Genomic features and computational identification of human microRNAs under long-range developmental regulation

Ying Sheng1, Christopher Previti1
1Computational Biology Unit, Bergen Center for Computational Science, and Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, 5008, Norway

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Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ: miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008, 36 (36 Database): D154-158.

Kim DH, Saetrom P, Snove O, Rossi JJ: MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci USA. 2008, 105 (42): 16230-16235. 10.1073/pnas.0808830105.

Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN: MicroRNA genes are transcribed by RNA polymerase II. Embo J. 2004, 23 (20): 4051-4060. 10.1038/sj.emboj.7600385.

Cai X, Hagedorn CH, Cullen BR: Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. Rna. 2004, 10 (12): 1957-1966. 10.1261/rna.7135204.

Bracht J, Hunter S, Eachus R, Weeks P, Pasquinelli AE: Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. Rna. 2004, 10 (10): 1586-1594. 10.1261/rna.7122604.

Houbaviy HB, Dennis L, Jaenisch R, Sharp PA: Characterization of a highly variable eutherian microRNA gene. Rna. 2005, 11 (8): 1245-1257. 10.1261/rna.2890305.

Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, et al: Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol Cell. 2007, 26 (5): 745-752. 10.1016/j.molcel.2007.05.010.

Woods K, Thomson JM, Hammond SM: Direct regulation of an oncogenic micro-RNA cluster by E2F transcription factors. J Biol Chem. 2007, 282 (4): 2130-2134.

Gu J, He T, Pei Y, Li F, Wang X, Zhang J, Zhang X, Li Y: Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences. Mamm Genome. 2006, 17 (10): 1033-1041. 10.1007/s00335-006-0007-9.

Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song JS, Fisher DE: Chromatin structure analyses identify miRNA promoters. Genes Dev. 2008, 22 (22): 3172-3183. 10.1101/gad.1706508.

He S, Su H, Liu C, Skogerbo G, He H, He D, Zhu X, Liu T, Zhao Y, Chen R: MicroRNA-encoding long non-coding RNAs. BMC Genomics. 2008, 9: 236-10.1186/1471-2164-9-236.

Saini HK, Griffiths-Jones S, Enright AJ: Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci USA. 2007, 104 (45): 17719-17724. 10.1073/pnas.0703890104.

Zhou X, Ruan J, Wang G, Zhang W: Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol. 2007, 3 (3): e37-10.1371/journal.pcbi.0030037.

Saini HK, Enright AJ, Griffiths-Jones S: Annotation of Mammalian Primary microRNAs. BMC Genomics. 2008, 9 (1): 564-10.1186/1471-2164-9-564.

Wang X, Xuan Z, Zhao X, Li Y, Zhang MQ: High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res. 2008

Erson AE, Petty EM: MicroRNAs in development and disease. Clin Genet. 2008, 74 (4): 296-306. 10.1111/j.1399-0004.2008.01076.x.

Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engstrom PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, et al: Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 2007, 17 (5): 545-555. 10.1101/gr.6086307.

de la Calle-Mustienes E, Feijoo CG, Manzanares M, Tena JJ, Rodriguez-Seguel E, Letizia A, Allende ML, Gomez-Skarmeta JL: A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res. 2005, 15 (8): 1061-1072. 10.1101/gr.4004805.

Loots GG, Kneissel M, Keller H, Baptist M, Chang J, Collette NM, Ovcharenko D, Plajzer-Frick I, Rubin EM: Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease. Genome Res. 2005, 15 (7): 928-935. 10.1101/gr.3437105.

Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K, et al: Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 2005, 3 (1): e7-10.1371/journal.pbio.0030007.

Jeong Y, El-Jaick K, Roessler E, Muenke M, Epstein DJ: A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers. Development. 2006, 133 (4): 761-772. 10.1242/dev.02239.

Sandelin A, Bailey P, Bruce S, Engstrom PG, Klos JM, Wasserman WW, Ericson J, Lenhard B: Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics. 2004, 5 (1): 99-10.1186/1471-2164-5-99.

Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, et al: In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006, 444 (7118): 499-502. 10.1038/nature05295.

Li Q, Ritter D, Yang N, Dong Z, Li H, Chuang JH, Guo S: A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev Biol. 2010, 337 (2): 484-495. 10.1016/j.ydbio.2009.10.019.

Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y, Lenhard B: Transcriptional features of genomic regulatory blocks. Genome Biol. 2009, 10 (4): R38-10.1186/gb-2009-10-4-r38.

Tanay A, O'Donnell AH, Damelin M, Bestor TH: Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci USA. 2007, 104 (13): 5521-5526. 10.1073/pnas.0609746104.

Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, et al: A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006, 125 (2): 315-326. 10.1016/j.cell.2006.02.041.

Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007, 448 (7153): 553-560. 10.1038/nature06008.

Engstrom PG, Fredman D, Lenhard B: Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol. 2008, 9 (2): R34-10.1186/gb-2008-9-2-r34.

Borchert GM, Lanier W, Davidson BL: RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol. 2006, 13 (12): 1097-1101. 10.1038/nsmb1167.

Maston GA, Evans SK, Green MR: Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet. 2006, 7: 29-59. 10.1146/annurev.genom.7.080505.115623.

Eckner R, Ewen ME, Newsome D, Gerdes M, DeCaprio JA, Lawrence JB, Livingston DM: Molecular cloning and functional analysis of the adenovirus E1A-associated 300-kD protein (p300) reveals a protein with properties of a transcriptional adaptor. Genes Dev. 1994, 8 (8): 869-884. 10.1101/gad.8.8.869.

Eckner R, Yao TP, Oldread E, Livingston DM: Interaction and functional collaboration of p300/CBP and bHLH proteins in muscle and B-cell differentiation. Genes Dev. 1996, 10 (19): 2478-2490. 10.1101/gad.10.19.2478.

Yao TP, Oh SP, Fuchs M, Zhou ND, Ch'ng LE, Newsome D, Bronson RT, Li E, Livingston DM, Eckner R: Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300. Cell. 1998, 93 (3): 361-372. 10.1016/S0092-8674(00)81165-4.

Merika M, Williams AJ, Chen G, Collins T, Thanos D: Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription. Mol Cell. 1998, 1 (2): 277-287. 10.1016/S1097-2765(00)80028-3.

Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, et al: ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009, 457 (7231): 854-858. 10.1038/nature07730.

Pan G, Tian S, Nie J, Yang C, Ruotti V, Wei H, Jonsdottir GA, Stewart R, Thomson JA: Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell. 2007, 1 (3): 299-312. 10.1016/j.stem.2007.08.003.

Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, et al: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007, 39 (3): 311-318. 10.1038/ng1966.

Juan AH, Kumar RM, Marx JG, Young RA, Sartorelli V: Mir-214-dependent regulation of the polycomb protein Ezh2 in skeletal muscle and embryonic stem cells. Mol Cell. 2009, 36 (1): 61-74. 10.1016/j.molcel.2009.08.008.

Wang H, Garzon R, Sun H, Ladner KJ, Singh R, Dahlman J, Cheng A, Hall BM, Qualman SJ, Chandler DS, et al: NF-kappaB-YY1-miR-29 regulatory circuitry in skeletal myogenesis and rhabdomyosarcoma. Cancer Cell. 2008, 14 (5): 369-381. 10.1016/j.ccr.2008.10.006.

Krichevsky AM, Sonntag KC, Isacson O, Kosik KS: Specific microRNAs modulate embryonic stem cell-derived neurogenesis. Stem Cells. 2006, 24 (4): 857-864. 10.1634/stemcells.2005-0441.

Coolen M, Bally-Cuif L: MicroRNAs in brain development and physiology. Curr Opin Neurobiol. 2009, 19 (5): 461-470. 10.1016/j.conb.2009.09.006.

Liu N, Okamura K, Tyler DM, Phillips MD, Chung WJ, Lai EC: The evolution and functional diversification of animal microRNA genes. Cell Res. 2008, 18 (10): 985-996. 10.1038/cr.2008.278.

Meyer A, Van de Peer Y: From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). Bioessays. 2005, 27 (9): 937-945. 10.1002/bies.20293.

Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, Stadler PF: The expansion of the metazoan microRNA repertoire. BMC Genomics. 2006, 7: 25-10.1186/1471-2164-7-25.

Navratilova P, Fredman D, Hawkins TA, Turner K, Lenhard B, Becker TS: Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev Biol. 2009, 327 (2): 526-540. 10.1016/j.ydbio.2008.10.044.

Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M: The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 2009, D755-761. 37 Database

Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S: Ensembl's 10th year. Nucleic Acids Res. 2010, D557-562. 38 Database

Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P: Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res. 2008, D5-12. 36 Database

Dong X, Fredman D, Lenhard B: Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biol. 2009, 10 (8): R86-10.1186/gb-2009-10-8-r86.

Chopra VS, Mishra RK: "Mir"acles in hox gene regulation. Bioessays. 2006, 28 (5): 445-448. 10.1002/bies.20401.

McGlinn E, Yekta S, Mansfield JH, Soutschek J, Bartel DP, Tabin CJ: In ovo application of antagomiRs indicates a role for miR-196 in patterning the chick axial skeleton through Hox gene regulation. Proc Natl Acad Sci USA. 2009, 106 (44): 18610-18615. 10.1073/pnas.0910374106.

Sehm T, Sachse C, Frenzel C, Echeverri K: miR-196 is an essential early-stage regulator of tail regeneration, upstream of key spinal cord patterning events. Dev Biol. 2009, 334 (2): 468-480. 10.1016/j.ydbio.2009.08.008.

Hou W, Tian Q, Zheng J, Bonkovsky HL: MicroRNA-196 represses Bach1 protein and hepatitis C virus gene expression in human hepatoma cells expressing hepatitis C viral proteins. Hepatology. 2009

Edbauer D, Neilson JR, Foster KA, Wang CF, Seeburg DP, Batterton MN, Tada T, Dolan BM, Sharp PA, Sheng M: Regulation of synaptic structure and function by FMRP-associated microRNAs miR-125b and miR-132. Neuron. 2010, 65 (3): 373-384. 10.1016/j.neuron.2010.01.005.

Lusardi TA, Farr CD, Faulkner CL, Pignataro G, Yang T, Lan J, Simon RP, Saugstad JA: Ischemic preconditioning regulates expression of microRNAs and a predicted target, MeCP2, in mouse cortex. J Cereb Blood Flow Metab. 2009

Shaked I, Meerson A, Wolf Y, Avni R, Greenberg D, Gilboa-Geffen A, Soreq H: MicroRNA-132 potentiates cholinergic anti-inflammatory signaling by targeting acetylcholinesterase. Immunity. 2009, 31 (6): 965-973. 10.1016/j.immuni.2009.09.019.

Nudelman AS, Dirocco DP, Lambert TJ, Garelick MG, Le J, Nathanson NM, Storm DR: Neuronal activity rapidly induces transcription of the CREB-regulated microRNA-132, in vivo. Hippocampus. 2009

Yuen T, Ruf F, Chu T, Sealfon SC: Microtranscriptome regulation by gonadotropin-releasing hormone. Mol Cell Endocrinol. 2009, 302 (1): 12-17. 10.1016/j.mce.2008.12.013.

Cheng HY, Papp JW, Varlamova O, Dziema H, Russell B, Curfman JP, Nakazawa T, Shimizu K, Okamura H, Impey S, et al: microRNA modulation of circadian-clock period and entrainment. Neuron. 2007, 54 (5): 813-829. 10.1016/j.neuron.2007.05.017.

Lukiw WJ: Micro-RNA speciation in fetal, adult and Alzheimer's disease hippocampus. Neuroreport. 2007, 18 (3): 297-300. 10.1097/WNR.0b013e3280148e8b.

Haller F, von Heydebreck A, Zhang JD, Gunawan B, Langer C, Ramadori G, Wiemann S, Sahin O: Localization- and mutation-dependent microRNA (miRNA) expression signatures in gastrointestinal stromal tumours (GISTs), with a cluster of co-expressed miRNAs located at 14q32.31. J Pathol. 2010, 220 (1): 71-86. 10.1002/path.2610.

Lund AH: miR-10 in development and cancer. Cell Death Differ. 2010, 17 (2): 209-214. 10.1038/cdd.2009.58.

Choong ML, Yang HH, McNiece I: MicroRNA expression profiling during human cord blood-derived CD34 cell erythropoiesis. Exp Hematol. 2007, 35 (4): 551-564. 10.1016/j.exphem.2006.12.002.

Huang ZM, Yang J, Shen XY, Zhang XY, Meng FS, Xu JT, Zhang BF, Gao HJ: MicroRNA expression profile in non-cancerous colonic tissue associated with lymph node metastasis of colon cancer. J Dig Dis. 2009, 10 (3): 188-194. 10.1111/j.1751-2980.2009.00384.x.

Silber J, Lim DA, Petritsch C, Persson AI, Maunakea AK, Yu M, Vandenberg SR, Ginzinger DG, James CD, Costello JF, et al: miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells. BMC Med. 2008, 6: 14-10.1186/1741-7015-6-14.

Bemis LT, Chen R, Amato CM, Classen EH, Robinson SE, Coffey DG, Erickson PF, Shellman YG, Robinson WA: MicroRNA-137 targets microphthalmia-associated transcription factor in melanoma cell lines. Cancer Res. 2008, 68 (5): 1362-1368. 10.1158/0008-5472.CAN-07-2912.

Baroukh NN, Van Obberghen E: Function of microRNA-375 and microRNA-124a in pancreas and brain. Febs J. 2009, 276 (22): 6509-6521. 10.1111/j.1742-4658.2009.07353.x.

Avissar M, Christensen BC, Kelsey KT, Marsit CJ: MicroRNA expression ratio is predictive of head and neck squamous cell carcinoma. Clin Cancer Res. 2009, 15 (8): 2850-2855. 10.1158/1078-0432.CCR-08-3131.

Mathe EA, Nguyen GH, Bowman ED, Zhao Y, Budhu A, Schetter AJ, Braun R, Reimers M, Kumamoto K, Hughes D, et al: MicroRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus: associations with survival. Clin Cancer Res. 2009, 15 (19): 6192-6200. 10.1158/1078-0432.CCR-09-1467.

Avissar M, McClean MD, Kelsey KT, Marsit CJ: MicroRNA expression in head and neck cancer associates with alcohol consumption and survival. Carcinogenesis. 2009, 30 (12): 2059-2063. 10.1093/carcin/bgp277.

Hui AB, Lenarduzzi M, Krushel T, Waldron L, Pintilie M, Shi W, Perez-Ordonez B, Jurisica I, O'Sullivan B, Waldron J, et al: Comprehensive MicroRNA profiling for head and neck squamous cell carcinomas. Clin Cancer Res. 2010, 16 (4): 1129-1139. 10.1158/1078-0432.CCR-09-2166.

Ladeiro Y, Couchy G, Balabaud C, Bioulac-Sage P, Pelletier L, Rebouissou S, Zucman-Rossi J: MicroRNA profiling in hepatocellular tumors is associated with clinical features and oncogene/tumor suppressor gene mutations. Hepatology. 2008, 47 (6): 1955-1963. 10.1002/hep.22256.

Avnit-Sagi T, Kantorovich L, Kredo-Russo S, Hornstein E, Walker MD: The promoter of the pri-miR-375 gene directs expression selectively to the endocrine pancreas. PLoS One. 2009, 4 (4): e5033-10.1371/journal.pone.0005033.

Visvanathan J, Lee S, Lee B, Lee JW, Lee SK: The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development. Genes Dev. 2007, 21 (7): 744-749. 10.1101/gad.1519107.

Tang X, Tang G, Ozcan S: Role of microRNAs in diabetes. Biochim Biophys Acta. 2008, 1779 (11): 697-701.

Toloubeydokhti T, Pan Q, Luo X, Bukulmez O, Chegini N: The expression and ovarian steroid regulation of endometrial micro-RNAs. Reprod Sci. 2008, 15 (10): 993-1001. 10.1177/1933719108324132.

Zhang MC, Lv Y, Qi YT, Zhang Z, Fu XN, Yuan CG, Lai LH: [Knockdown and overexpression of miR-219 lead to embryonic defects in zebrafish development]. Fen Zi Xi Bao Sheng Wu Xue Bao. 2008, 41 (5): 341-348.

Schotte D, Chau JC, Sylvester G, Liu G, Chen C, van der Velden VH, Broekhuis MJ, Peters TC, Pieters R, den Boer ML: Identification of new microRNA genes and aberrant microRNA profiles in childhood acute lymphoblastic leukemia. Leukemia. 2009, 23 (2): 313-322. 10.1038/leu.2008.286.

Ohlsson Teague EM, Van der Hoek KH, Van der Hoek MB, Perry N, Wagaarachchi P, Robertson SA, Print CG, Hull LM: MicroRNA-regulated pathways associated with endometriosis. Mol Endocrinol. 2009, 23 (2): 265-275.

Decembrini S, Bressan D, Vignali R, Pitto L, Mariotti S, Rainaldi G, Wang X, Evangelista M, Barsacchi G, Cremisi F: MicroRNAs couple cell fate and developmental timing in retina. Proc Natl Acad Sci USA. 2009, 106 (50): 21179-21184. 10.1073/pnas.0909167106.

Liu SP, Fu RH, Yu HH, Li KW, Tsai CH, Shyu WC, Lin SZ: MicroRNAs regulation modulated self-renewal and lineage differentiation of stem cells. Cell Transplant. 2009, 18 (9): 1039-1045. 10.3727/096368909X471224.

Katada T, Ishiguro H, Kuwabara Y, Kimura M, Mitui A, Mori Y, Ogawa R, Harata K, Fujii Y: microRNA expression profile in undifferentiated gastric cancer. Int J Oncol. 2009, 34 (2): 537-542.

Dyrskjot L, Ostenfeld MS, Bramsen JB, Silahtaroglu AN, Lamy P, Ramanathan R, Fristrup N, Jensen JL, Andersen CL, Zieger K, et al: Genomic profiling of microRNAs in bladder cancer: miR-129 is associated with poor outcome and promotes cell death in vitro. Cancer Res. 2009, 69 (11): 4851-4860. 10.1158/0008-5472.CAN-08-4043.

Bandres E, Agirre X, Bitarte N, Ramirez N, Zarate R, Roman-Gomez J, Prosper F, Garcia-Foncillas J: Epigenetic regulation of microRNA expression in colorectal cancer. Int J Cancer. 2009, 125 (11): 2737-2743. 10.1002/ijc.24638.

Ogawa R, Ishiguro H, Kuwabara Y, Kimura M, Mitsui A, Katada T, Harata K, Tanaka T, Fujii Y: Expression profiling of micro-RNAs in human esophageal squamous cell carcinoma using RT-PCR. Med Mol Morphol. 2009, 42 (2): 102-109. 10.1007/s00795-009-0443-1.

Merkerova M, Vasikova A, Belickova M, Bruchova H: MicroRNA expression profiles in umbilical cord blood cell lineages. Stem Cells Dev. 2010, 19 (1): 17-26. 10.1089/scd.2009.0071.

Schmidt WM, Spiel AO, Jilma B, Wolzt M, Muller M: In vivo profile of the human leukocyte microRNA response to endotoxemia. Biochem Biophys Res Commun. 2009, 380 (3): 437-441. 10.1016/j.bbrc.2008.12.190.

Taganov KD, Boldin MP, Chang KJ, Baltimore D: NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci USA. 2006, 103 (33): 12481-12486. 10.1073/pnas.0605298103.

Patnaik SK, Kannisto E, Knudsen S, Yendamuri S: Evaluation of microRNA expression profiles that may predict recurrence of localized stage I non-small cell lung cancer after surgical resection. Cancer Res. 2010, 70 (1): 36-45. 10.1158/0008-5472.CAN-09-3153.

Hussein K, Theophile K, Dralle W, Wiese B, Kreipe H, Bock O: MicroRNA expression profiling of megakaryocytes in primary myelofibrosis and essential thrombocythemia. Platelets. 2009, 20 (6): 391-400. 10.1080/09537100903114537.

Melkamu T, Zhang X, Tan J, Zeng Y, Kassie F: Alteration of microRNA expression in vinyl carbamate-induced mouse lung tumors and modulation by the chemopreventive agent indole-3-carbinol. Carcinogenesis. 2010, 31 (2): 252-258. 10.1093/carcin/bgp208.

Raponi M, Dossey L, Jatkoe T, Wu X, Chen G, Fan H, Beer DG: MicroRNA classifiers for predicting prognosis of squamous cell lung cancer. Cancer Res. 2009, 69 (14): 5776-5783. 10.1158/0008-5472.CAN-09-0587.

Iliopoulos D, Drosatos K, Hiyama Y, Goldberg IJ, Zannis VI: MicroRNA-370 controls the expression of microRNA-122 and Cpt1{alpha} and affects lipid metabolism. J Lipid Res. 2010

Xu CF, Yu CH, Li YM: Regulation of hepatic MicroRNA expression in response to ischemic preconditioning following ischemia/reperfusion injury in mice. Omics. 2009, 13 (6): 513-520. 10.1089/omi.2009.0035.

Dixon-McIver A, East P, Mein CA, Cazier JB, Molloy G, Chaplin T, Andrew Lister T, Young BD, Debernardi S: Distinctive patterns of microRNA expression associated with karyotype in acute myeloid leukaemia. PLoS One. 2008, 3 (5): e2141-10.1371/journal.pone.0002141.

Meng F, Wehbe-Janek H, Henson R, Smith H, Patel T: Epigenetic regulation of microRNA-370 by interleukin-6 in malignant human cholangiocytes. Oncogene. 2008, 27 (3): 378-386. 10.1038/sj.onc.1210648.

Volinia S, Galasso M, Costinean S, Tagliavini L, Gamberoni G, Drusco A, Marchesini J, Mascellani N, Sana ME, Abu Jarour R, et al: Reprogramming of miRNA networks in cancer and leukemia. Genome Res. 2010, 20 (5): 589-599. 10.1101/gr.098046.109.

Sun Y, Fang R, Li C, Li L, Li F, Ye X, Chen H: Hsa-mir-182 suppresses lung tumorigenesis through down regulation of RGS17 expression in vitro. Biochem Biophys Res Commun. 2010

Ivey KN, Muth A, Arnold J, King FW, Yeh RF, Fish JE, Hsiao EC, Schwartz RJ, Conklin BR, Bernstein HS, et al: MicroRNA regulation of cell lineages in mouse and human embryonic stem cells. Cell Stem Cell. 2008, 2 (3): 219-229. 10.1016/j.stem.2008.01.016.

Yi R, Poy MN, Stoffel M, Fuchs E: A skin microRNA promotes differentiation by repressing 'stemness'. Nature. 2008, 452 (7184): 225-229. 10.1038/nature06642.

Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, et al: Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA. 2002, 99 (24): 15524-15529. 10.1073/pnas.242606799.

Sampson VB, Rong NH, Han J, Yang Q, Aris V, Soteropoulos P, Petrelli NJ, Dunn SP, Krueger LJ: MicroRNA let-7a down-regulates MYC and reverts MYC-induced growth in Burkitt lymphoma cells. Cancer Res. 2007, 67 (20): 9762-9770. 10.1158/0008-5472.CAN-07-2462.

Schultz J, Lorenz P, Gross G, Ibrahim S, Kunz M: MicroRNA let-7b targets important cell cycle molecules in malignant melanoma cells and interferes with anchorage-independent growth. Cell Res. 2008, 18 (5): 549-557. 10.1038/cr.2008.45.