(7423), 284-287.
[http://dx.doi.org/10.1038/nature11509] [PMID: 23064230]
[88]
Kawaoka, S.; Izumi, N.; Katsuma, S.; Tomari, Y. 3′ end formation of PIWI-interacting RNAs in vitro. Mol. Cell, 2011, 43(6), 1015-1022.
[http://dx.doi.org/10.1016/j.molcel.2011.07.029] [PMID: 21925389]
[89]
Ohara, T.; Sakaguchi, Y.; Suzuki, T.; Ueda, H.; Miyauchi, K.; Suzuki, T. The 3′ termini of mouse Piwi-interacting RNAs are 2′-O-methylated. Nat. Struct. Mol. Biol., 2007, 14(4), 349-350.
[http://dx.doi.org/10.1038/nsmb1220] [PMID: 17384646]
[90]
Cosacak, M.I. Yiğit, H.; Kizil, C.; Akgül, B. Re-Arrangements in the cytoplasmic distribution of small RNAs following the maternal-to-zygotic transition in drosophila embryos. Genes, 2018, 9(2), 22.
[http://dx.doi.org/10.3390/genes9020082] [PMID: 29439397]
[91]
Zhang, Z.; Xu, J.; Koppetsch, B.S.; Wang, J.; Tipping, C.; Ma, S.; Weng, Z.; Theurkauf, W.E.; Zamore, P.D. Heterotypic piRNA Ping-Pong requires qin, a protein with both E3 ligase and Tudor domains. Mol. Cell, 2011, 44(4), 572-584.
[http://dx.doi.org/10.1016/j.molcel.2011.10.011] [PMID: 22099305]
[92]
Luo, S.; Lu, J. Silencing of transposable elements by piRNAs in Drosophila: An evolutionary perspective. Authors, 2017, 15(3), 164-176.
[http://dx.doi.org/10.1016/j.gpb.2017.01.006] [PMID: 28602845]
[93]
Czech, B.; Munafò, M.; Ciabrelli, F.; Eastwood, E.L.; Fabry, M.H.; Kneuss, E.; Hannon, G.J. piRNA-Guided genome defense: From biogenesis to silencing. Annu. Rev. Genet., 2018, 52(1), 131-157.
[http://dx.doi.org/10.1146/annurev-genet-120417-031441] [PMID: 30476449]
[94]
Brown, C.J.; Ballabio, A.; Rupert, J.L.; Lafreniere, R.G.; Grompe, M.; Tonlorenzi, R.; Willard, H.F. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature, 1991, 349(6304), 38-44.
[http://dx.doi.org/10.1038/349038a0] [PMID: 1985261]
[95]
Cao, H.; Wahlestedt, C.; Kapranov, P. Strategies to annotate and characterize long noncoding RNAs: Advantages and pitfalls. Trends Genet., 2018, 34(9), 704-721.
[http://dx.doi.org/10.1016/j.tig.2018.06.002] [PMID: 30017313]
[96]
Fernandes, J.C.R.; Acuña, S.M.; Aoki, J.I.; Floeter-Winter, L.M.; Muxel, S.M. Long non-coding RNAs in the regulation of gene expression: Physiology and disease. Noncoding RNA, 2019, 5(1)E17
[http://dx.doi.org/10.3390/ncrna5010017] [PMID: 30781588]
[97]
Yao, R.W.; Wang, Y.; Chen, L.L. Cellular functions of long noncoding RNAs. Nat. Cell Biol., 2019, 21(5), 542-551.
[http://dx.doi.org/10.1038/s41556-019-0311-8] [PMID: 31048766]
[98]
Gurer, D.C. Erdogan, İ.; Ahmadov, U.; Basol, M.; Sweef, O.; Cakan-Akdogan, G.; Akgül, B. Transcriptomics profiling identifies cisplatin-inducible death receptor 5 antisense long non-coding RNA as a modulator of proliferation and metastasis in hela cells. Front. Cell Dev. Biol., 2021, 9688855
[http://dx.doi.org/10.3389/fcell.2021.688855] [PMID: 34497804]
[99]
Distefano, J.K. The emerging role of long noncoding RNAs in human disease. In: Disease gene identification., 2018, 1706, pp. 91-110.
[http://dx.doi.org/10.1007/978-1-4939-7471-9_6]
[100]
Erdoğan, İ Sweef, O.; Akgül, B. Human long noncoding RNAs in apoptosis and cancer. Curr. Pharm. Biotechnol., 2021.
[101]
Caron, M.; St-Onge, P.; Drouin, S.; Richer, C.; Sontag, T.; Busche, S.; Bourque, G.; Pastinen, T.; Sinnett, D. Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes. PLoS One, 2018, 13(11)e0207250
[http://dx.doi.org/10.1371/journal.pone.0207250] [PMID: 30440012]
[102]
Latgé, G.; Poulet, C.; Bours, V.; Josse, C.; Jerusalem, G. Natural antisense transcripts: Molecular mechanisms and implications in breast cancers. Int. J. Mol. Sci., 2018, 19(1)E123
[http://dx.doi.org/10.3390/ijms19010123] [PMID: 29301303]
[103]
Ma, L.; Bajic, V.B.; Zhang, Z. On the classification of long non-coding RNAs. RNA Biol., 2013, 10(6), 925-933.
[http://dx.doi.org/10.4161/rna.24604] [PMID: 23696037]
[104]
Gudenas, B.L.; Wang, L. Prediction of LncRNA subcellular localization with deep learning from sequence features. Sci. Rep., 2018, 8(1), 16385.
[http://dx.doi.org/10.1038/s41598-018-34708-w] [PMID: 30401954]
[105]
Wang, K.C.; Chang, H.Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell, 2011, 43(6), 904-914.
[http://dx.doi.org/10.1016/j.molcel.2011.08.018] [PMID: 21925379]
[106]
Briata, P.; Gherzi, R. Long non-coding RNA-ribonucleoprotein networks in the post-transcriptional control of gene expression. Noncoding RNA, 2020, 6(3)E40
[http://dx.doi.org/10.3390/ncrna6030040] [PMID: 32957640]
[107]
Li, Y.; Syed, J.; Sugiyama, H. RNA-DNA triplex formation by long noncoding RNAs. Cell Chem. Biol., 2016, 23(11), 1325-1333.
[http://dx.doi.org/10.1016/j.chembiol.2016.09.011] [PMID: 27773629]
[108]
Liu, Y.; Xue, M.; Du, S.; Feng, W.; Zhang, K.; Zhang, L.; Liu, H.; Jia, G.; Wu, L.; Hu, X.; Chen, L.; Wang, P. Competitive endogenous RNA is an intrinsic component of EMT regulatory circuits and modulates EMT. Nat. Commun., 2019, 10(1), 1637.
[http://dx.doi.org/10.1038/s41467-019-09649-1] [PMID: 30967542]
[109]
Salmena, L.; Poliseno, L.; Tay, Y.; Kats, L.; Pandolfi, P.P. A ceRNA hypothesis: The Rosetta Stone of a hidden RNA language? Cell, 2011, 146(3), 353-358.
[http://dx.doi.org/10.1016/j.cell.2011.07.014] [PMID: 21802130]
[110]
Alkan, A.H.; Akgül, B. Endogenous MiRNA sponges. In: miRNomics: MicroRNA Biology and Computational Analysis; Allmer, J.; Yousef, M., Eds.; Springer US: New York, NY, 2022, pp. 91-104.
[http://dx.doi.org/10.1007/978-1-0716-1170-8_5]
[111]
Thomson, D.W.; Dinger, M.E. Endogenous microRNA sponges: Evidence and controversy. Nat. Rev. Genet., 2016, 17(5), 272-283.
[http://dx.doi.org/10.1038/nrg.2016.20] [PMID: 27040487]
[112]
Tay, Y.; Rinn, J.; Pandolfi, P.P. The multilayered complexity of ceRNA crosstalk and competition. Nature, 2014, 505(7483), 344-352.
[http://dx.doi.org/10.1038/nature12986] [PMID: 24429633]
[113]
Kopp, F.; Mendell, J.T. Functional classification and experimental dissection of long noncoding RNAs. Cell, 2018, 172(3), 393-407.
[http://dx.doi.org/10.1016/j.cell.2018.01.011] [PMID: 29373828]
[114]
Bousard, A. Raposo, A.C.; Żylicz, J.J.; Picard, C.; Pires, V.B.; Qi, Y.; Gil, C.; Syx, L.; Chang, H.Y.; Heard, E.; da Rocha, S.T. The role of Xist-mediated polycomb recruitment in the initiation of X-chromosome inactivation. EMBO Rep., 2019, 20(10)e48019
[http://dx.doi.org/10.15252/embr.201948019] [PMID: 31456285]
[115]
Latos, P.A. Pauler, F. M.; Koerner, M. V.; Şenergin, H. B.; Hudson, Q. J.; Stocsits, R. R.; Allhoff, W.; Stricker, S. H.; Klement, R. M.; Warczok, K. E. Airn transcriptional overlap, but not its LncRNA products, induces imprinted Igf2r silencing. Science, 2012, 338(6113), 1469-1472.
[http://dx.doi.org/10.1126/science.1228110]
[116]
Bernard, D.; Prasanth, K.V.; Tripathi, V.; Colasse, S.; Nakamura, T.; Xuan, Z.; Zhang, M.Q.; Sedel, F.; Jourdren, L.; Coulpier, F.; Triller, A.; Spector, D.L.; Bessis, A. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J., 2010, 29(18), 3082-3093.
[http://dx.doi.org/10.1038/emboj.2010.199] [PMID: 20729808]
[117]
Lee, S.; Kopp, F.; Chang, T.C.; Sataluri, A.; Chen, B.; Sivakumar, S.; Yu, H.; Xie, Y.; Mendell, J.T. Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins. Cell, 2016, 164(1-2), 69-80.
[http://dx.doi.org/10.1016/j.cell.2015.12.017] [PMID: 26724866]
[118]
Pang, Y.; Mao, C.; Liu, S. Encoding activities of non-coding RNAs. Theranostics, 2018, 8(9), 2496-2507.
[http://dx.doi.org/10.7150/thno.24677] [PMID: 29721095]
[119]
Han, C.; Sun, L.; Pan, Q.; Sun, Y.; Wang, W.; Chen, Y. Polysome profiling followed by quantitative PCR for identifying potential micropeptide encoding long non-coding RNAs in suspension cell lines. STAR Protoc., 2021, 3(1)101037
[http://dx.doi.org/10.1016/j.xpro.2021.101037] [PMID: 34977682]
[120]
Wang, S.; Mao, C.; Liu, S. Peptides encoded by noncoding genes: Challenges and perspectives. Signal Transduct. Target. Ther., 2019, 4(1), 57.
[http://dx.doi.org/10.1038/s41392-019-0092-3] [PMID: 31871775]
[121]
Xing, J.; Liu, H.; Jiang, W.; Wang, L. LncRNA-encoded peptide: Functions and predicting methods. Front. Oncol., 2021, 10622294
[http://dx.doi.org/10.3389/fonc.2020.622294] [PMID: 33520729]
[122]
Anderson, D.M.; Anderson, K.M.; Chang, C-L.; Makarewich, C.A.; Nelson, B.R.; McAnally, J.R.; Kasaragod, P.; Shelton, J.M.; Liou, J.; Bassel-Duby, R.; Olson, E.N. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell, 2015, 160(4), 595-606.
[http://dx.doi.org/10.1016/j.cell.2015.01.009] [PMID: 25640239]
[123]
Pang, Y.; Liu, Z.; Han, H.; Wang, B.; Li, W.; Mao, C.; Liu, S. Peptide SMIM30 promotes HCC development by inducing SRC/YES1 membrane anchoring and MAPK pathway activation. J. Hepatol., 2020, 73(5), 1155-1169.
[http://dx.doi.org/10.1016/j.jhep.2020.05.028] [PMID: 32461121]
[124]
Ye, M.; Zhang, J.; Wei, M.; Liu, B.; Dong, K. Emerging role of long noncoding RNA-encoded micropeptides in cancer. Cancer Cell Int., 2020, 20(1), 506.
[http://dx.doi.org/10.1186/s12935-020-01589-x] [PMID: 33088214]
[125]
Wu, S.; Guo, B.; Zhang, L.; Zhu, X.; Zhao, P.; Deng, J.; Zheng, J.; Li, F.; Wang, Y.; Zhang, S.; Zhang, Z.; Lu, J.; Zhou, Y. A micropeptide XBP1SBM encoded by lncRNA promotes angiogenesis and metastasis of TNBC via XBP1s pathway. Oncogene, 2022, 41(15), 2163-2172.
[http://dx.doi.org/10.1038/s41388-022-02229-6] [PMID: 35197570]
[126]
Lin, N.; Chang, K-Y.; Li, Z.; Gates, K.; Rana, Z.A.; Dang, J.; Zhang, D.; Han, T.; Yang, C-S.; Cunningham, T.J.; Head, S.R.; Duester, G.; Dong, P.D.; Rana, T.M. An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol. Cell, 2014, 53(6), 1005-1019.
[http://dx.doi.org/10.1016/j.molcel.2014.01.021] [PMID: 24530304]
[127]
Senís, E.; Esgleas, M.; Najas, S.; Jiménez-Sábado, V.; Bertani, C.; Giménez-Alejandre, M.; Escriche, A.; Ruiz-Orera, J.; Hergueta-Redondo, M.; Jiménez, M.; Giralt, A.; Nuciforo, P.; Albà, M.M.; Peinado, H.; Del Toro, D.; Hove-Madsen, L.; Götz, M.; Abad, M. TUNAR lncRNA encodes a microprotein that regulates neural differentiation and neurite formation by modulating calcium dynamics. Front. Cell Dev. Biol., 2021, 9747667
[http://dx.doi.org/10.3389/fcell.2021.747667] [PMID: 35036403]
[128]
Li, M.; Shao, F.; Qian, Q.; Yu, W.; Zhang, Z.; Chen, B.; Su, D.; Guo, Y.; Phan, A-V.; Song, L-S.; Stephens, S.B.; Sebag, J.; Imai, Y.; Yang, L.; Cao, H. A putative long noncoding RNA-encoded micropeptide maintains cellular homeostasis in pancreatic β cells. Mol. Ther. Nucleic Acids, 2021, 26, 307-320.
[http://dx.doi.org/10.1016/j.omtn.2021.06.027] [PMID: 34513312]
[129]
Sanger, H.L.; Klotz, G.; Riesner, D.; Gross, H.J.; Kleinschmidt, A.K. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc. Natl. Acad. Sci.USA, 1976, 73(11), 3852-3856.
[http://dx.doi.org/10.1073/pnas.73.11.3852] [PMID: 1069269]
[130]
Nigro, J.M.; Cho, K.R.; Fearon, E.R.; Kern, S.E.; Ruppert, J.M.; Oliner, J.D.; Kinzler, K.W.; Vogelstein, B. Scrambled exons. Cell, 1991, 64(3), 607-613.
[http://dx.doi.org/10.1016/0092-8674(91)90244-S] [PMID: 1991322]
[131]
Capel, B.; Swain, A.; Nicolis, S.; Hacker, A.; Walter, M.; Koopman, P.; Goodfellow, P.; Lovell-Badge, R. Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell, 1993, 73(5), 1019-1030.
[http://dx.doi.org/10.1016/0092-8674(93)90279-Y] [PMID: 7684656]
[132]
Zaphiropoulos, P.G. Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: Correlation with exon skipping. Proc. Natl. Acad. Sci., 1996, 93(13), 6536-6541.
[http://dx.doi.org/10.1073/pnas.93.13.6536]
[133]
Cocquerelle, C.; Daubersies, P.; Majérus, M.A.; Kerckaert, J.P.; Bailleul, B. Splicing with inverted order of exons occurs proximal to large introns. EMBO J., 1992, 11(3), 1095-1098.
[http://dx.doi.org/10.1002/j.1460-2075.1992.tb05148.x] [PMID: 1339341]
[134]
Surono, A.; Takeshima, Y.; Wibawa, T.; Ikezawa, M.; Nonaka, I.; Matsuo, M. Circular dystrophin RNAs consisting of exons that were skipped by alternative splicing. Hum. Mol. Genet., 1999, 8(3), 493-500.
[http://dx.doi.org/10.1093/hmg/8.3.493] [PMID: 9949208]
[135]
Burd, C.E.; Jeck, W.R.; Liu, Y.; Sanoff, H.K.; Wang, Z.; Sharpless, N.E. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet., 2010, 6(12)e1001233
[http://dx.doi.org/10.1371/journal.pgen.1001233] [PMID: 21151960]
[136]
Salzman, J.; Gawad, C.; Wang, P.L.; Lacayo, N.; Brown, P.O. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One, 2012, 7(2)e30733
[http://dx.doi.org/10.1371/journal.pone.0030733] [PMID: 22319583]
[137]
Szabo, L.; Salzman, J. Detecting circular RNAs: Bioinformatic and experimental challenges. Nat. Rev. Genet., 2016, 17(11), 679-692.
[http://dx.doi.org/10.1038/nrg.2016.114] [PMID: 27739534]
[138]
Memczak, S.; Jens, M.; Elefsinioti, A.; Torti, F.; Krueger, J.; Rybak, A.; Maier, L.; Mackowiak, S.D.; Gregersen, L.H.; Munschauer, M.; Loewer, A.; Ziebold, U.; Landthaler, M.; Kocks, C.; le Noble, F.; Rajewsky, N. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 2013, 495(7441), 333-338.
[http://dx.doi.org/10.1038/nature11928] [PMID: 23446348]
[139]
Hansen, T.B.; Venø, M.T.; Damgaard, C.K.; Kjems, J. Comparison of circular RNA prediction tools. Nucleic Acids Res., 2016, 44(6)e58
[http://dx.doi.org/10.1093/nar/gkv1458] [PMID: 26657634]
[140]
Zeng, X.; Lin, W.; Guo, M.; Zou, Q. A comprehensive overview and evaluation of circular RNA detection tools. PLOS Comput. Biol., 2017, 13(6)e1005420
[http://dx.doi.org/10.1371/journal.pcbi.1005420] [PMID: 28594838]
[141]
Nielsen, H.; Fiskaa, T.; Birgisdottir, Å.B.; Haugen, P.; Einvik, C.; Johansen, S. The ability to form full-length intron RNA circles is a general property of nuclear group I introns. RNA, 2003, 9(12), 1464-1475.
[http://dx.doi.org/10.1261/rna.5290903] [PMID: 14624003]
[142]
Guo, J.U.; Agarwal, V.; Guo, H.; Bartel, D.P. Expanded identification and characterization of mammalian circular RNAs. Genome Biol., 2014, 15(7), 409.
[http://dx.doi.org/10.1186/s13059-014-0409-z] [PMID: 25070500]
[143]
Xu, S.; Zhou, L.; Ponnusamy, M.; Zhang, L.; Dong, Y.; Zhang, Y.; Wang, Q.; Liu, J.; Wang, K. A comprehensive review of circRNA: From purification and identification to disease marker potential. PeerJ, 2018, 6(8)e5503
[http://dx.doi.org/10.7717/peerj.5503] [PMID: 30155370]
[144]
Yang, Y.; Fan, X.; Mao, M.; Song, X.; Wu, P.; Zhang, Y.; Jin, Y.; Yang, Y.; Chen, L.L.; Wang, Y.; Wong, C.C.; Xiao, X.; Wang, Z. Extensive translation of circular RNAs driven by N6-methyladenosine. Cell Res., 2017, 27(5), 626-641.
[http://dx.doi.org/10.1038/cr.2017.31] [PMID: 28281539]
[145]
Li, Z.; Huang, C.; Bao, C.; Chen, L.; Lin, M.; Wang, X.; Zhong, G.; Yu, B.; Hu, W.; Dai, L.; Zhu, P.; Chang, Z.; Wu, Q.; Zhao, Y.; Jia, Y.; Xu, P.; Liu, H.; Shan, G. Exon-intron circular RNAs regulate transcription in the nucleus. Nat. Struct. Mol. Biol., 2015, 22(3), 256-264.
[http://dx.doi.org/10.1038/nsmb.2959] [PMID: 25664725]
[146]
Venø, M.T.; Hansen, T.B.; Venø, S.T.; Clausen, B.H.; Grebing, M.; Finsen, B.; Holm, I.E.; Kjems, J. Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development. Genome Biol., 2015, 16(1), 245.
[http://dx.doi.org/10.1186/s13059-015-0801-3] [PMID: 26541409]
[147]
Haque, S.; Harries, L.W. Circular RNAs (circRNAs) in health and disease. Genes, 2017, 8(12), 1-17.
[http://dx.doi.org/10.3390/genes8120353] [PMID: 29182528]
[148]
Yaylak, B.; Erdogan, I.; Akgul, B. Transcriptomics analysis of circular RNAs differentially expressed in apoptotic hela cells. Front. Genet., 2019, 10(176), 176.
[http://dx.doi.org/10.3389/fgene.2019.00176] [PMID: 30918512]
[149]
Ashwal-Fluss, R.; Meyer, M.; Pamudurti, N.R.; Ivanov, A.; Bartok, O.; Hanan, M.; Evantal, N.; Memczak, S.; Rajewsky, N.; Kadener, S. circRNA biogenesis competes with pre-mRNA splicing. Mol. Cell, 2014, 56(1), 55-66.
[http://dx.doi.org/10.1016/j.molcel.2014.08.019] [PMID: 25242144]
[150]
Liang, D.; Tatomer, D.C.; Luo, Z.; Wu, H.; Yang, L.; Chen, L.L.; Cherry, S.; Wilusz, J.E. The output of protein-coding genes shifts to circular RNAs when the Pre-mRNA processing machinery is limiting. Mol. Cell, 2017, 68(5), 940-954.e3.
[http://dx.doi.org/10.1016/j.molcel.2017.10.034] [PMID: 29174924]
[151]
Chen, L.L.; Yang, L. Regulation of circRNA biogenesis. RNA Biol., 2015, 12(4), 381-388.
[http://dx.doi.org/10.1080/15476286.2015.1020271] [PMID: 25746834]
[152]
Zhang, X.O.; Wang, H.B.; Zhang, Y.; Lu, X.; Chen, L.L.; Yang, L. Complementary sequence-mediated exon circularization. Cell, 2014, 159(1), 134-147.
[http://dx.doi.org/10.1016/j.cell.2014.09.001] [PMID: 25242744]
[153]
Conn, S.J.; Pillman, K.A.; Toubia, J.; Conn, V.M.; Salmanidis, M.; Phillips, C.A.; Roslan, S.; Schreiber, A.W.; Gregory, P.A.; Goodall, G.J. The RNA binding protein quaking regulates formation of circRNAs. Cell, 2015, 160(6), 1125-1134.
[http://dx.doi.org/10.1016/j.cell.2015.02.014] [PMID: 25768908]
[154]
Errichelli, L.; Dini Modigliani, S.; Laneve, P.; Colantoni, A.; Legnini, I.; Capauto, D.; Rosa, A.; De Santis, R.; Scarfò, R.; Peruzzi, G.; Lu, L.; Caffarelli, E.; Shneider, N.A.; Morlando, M.; Bozzoni, I. FUS affects circular RNA expression in murine embryonic stem cell-derived motor neurons. Nat. Commun., 2017, 8(1), 14741.
[http://dx.doi.org/10.1038/ncomms14741] [PMID: 28358055]
[155]
Holdt, L.M.; Kohlmaier, A.; Teupser, D. Circular RNAs as therapeutic agents and targets. Front. Physiol., 2018, 9, 1262.
[http://dx.doi.org/10.3389/fphys.2018.01262] [PMID: 30356745]
[156]
Zhang, Y.; Zhang, X.O.; Chen, T.; Xiang, J.F.; Yin, Q.F.; Xing, Y.H.; Zhu, S.; Yang, L.; Chen, L.L. Circular intronic long noncoding RNAs. Mol. Cell, 2013, 51(6), 792-806.
[http://dx.doi.org/10.1016/j.molcel.2013.08.017] [PMID: 24035497]
[157]
Huang, C.; Liang, D.; Tatomer, D.C.; Wilusz, J.E. A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs. Genes Dev., 2018, 32(9-10), 639-644.
[http://dx.doi.org/10.1101/gad.314856.118] [PMID: 29773557]
[158]
Yu, L.; Gong, X.; Sun, L.; Zhou, Q.; Lu, B.; Zhu, L. The circular RNA Cdr1as act as an oncogene in hepatocellular carcinoma through targeting miR-7 expression. PLoS One, 2016, 11(7)e0158347
[http://dx.doi.org/10.1371/journal.pone.0158347] [PMID: 27391479]
[159]
Hansen, T.B.; Jensen, T.I.; Clausen, B.H.; Bramsen, J.B.; Finsen, B.; Damgaard, C.K.; Kjems, J. Natural RNA circles function as efficient microRNA sponges. Nature, 2013, 495(7441), 384-388.
[http://dx.doi.org/10.1038/nature11993] [PMID: 23446346]
[160]
Abe, N.; Matsumoto, K.; Nishihara, M.; Nakano, Y.; Shibata, A.; Maruyama, H.; Shuto, S.; Matsuda, A.; Yoshida, M.; Ito, Y.; Abe, H. Rolling circle translation of circular RNA in living human cells. Sci. Rep., 2015, 5(1), 16435.
[http://dx.doi.org/10.1038/srep16435] [PMID: 26553571]
[161]
Meyer, K.D.; Patil, D.P.; Zhou, J.; Zinoviev, A.; Skabkin, M.A.; Elemento, O.; Pestova, T.V.; Qian, S-B.; Jaffrey, S.R. 5′ UTR m(6)A promotes cap-independent translation. Cell, 2015, 163(4), 999-1010.
[http://dx.doi.org/10.1016/j.cell.2015.10.012] [PMID: 26593424]
[162]
Pamudurti, N.R.; Bartok, O.; Jens, M.; Ashwal-Fluss, R.; Stottmeister, C.; Ruhe, L.; Hanan, M.; Wyler, E.; Perez-Hernandez, D.; Ramberger, E.; Shenzis, S.; Samson, M.; Dittmar, G.; Landthaler, M.; Chekulaeva, M.; Rajewsky, N.; Kadener, S. Translation of CircRNAs. Mol. Cell, 2017, 66(1), 9-21.e7.
[http://dx.doi.org/10.1016/j.molcel.2017.02.021] [PMID: 28344080]
[163]
Huang, G.; Li, S.; Yang, N.; Zou, Y.; Zheng, D.; Xiao, T. Recent progress in circular RNAs in human cancers. Cancer Lett., 2017, 404(7), 8-18.
[http://dx.doi.org/10.1016/j.canlet.2017.07.002] [PMID: 28705773]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy