Expression of miR-15/107 family microRNAs in human tissues and cultured rat brain cells

Genomics, Proteomics and Bioinformatics

Volumn 12, Issue 1, 2014, Pages 19-30

  Wang, Wang Xia ^a   Danaher, Robert J ^b   Miller, Craig S ^b   Berger, Joseph R ^a   Nubia, Vega G ^a   Wilfred, Bernard S ^a   Neltner, Janna H ^a,c   Norris, Christopher M ^c   Nelson, Peter T ^a,c  

^a UNIVERSITY OF KENTUCKY   (United States)

^b UNIVERSITY OF KENTUCKY COLLEGE OF DENTISTRY   (United States)

^c UNIVERSITY OF KENTUCKY   (United States)

Author keywords

MiR 15; MiR 16; MiR 424; MiR 503; Normalization; Target prediction

Indexed keywords

MIR-15; MIR-16; MIR-424; MIR-503; NORMALIZATION; TARGET PREDICTION;

ANIMALS; BRAIN; CELLS, CULTURED; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; HUMANS; MICROGLIA; MICRORNAS; NEURONS; RATS;

EID: 84894262662     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2013.10.003     Document Type: Article

References (52)

1. Lewis B.P., Burge C.B., Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
2. Friedman R.C., Farh K.K., Burge C.B., Bartel D.P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009, 19:92-105.
3. Miranda K.C., Huynh T., Tay Y., Ang Y.S., Tam W.L., Thomson A.M., et al. A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 2006, 126:1203-1217.
4. Liu X., Fortin K., Mourelatos Z. MicroRNAs: biogenesis and molecular functions. Brain Pathol 2008, 18:113-121.
5. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
6. Mourelatos Z. Small RNAs: the seeds of silence. Nature 2008, 455:44-45.
7. Finnerty J.R., Wang W.X., Hebert S.S., Wilfred B.R., Mao G., Nelson P.T. The miR-15/107 group of microRNA genes: evolutionary biology, cellular functions, and roles in human diseases. J Mol Biol 2010, 402:491-509.
8. Zhu W., Zhu D., Lu S., Wang T., Wang J., Jiang B., et al. miR-497 modulates multidrug resistance of human cancer cell lines by targeting BCL2. Med Oncol 2012, 29:384-391.
9. Moncini S., Salvi A., Zuccotti P., Viero G., Quattrone A., Barlati S., et al. The role of miR-103 and miR-107 in regulation of CDK5R1 expression and in cellular migration. PLoS One 2011, 6:e20038.
10. Nelson P.T., Wang W.X., Mao G., Wilfred B.R., Xie K., Jennings M.H., et al. Specific sequence determinants of miR-15/107 microRNA gene group targets. Nucleic Acids Res 2011, 39:8163-8172.
11. Wang W.X., Kyprianou N., Wang X., Nelson P.T. Dysregulation of the mitogen granulin in human cancer through the miR-15/107 microRNA gene group. Cancer Res 2010, 70:9137-9142.
12. Hebert S.S., Wang W.X., Zhu Q., Nelson P.T. A study of small RNAs from cerebral neocortex of pathology-verified Alzheimer's disease, dementia with lewy bodies, hippocampal sclerosis, frontotemporal lobar dementia, and non-demented human controls. J Alzheimers Dis 2013, 35:335-348.
13. Wilfred B.R., Wang W.X., Nelson P.T. Energizing miRNA research: a review of the role of miRNAs in lipid metabolism, with a prediction that miR-103/107 regulates human metabolic pathways. Mol Genet Metab 2007, 91:209-217.
14. Kriegel A.J., Liu Y., Fang Y., Ding X., Liang M. The miR-29 family: genomics, cell biology, and relevance to renal and cardiovascular injury. Physiol Genomics 2012, 44:237-244.
15. Mott J.L., Kurita S., Cazanave S.C., Bronk S.F., Werneburg N.W., Fernandez-Zapico M.E. Transcriptional suppression of mir-29b-1/mir-29a promoter by c-Myc, hedgehog, and NF-kappaB. J Cell Biochem 2010, 110:1155-1164.
16. Wang W.X., Wilfred B.R., Xie K., Jennings M.H., Hu Y.H., Stromberg A.J., et al. Individual microRNAs (miRNAs) display distinct mRNA targeting "rules". RNA Biol 2010, 7:373-380.
17. Git A., Dvinge H., Salmon-Divon M., Osborne M., Kutter C., Hadfield J., et al. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 2010, 16:991-1006.
18. Wang W.X., Wilfred B.R., Baldwin D.A., Isett R.B., Ren N., Stromberg A., et al. Focus on RNA isolation: obtaining RNA for microRNA (miRNA) expression profiling analyses of neural tissue. Biochim Biophys Acta 2008, 1779:749-757.
19. Chen Y., Gelfond J.A., McManus L.M., Shireman P.K. Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis. BMC Genomics 2009, 10:407.
20. Ach R.A., Wang H., Curry B. Measuring microRNAs: comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods. BMC Biotechnol 2008, 8:69.
21. Willenbrock H., Salomon J., Sokilde R., Barken K.B., Hansen T.N., Nielsen F.C., et al. Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing. RNA 2009, 15:2028-2034.
22. Bruchova H., Yoon D., Agarwal A.M., Mendell J., Prchal J.T. Regulated expression of microRNAs in normal and polycythemia vera erythropoiesis. Exp Hematol 2007, 35:1657-1667.
23. Choong M.L., Yang H.H., McNiece I. MicroRNA expression profiling during human cord blood-derived CD34 cell erythropoiesis. Exp Hematol 2007, 35:551-564.
24. Nelson P.T., Baldwin D.A., Kloosterman W.P., Kauppinen S., Plasterk R.H., Mourelatos Z. RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA 2006, 12:187-191.
25. Bargaje R., Hariharan M., Scaria V., Pillai B. Consensus miRNA expression profiles derived from interplatform normalization of microarray data. RNA 2010, 16:16-25.
26. Shingara J., Keiger K., Shelton J., Laosinchai-Wolf W., Powers P., Conrad R., et al. An optimized isolation and labeling platform for accurate microRNA expression profiling. RNA 2005, 11:1461-1470.
27. Baskerville S., Bartel D.P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 2005, 11:241-247.
28. Sempere L.F., Freemantle S., Pitha-Rowe I., Moss E., Dmitrovsky E., Ambros V. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol 2004, 5:R13.
29. Babak T., Zhang W., Morris Q., Blencowe B.J., Hughes T.R. Probing microRNAs with microarrays: tissue specificity and functional inference. RNA 2004, 10:1813-1819.
30. Liu C.G., Spizzo R., Calin G.A., Croce C.M. Expression profiling of microRNA using oligo DNA arrays. Methods 2008, 44:22-30.
31. Peltier H.J., Latham G.J. Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues. RNA 2008, 14:844-852.
32. Wu H., Neilson J.R., Kumar P., Manocha M., Shankar P., Sharp P.A., et al. miRNA profiling of naive, effector and memory CD8 T cells. PLoS One 2007, 2:e1020.
33. Merkerova M., Belickova M., Bruchova H. Differential expression of microRNAs in hematopoietic cell lineages. Eur J Haematol 2008, 81:304-310.
34. Liu C.G., Calin G.A., Meloon B., Gamliel N., Sevignani C., Ferracin M., et al. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci U S A 2004, 101:9740-9744.
35. Wang Y., Weng T., Gou D., Chen Z., Chintagari N.R., Liu L. Identification of rat lung-specific microRNAs by micoRNA microarray: valuable discoveries for the facilitation of lung research. BMC Genomics 2007, 8:29.
36. Soares A.R., Pereira P.M., Santos B., Egas C., Gomes A.C., Arrais J., et al. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genomics 2009, 10:195.
37. Polster B.J., Westaway S.K., Nguyen T.M., Yoon M.Y., Hayflick S.J. Discordant expression of miR-103/7 and pantothenate kinase host genes in mouse. Mol Genet Metab 2010, 101:292-295.
38. Ason B., Darnell D.K., Wittbrodt B., Berezikov E., Kloosterman W.P., Wittbrodt J., et al. Differences in vertebrate microRNA expression. Proc Natl Acad Sci U S A 2006, 103:14385-14389.
39. Lee E.J., Baek M., Gusev Y., Brackett D.J., Nuovo G.J., Schmittgen T.D. Systematic evaluation of microRNA processing patterns in tissues, cell lines, and tumors. RNA 2008, 14:35-42.
40. Lagos-Quintana M., Rauhut R., Yalcin A., Meyer J., Lendeckel W., Tuschl T. Identification of tissue-specific microRNAs from mouse. Curr Biol 2002, 12:735-739.
41. Linsley P.S., Schelter J., Burchard J., Kibukawa M., Martin M.M., Bartz S.R., et al. Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression. Mol Cell Biol 2007, 27:2240-2252.
42. Schmittgen T.D., Lee E.J., Jiang J., Sarkar A., Yang L., Elton T.S., et al. Real-time PCR quantification of precursor and mature microRNA. Methods 2008, 44:31-38.
43. Wylie D., Shelton J., Choudhary A., Adai A.T. A novel mean-centering method for normalizing microRNA expression from high-throughput RT-qPCR data. BMC Res Notes 2011, 4:555.
44. Lin Y.L., Lai Z.X. Evaluation of suitable reference genes for normalization of microRNA expression by real-time reverse transcription PCR analysis during longan somatic embryogenesis. Plant Physiol Biochem 2013, 66:20-25.
45. Lim Q.E., Zhou L., Ho Y.K., Wan G., Too H.P. SnoU6 and 5S RNAs are not reliable miRNA reference genes in neuronal differentiation. Neuroscience 2011, 199:32-43.
46. Brattelid T., Aarnes E.K., Helgeland E., Guvaag S., Eichele H., Jonassen A.K. Normalization strategy is critical for the outcome of miRNA expression analyses in the rat heart. Physiol Genomics 2011, 43:604-610.
47. Nelson P.T., Wang W.X., Wilfred B.R., Tang G. Technical variables in high-throughput miRNA expression profiling: much work remains to be done. Biochim Biophys Acta 2008, 1779:758-765.
48. Mestdagh P., Van Vlierberghe P., De Weer A., Muth D., Westermann F., Speleman F., et al. A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol 2009, 10:R64.
49. Wang W.X., Wilfred B.R., Hu Y., Stromberg A.J., Nelson P.T. Anti-Argonaute RIP-Chip shows that miRNA transfections alter global patterns of mRNA recruitment to microribonucleoprotein complexes. RNA 2010, 16:394-404.
50. Wang W.X., Wilfred B.R., Madathil S.K., Tang G., Hu Y., Dimayuga J., et al. MiR-107 regulates granulin/progranulin with implications for traumatic brain injury and neurodegenerative disease. Am J Pathol 2010, 177:334-345.
51. Norris C.M., Blalock E.M., Thibault O., Brewer L.D., Clodfelter G.V., Porter N.M., et al. Electrophysiological mechanisms of delayed excitotoxicity: positive feedback loop between NMDA receptor current and depolarization-mediated glutamate release. J Neurophysiol 2006, 96:2488-2500.
52. Sama M.A., Mathis D.M., Furman J.L., Abdul H.M., Artiushin I.A., Kraner S.D., et al. Interleukin-1beta-dependent signaling between astrocytes and neurons depends critically on astrocytic calcineurin/NFAT activity. J Biol Chem 2008, 283:21953-21964.