[1] Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 2009; 23(13): 1494-504.
[2] ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447(7146): 799-816.
[3] Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J,
Hertel J,
Lindemeyer M,
Reiche K,
Tanzer A,
Ucla C,
Wyss C,
Antonarakis SE,
Denoeud F,
Lagarde J,
Drenkow J,
Kapranov P,
Gingeras TR,
Guigó R,
Snyder M,
Gerstein MB,
Reymond A,
Hofacker IL,
Stadler PF. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 2007; 17: 852-64.
[4] Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res 2004; 14(10A): 1902-10.
[5] Carthew RW, Sontheimer EJ. Origins and Mechanisms of miRNAs and siRNAs. Cell 2009; 136(4): 642-55.
[6] Cullen BR. Transcription and processing of human microRNA precursors. Mol Cell 2004; 16(6): 861-5.
[7] Ekhteraei-Tousi S, Mohammad-Soltani B, Sadeghizadeh M, Mowla SJ, Parsi S, Soleimani M. Inhibitory effect of hsa-miR-590-5p on cardiosphere-derived stem cells differentiation through downregulation of TGFB signaling. J Cell Biochem 2015; 116(1): 179-91.
[8] Azimzadeh Jamalkandi S, Masoudi-Nejad A. RNAi pathway integration in Caenorhabditis elegans development. Funct Integr Genomics 2011; 11(3): 389-405.
[9] Lee RC, Feinbaum RL, Ambros V. The C. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993; 75(5): 843-54.
[10] van Rooij E, Sutherland LB, Liu N, Williams AH, McAnally J, Gerard RD, Richardson JA, Olson EN. A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure. Proc Natl Acad Sci U S A 2006; 103(48): 18255-60.
[11] Slack FJ, Basson M, Liu Z, Ambros V, Horvitz HR, Ruvkun G. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol Cell. 2000 Apr;5(4):659-69.
[12] Vella MC, Slack FJ. C. elegans microRNAs. WormBook, ed. The C. elegans Research Community, WormBook, 2005; Available at: http://www.wormbook.org.
[13] Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000; 408(6808): 86-9.
[14] Zamore PD, Tuschl T, Sharp PA, Bartel DP. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 2000; 101(1): 25-33.
[15] Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 2001; 106(1): 23-34.
[16] Lund E, Güttinger S, Calado A, Dahlberg JE, Kutay U. Nuclear export of microRNA precursors. Science 2004; 303(5654): 95-8.
[17] Ekhteraei Tousi S, Mohammad Soltani B, Sadeghizadeh M, Hoseini S, Soleimani M. Hsa-miR-133b expression profile during cardiac progenitor cell differentiation and its inhibitory effect on srf expression. Modares Journal of Medical Sciences: Pathobiology 2013; 16(1): 1-9.
[18] Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010; 466(7308): 835-40.
[19] Thomson DW, Bracken CP, Goodall GJ. Experimental strategies for microRNA target identification. Nucleic Acids Res 2011; 39(16): 6845-53.
[20] Fabian MR, Sonenberg N, Filipowicz W. Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 2010; 79: 351-79.
[21] Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W, Cui Q. An analysis of human microRNA and disease associations. PLoS One 2008; 3(10): e3420.
[22] Creighton CJ, Reid JG, Gunaratne PH. Expression profiling of microRNAs by deep sequencing. Brief Bioinform 2009; 10(5): 490-7.
[23] Dokanehiifard S, Soltani BM, Parsi S, Hosseini F, Javan M, Mowla SJ. Exprimental verification of a conserved intronic microRNA located in the human TrKC gene with a cell type-dependent apoptotic function. Cellular and Molecular life Science 2015.
[24] Lu C, Meyers BC, Green PJ. Construction of small RNA cDNA libraries for deep sequencing. Methods 2007; 43(2): 110-7.
[25] Eiring AM, Harb JG, Neviani P, Garton C, Oaks JJ, Spizzo R, Liu S, Schwind S, Santhanam R, Hickey CJ, Becker H, Chandler JC, Andino R, Cortes J, Hokland P, Huettner CS, Bhatia R, Roy DC, Liebhaber SA, Caligiuri MA, Marcucci G, Garzon R, Croce CM, Calin GA, Perrotti D. miR-328 functions as an RNA decoy to modulate hnRNP E2 regulation of mRNA translation in leukemic blasts. Cell 2010; 140(5): 652-65.
[26] Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, Endoh H, Harano T, Yatabe Y, Nagino M, Nimura Y, Mitsudomi T, Takahashi T. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 2004; 64(11): 3753-6.
[27] Ghanbari R, Mosakhani N, Asadi J, Nouraee N, Mowla SJ, Poustchi H, Malekzadeh R, Knuutila S. Decreased expression of fecal miR-4478 and miR-1295b-3p in early-stage colorectal cancer. Cancer Biomark 2015; 15(2): 195-201.
[28] Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A, Labourier E, Reinert KL, Brown D, Slack FJ. RAS is regulated by the let-7 microRNA family. Cell 2005; 120(5): 635-47.
[29] Khalili M, Sadeghizadeh M, Ghorbanian K, Malekzadeh R, Vasei M, Mowla SJ. Down-regulation of miR-302b, an ESC-specific microRNA, in Gastric Adenocarcinoma. Cell J 2012; 13(4): 251-8.
[30] He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, Hammond SM. A microRNA polycistron as a potential human oncogene. Nature 2005; 435(7043): 828-33.
[31] Almeida MI, Reis RM, Calin GA. MicroRNA history: discovery, recent applications, and next frontiers. Mutat Res 2011; 717(1-2): 1-8.
[32] O'Donnell KA, Wentzel EA, Zeller KI, Dang CV, Mendell JT. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 2005; 435(7043): 839-43.
[33] Ma R, Jiang T, Kang X. Circulating microRNAs in cancer: origin, function and application. J Exp Clin Cancer Res 2012; 31: 38.
[34] Turchinovich A, Samatov TR, Tonevitsky AG, Burwinkel B. Circulating miRNAs: cell-cell communication function?. Front Genet 2013; 4: 119.
[35] Turchinovich A, Weiz L, Burwinkel B. Extracellular miRNAs: the mystery of their origin and function. Trends Biochem Sci 2012; 37(11): 460-5.
[36] Liu X, Fortin K, Mourelatos Z. MicroRNAs: biogenesis and molecular functions. Brain Pathol 2008; 18(1): 113-21.
[37] Olena AF, Patton JG. Genomic organization of microRNAs. J Cell Physiol 2010; 222(3): 540-5.
[38] Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 2007; 130(1): 89-100.
[39] Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 2005; 33(8): 2697-706.
[40] Jiang P, Wu H, Wang W, Ma W, Sun X, Lu Z. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res 2007; 35(Web Server issue): W339-44.
[41] Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, Dreyfuss G. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 2002; 16(6): 720-8.
[42] Berezikov E, Cuppen E, Plasterk RH. Approaches to microRNA discovery. Nat Genet 2006; 38 Suppl: S2-7.
[43] Mendes ND, Freitas AT, Sagot MF. Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res 2009; 37(8): 2419-33.
[44] Parsi S, Soltani BM, Hosseini E, Tousi SE, Mowla SJ. Experimental verification of a predicted intronic microRNA in human NGFR gene with a potential pro-apoptotic function. PLoS One 2012; 7(4): e35561.
[45] Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001; 294(5543): 853-8.
[46] Seitz H, Royo H, Bortolin ML, Lin SP, Ferguson-Smith AC, Cavaillé J. A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Res 2004; 14(9): 1741-8.
[47] Nelson PT, Baldwin DA, Scearce LM, Oberholtzer JC, Tobias JW, Mourelatos Z. Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 2004; 1(2): 155-61.
[48] Brennecke J, Stark A, Russell RB, Cohen SM. Principles of microRNA-target recognition. PLoS Biol 2005; 3(3): e85.
[49] Kuhn DE, Martin MM, Feldman DS, Terry Jr AV, Nuovo GJ, Elton TS. Experimental validation of miRNA targets. Methods 2008; 44(1): 47-54.
[50] Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 2009; 27(6): 549-55.
[51] Le Brigand K, Robbe-Sermesant K, Mari B, Barbry P. MiRonTop: mining microRNAs targets across large scale gene expression studies. Bioinformatics 2010; 26(24): 3131-2.
[52] Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010; 141(1): 129-41.
[53] Oulas A, Boutla A, Gkirtzou K, Reczko M, Kalantidis K, Poirazi P. Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach. Nucleic Acids Res 2009; 37(10): 3276-87.
[54] 54-. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP. Vertebrate microRNA genes. Science 2003; 299(5612): 1540.
[55] Lai EC, Tomancak P, Williams RW, Rubin GM. Computational identification of Drosophila microRNA genes. Genome Biol 2003; 4(7): R42.
[56] Jones-Rhoades MW, Bartel DP. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 2004; 14(6): 787-99.
[57] Bonnet E, Wuyts J, Rouzé P, Van de Peer Y. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci U S A 2004; 101(31): 11511-6.
[58] Bentwich I. Prediction and validation of microRNAs and their targets. FEBS Lett 2005; 579(26): 5904-10.
[59] Sadeghi B, Ahmadi H, Azimzadeh-Jamalkandi S, Nassiri MR, Masoudi-Nejad A. BosFinder: a novel pre-microRNA gene prediction algorithm in Bos taurus. Anim Genet 2014; 45(4): 479-84.
[60] Ritchie W, Théodule FX, Gautheret D. Mireval: a web tool for simple microRNA prediction in genome sequences. Bioinformatics 2008; 24(11): 1394-6.
[61] Helvik SA, Snøve O Jr, Saetrom P. Reliable prediction of Drosha processing sites improves microRNA gene prediction. Bioinformatics 2007; 23(2): 142-9.
[62] Tyagi S, Vaz C, Gupta V, Bhatia R, Maheshwari S, Srinivasan A, Bhattacharya A. CID-miRNA: a web server for prediction of novel miRNA precursors in human genome. Biochem Biophys Res Commun 2008; 372(4): 831-4.
[63] Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005; 120(1): 15-20.
[64] Ahmadi H, Ahmadi A, Azimzadeh-Jamalkandi S, Shoorehdeli MA, Salehzadeh-Yazdi A, Bidkhori G, Masoudi-Nejad A. HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens. Genomics 2013; 101(2): 94-100.
[65] Cai X, Hagedorn CH, Cullen BR. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 2004; 10(12): 1957-66.
[66] 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.
[67] Mazière P, Enright AJ. Prediction of microRNA targets. Drug Discov Today 2007; 12(11-12): 452-8.
[68] Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol 2003; 5(1): R1.
[69] Dweep H, Sticht C, Pandey P, Gretz N. miRWalk--database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Inform 2011; 44(5): 839-47.
[70] Thirion M, Ochiya T. Roles of microRNAs in the hepatitis B virus infection and related diseases. Viruses 2013; 5(11): 2690-703.
[71] Raymond CK, Roberts BS, Garrett-Engele P, Lim LP, Johnson JM. Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. RNA 2005; 11(11): 1737-44.
Pathobiology Reserach