Simultaneous detection of different MicroRNA types using the ZIP-code array system

Journal of Nucleic Acids

Volumn 2013, Issue , 2013, Pages

  Weishaupt, Sonja U ^a   Rupp, Steffen ^b   Lemuth, Karin ^b  

^a UNIVERSITY OF STUTTGART   (Germany)

^b FRAUNHOFER INSTITUTE FOR INTERFACIAL ENGINEERING AND BIOTECHNOLOGY IGB   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DEOXYURIDINE TRIPHOSPHATE PYROPHOSPHATASE; MICRORNA; MICRORNA 100; MICRORNA 139; MICRORNA 139 5P; MICRORNA 16; MICRORNA 199B; MICRORNA 199B 5P; MICRORNA 19B; MICRORNA 19B 3P; MICRORNA 29A; MICRORNA 29A 3P; MICRORNA 9; MICRORNA 92A; MICRORNA 92A 3P; MICRORNA 99A; MICRORNA 99A 5P; MICRORNA 99B; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CELL CULTURE; CELL ISOLATION; CONTROLLED STUDY; DNA MICROARRAY; DNA SYNTHESIS; ENZYME MECHANISM; GENE AMPLIFICATION; GENE EXPRESSION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION; TUMOR CELL; ZIP CODE DNA MICROARRAY SYSTEM;

EID: 84884844520     PISSN: 20900201     EISSN: 2090021X     Source Type: Journal    
DOI: 10.1155/2013/496425     Document Type: Article

References (44)

1. Bartel D. P., MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004 116 2 281 297 2-s2.0-0347444723 10.1016/S0092-8674(04)00045-5 (Pubitemid 38167318)
2. Bushati N., Cohen S. M., MicroRNA functions. Annual Review of Cell and Developmental Biology 2007 23 175 205 2-s2.0-34547960488 10.1146/annurev. cellbio.23.090506.123406
3. Calin G. A., Croce C. M., MicroRNA signatures in human cancers. Nature Reviews Cancer 2006 6 11 857 866 2-s2.0-33750370444 10.1038/nrc1997 (Pubitemid 44629897)
4. Esquela-Kerscher A., Slack F. J., Oncomirs-microRNAs with a role in cancer. Nature Reviews Cancer 2006 6 4 259 269 2-s2.0-33645294070 10.1038/nrc1840
5. Barbarotto E., Schmittgen T. D., Calin G. A., MicroRNAs and cancer: profile, profile, profile. International Journal of Cancer 2008 122 5 969 977 2-s2.0-38749083425 10.1002/ijc.23343 (Pubitemid 351213993)
6. Kim V. N., Nam J. W., Genomics of microRNA. Trends in Genetics 2006 22 3 165 173 2-s2.0-33344477448 10.1016/j.tig.2006.01.003 (Pubitemid 43290020)
7. Yu J., Wang F., Yang G. H., Wang F. L., Ma Y. N., Du Z. W., Zhang J. W., Human microRNA clusters: genomic organization and expression profile in leukemia cell lines. Biochemical and Biophysical Research Communications 2006 349 1 59 68 2-s2.0-33748286897 10.1016/j.bbrc.2006.07.207 (Pubitemid 44331762)
8. Lee Y., Kim M., Han J., Yeom K., Lee S., Baek S. H., Kim V. N., MicroRNA genes are transcribed by RNA polymerase II. EMBO Journal 2004 23 20 4051 4060 2-s2.0-8144225486 10.1038/sj.emboj.7600385 (Pubitemid 39472426)
9. Borchert G. M., Lanier W., Davidson B. L., RNA polymerase III transcribes human microRNAs. Nature Structural and Molecular Biology 2006 13 12 1097 1101 2-s2.0-33845370280 10.1038/nsmb1167 (Pubitemid 44885920)
10. 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 2-s2.0-0141843656 10.1038/nature01957 (Pubitemid 37187272)
11. Han J., Lee Y., Yeom K. H., Nam J. W., Heo I., Rhee J. K., Sohn S. Y., Cho Y., Zhang B. T., Kim V. N., Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 2006 125 5 887 901 2-s2.0-33744520104 10.1016/j.cell.2006.03.043 (Pubitemid 43810154)
12. Lund E., Güttinger S., Calado A., Dahlberg J. E., Kutay U., Nuclear export of microRNA precursors. Science 2004 303 5654 95 98 2-s2.0-0347988235 10.1126/science.1090599 (Pubitemid 38055779)
13. Bernstein E., Caudy A. A., Hammond S. M., Hannon G. J., Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001 409 6818 363 366 2-s2.0-0035905766 10.1038/35053110 (Pubitemid 32151243)
14. Kurihara Y., Watanabe Y., Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proceedings of the National Academy of Sciences of the United States of America 2004 101 34 12753 12758 2-s2.0-4344637081 10.1073/pnas.0403115101 (Pubitemid 39122095)
15. Förstemann K., Tomari Y., Du T., Vagin V. V., Denli A. M., Bratu D. P., Klattenhoff C., Theurkauf W. E., Zamore P. D., Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biology 2005 3 7, article e236 2-s2.0-22144497499
16. Meister G., Tuschl T., Mechanisms of gene silencing by double-stranded RNA. Nature 2004 431 7006 343 349 2-s2.0-4644223259 10.1038/nature02873 (Pubitemid 39265674)
17. Filipowicz W., Bhattacharyya S. N., Sonenberg N., Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Reviews Genetics 2008 9 2 102 114 2-s2.0-38349169664 10.1038/nrg2290
18. Schmittgen T. D., Regulation of microRNA processing in development, differentiation and cancer. Journal of Cellular and Molecular Medicine 2008 12 5 1811 1819 2-s2.0-55149109188 10.1111/j.1582-4934.2008.00483.x
19. Ambros V., Lee R. C., Lavanway A., Williams P. T., Jewell D., MicroRNAs and other tiny endogenous RNAs in C. elegans. Current Biology 2003 13 10 807 818 2-s2.0-0037737975 10.1016/S0960-9822(03)00287-2 (Pubitemid 36573248)
20. Thomson J. M., Newman M., Parker J. S., Morin-Kensicki E. M., Wright T., Hammond S. M., Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes and Development 2006 20 16 2202 2207 2-s2.0-33747334621 10.1101/gad.1444406
21. Wulczyn F. G., Smirnova L., Rybak A., Brandt C., Kwidzinski E., Ninnemann O., Strehle M., Seiler A., Schumacher S., Nitsch R., Post-transcriptional regulation of the let-7 microRNA during neural cell specification. FASEB Journal 2007 21 2 415 426 2-s2.0-33846833594 10.1096/fj.06-6130com (Pubitemid 46213489)
22. Yanaihara N., Caplen N., Bowman E., Seike M., Kumamoto K., Yi M., Stephens R. M., Okamoto A., Yokota J., Tanaka T., Calin G. A., Liu C., Croce C. M., Harris C. C., Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 2006 9 3 189 198 2-s2.0-33644819964 10.1016/j.ccr.2006.01.025 (Pubitemid 43357945)
23. O'Hara A. J., Vahrson W., Dittmer D. P., Gene alteration and precursor and mature microRNA transcription changes contribute to the miRNA signature of primary effusion lymphoma. Blood 2008 111 4 2347 2353 2-s2.0-41349103219 10.1182/blood-2007-08-104463 (Pubitemid 351451443)
24. Jaffe E. S., The 2008 WHO classification of lymphomas: implications for clinical practice and translational research. Hematology/the Education Program of the American Society of Hematology 2009 523 531 2-s2.0-77949453079
25. Lagos-Quintana M., Rauhut R., Lendeckel W., Tuschl T., Identification of novel genes coding for small expressed RNAs. Science 2001 294 5543 853 858 2-s2.0-0035955374 10.1126/science.1064921 (Pubitemid 33032103)
26. Válóczi A., Hornyik C., Varga N., Burgyán J., Kauppinen S., Havelda Z., Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Research 2004 32 22, article e175 2-s2.0-16544365954
27. Várallyay E., Burgyán J., Havelda Z., MicroRNA detection by northern blotting using locked nucleic acid probes. Nature Protocols 2008 3 2 190 196 2-s2.0-39549110203 10.1038/nprot.2007.528 (Pubitemid 351276798)
28. Farazi T. A., Spitzer J. I., Morozov P., Tuschl T., MiRNAs in human cancer. Journal of Pathology 2011 223 2 102 115 2-s2.0-78650034475 10.1002/path.2806
29. Chen C., Ridzon D. A., Broomer A. J., Zhou Z., Lee D. H., Nguyen J. T., Barbisin M., Xu N. L., Mahuvakar V. R., Andersen M. R., Lao K. Q., Livak K. J., Guegler K. J., Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research 2005 33 20, article e179 2-s2.0-29144470346 10.1093/nar/gni178 (Pubitemid 41806407)
30. Schmittgen T. D., Jiang J., Liu Q., Yang L., A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Research 2004 32 4, article e43 2-s2.0-2342642197
31. Li W., Ruan K., MicroRNA detection by microarray. Analytical and Bioanalytical Chemistry 2009 394 4 1117 1124 2-s2.0-67349176636 10.1007/s00216-008-2570-2
32. Liu C. G., Spizzo R., Calin G. A., Croce C. M., Expression profiling of microRNA using oligo DNA arrays. Methods 2008 44 1 22 30 2-s2.0-37349040713 10.1016/j.ymeth.2007.10.010 (Pubitemid 350297989)
33. Cissell K. A., Deo S. K., Trends in microRNA detection. Analytical and Bioanalytical Chemistry 2009 394 4 1109 1116 2-s2.0-67349244926 10.1007/s00216-009-2744-6
34. de Planell-Saguer M., Rodicio M. C., Analytical aspects of microRNA in diagnostics: a review. Analytica Chimica Acta 2011 699 2 134 152 2-s2.0-79959546069 10.1016/j.aca.2011.05.025
35. Hauser N. C., Martinez R., Jacob A., Rupp S., Hoheisel J. D., Matysiak S., Utilising the left-helical conformation of L-DNA for analysing different marker types on a single universal microarray platform. Nucleic Acids Research 2006 34 18 5101 5111 2-s2.0-33751014553 10.1093/nar/gkl671 (Pubitemid 44742475)
36. Mattie M. D., Benz C. C., Bowers J., Sensinger K., Wong L., Scott G. K., Fedele V., Ginzinger D., Getts R., Haqq C., Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Molecular Cancer 2006 5 article 24 2-s2.0-33748624597 10.1186/1476-4598-5-24 (Pubitemid 44376886)
37. Qiagen, MiScript PCR System Handbook 2011 4th
38. Plaisance V., Abderrahmani A., Perret-Menoud V., Jacquemin P., Lemaigre F., Regazzi R., MicroRNA-9 controls the expression of Granuphilin/Slp4 and the secretory response of insulin-producing cells. The Journal of Biological Chemistry 2006 281 37 26932 26942 2-s2.0-33748749597 10.1074/jbc.M601225200 (Pubitemid 44401722)
39. Landgraf P., Rusu M., Sheridan R., Sewer A., Iovino N., Aravin A., Pfeffer S., Rice A., Kamphorst A. O., Landthaler M., Lin C., Socci N. D., Hermida L., Fulci V., Chiaretti S., Foà R., Schliwka J., Fuchs U., Novosel A., Müller R., Schermer B., Bissels U., Inman J., Phan Q., Chien M., Weir D. B., Choksi R., De Vita G., Frezzetti D., Trompeter H., Hornung V., Teng G., Hartmann G., Palkovits M., Di Lauro R., Wernet P., Macino G., Rogler C. E., Nagle J. W., Ju J., Papavasiliou F. N., Benzing T., Lichter P., Tam W., Brownstein M. J., Bosio A., Borkhardt A., Russo J. J., Sander C., Zavolan M., Tuschl T., A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007 129 7 1401 1414 2-s2.0-34250877841 10.1016/j.cell.2007.04. 040 (Pubitemid 46970709)
40. Lagana A., Forte S., Giudice A., Arena M. R., Puglisi P. L., Giugno R., Pulvirenti A., Shasha D., Ferro A., miRò: a miRNA knowledge base. Database 2009 2009 bap008 10.1093/database/bap008
41. Lemuth K., Steuer K., Albermann C., Engineering of a plasmid-free Escherichia coli strain for improved in vivo biosynthesis of astaxanthin. Microbial Cell Factories 2011 10 article 29 2-s2.0-79955103635 10.1186/1475-2859-10-29
42. Griffiths-Jones S., Saini H. K., van Dongen S., Enright A. J., miRBase: tools for microRNA genomics. Nucleic Acids Research 2008 36 1 D154 D158 2-s2.0-38549150275 10.1093/nar/gkm952 (Pubitemid 351149713)
43. Starega-Roslan J., Krol J., Koscianska E., Kozlowski P., Szlachcic W. J., Sobczak K., Krzyzosiak W. J., Structural basis of microRNA length variety. Nucleic Acids Research 2011 39 1 257 268 2-s2.0-78651269517 10.1093/nar/gkq727
44. Kozomara A., Griffiths-Jones S., miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research 2011 39 1 D152 D157 2-s2.0-78651293534 10.1093/nar/gkq1027