Integrated miRNA and mRNA expression profiling to identify mRNA targets of dysregulated miRNAs in non-obstructive azoospermia

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Zhuang, Xuan ^a   Li, Zhiming ^b   Lin, Huinuan ^b   Gu, Long ^b   Lin, Qing ^b   Lu, Zhongxian ^b   Tzeng, Chi Meng ^b  

^a THE FIRST AFFILIATED HOSPITAL OF XIAMEN UNIVERSITY   (China)

^b XIAMEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

ADULT; AZOOSPERMIA; CLUSTER ANALYSIS; DNA MICROARRAY; DOWN REGULATION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETICS; HUMAN; MALE; METABOLISM; PATHOLOGY; REAL TIME POLYMERASE CHAIN REACTION; SPERMATOGENESIS; TESTIS; UPREGULATION;

ADULT; AZOOSPERMIA; CLUSTER ANALYSIS; DOWN-REGULATION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; MALE; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REAL-TIME POLYMERASE CHAIN REACTION; RNA, MESSENGER; SPERMATOGENESIS; TESTIS; UP-REGULATION;

EID: 84940719552     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep07922     Document Type: Article

References (39)

1. Hirsh, A. Male subfertility. BMJ 327, 669-672, doi:10.1136/bmj.327.7416.669 (2003).
2. Maduro, M. R.& Lamb, D. J. Understanding new genetics of male infertility. JUrol 168, 2197-2205, doi:10.1097/07.ju.0000023290.61978.b2 (2002).
3. Moghissi, K. S., Wallach, E. E. Unexplained infertility. Fertil Steril 39, 5-21 (1983).
4. Hamada, A., Esteves, S. C., Nizza, M., Agarwal, A. Unexplained male infertility: diagnosis and management. International braz j urol : official journal of the Brazilian Society of Urology 38, 576-594 (2012).
5. Ferlin, A. et al.Male infertility: role of genetic background. Reprod Biomed Online 14, 734-745 (2007).
6. Dube, E.,Hermo, L., Chan, P. T., Cyr,D. G. Alterations in gene expression in the caput epididymides of nonobstructive azoospermic men. Biol Reprod 78, 342-351, doi:10.1095/biolreprod.107.062760 (2008).
7. Hu, Z. et al. A genome-wide association study in Chinese men identifies three risk loci for non-obstructive azoospermia. Nat Genet 44, 183-186, doi:10.1038/ng.1040 (2012).
8. Ellis, P. J. et al. Coordinated transcriptional regulation patterns associated with infertility phenotypes in men. J Med Genet 44, 498-508, doi:10.1136/jmg.2007.049650 (2007).
9. Siomi, M. C., Sato, K., Pezic, D., Aravin, A. A. PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12, 246-258, doi:10.1038/nrm3089 (2011).
10. He, Z., Kokkinaki, M., Pant, D., Gallicano, G. I., Dym,M. Small RNA molecules in the regulation of spermatogenesis. Reproduction 137, 901-911, doi:10.1530/REP-08-0494 (2009).
11. Hayashi, K. et al.MicroRNAbiogenesis is required for mouse primordial germ cell development and spermatogenesis. PLoS One 3, e1738, doi:10.1371/journal.pone.0001738 (2008).
12. Betel, D., Wilson, M., Gabow, A., Marks, D. S., Sander, C. The microRNA.org resource: targets and expression. Nucleic Acids Res 36, D149-153, doi:10.1093/nar/gkm995 (2008).
13. Krek, A. et al. Combinatorial microRNA target predictions. Nat Genet 37, 495-500, doi:10.1038/ng1536 (2005).
14. 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 120, 15-20, doi:10.1016/j.cell.2004.12.035 (2005).
15. Maragkakis, M. et al. Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10, 295, doi:10.1186/1471-2105-10-295 (2009).
16. Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., Segal, E. The role of site accessibility in microRNA target recognition. Nat Genet 39, 1278-1284, doi:10.1038/ng2135 (2007).
17. Maragkakis, M. et al. DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res 37, W273-276, doi:10.1093/nar/gkp292(2009).
18. Miranda, K. C. et al. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126, 1203-1217, doi: 10.1016/j.cell.2006.07.031 (2006).
19. Mansson, R. et al. Pearson correlation analysis of microarray data allows for the identification of genetic targets for early B-cell factor. The Journal of biological chemistry 279, 17905-17913, doi:10.1074/jbc.M400589200 (2004).
20. Sethupathy, P., Corda, B., Hatzigeorgiou, A. G. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 12, 192-197, doi:10.1261/rna.2239606 (2006).
21. Keshava Prasad, T. S. et al. Human Protein Reference Database-2009 update. Nucleic Acids Res 37, D767-772, doi:10.1093/nar/gkn892 (2009).
22. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-2504, doi:10.1101/gr.1239303 (2003).
23. Galluccio, A., Loebl, M., Vondrak, J. New algorithm for the Ising problem: partition function for finite lattice graphs. Phys Rev Lett 84, 5924-5927 (2000).
24. Garzon, R., Calin, G. A., Croce, C. M. MicroRNAs in Cancer. Annu RevMed 60, 167-179, doi:10.1146/annurev.med.59.053006.104707 (2009).
25. Aravin, A. A. et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 31, 785-799, doi:10.1016/j.molcel.2008.09.003 (2008).
26. Wang, G., Reinke, V. A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis. Curr Biol 18, 861-867, doi:10.1016/j.cub.2008.05.009 (2008).
27. Aiman, J., Griffin, J. E., Gazak, J. M.,Wilson, J. D.,MacDonald, P. C. Androgen insensitivity as a cause of infertility in otherwise normal men. N Engl J Med 300, 223-227, doi:10.1056/NEJM197902013000503 (1979).
28. Cappallo-Obermann, H., Feig, C., Schulze, W., Spiess, A. N. Fold-change correction values for testicular somatic transcripts in gene expression studies of human spermatogenesis. Human reproduction 28, 590-598, doi:10.1093/humrep/des433 (2013).
29. Males, J. L., Turkington, R. W. Hormonal control of lysosomal enzymes during spermatogenesis in the rat. Endocrinology 88, 578-588 (1971).
30. Berruti, G., Ripolone, M., Ceriani, M. USP8, a regulator of endosomal sorting, is involved in mouse acrosome biogenesis through interaction with the spermatid ESCRT-0 complex and microtubules. Biol Reprod 82, 930-939, doi:10.1095/biolreprod.109.081679 (2010).
31. Lian, J. et al. Altered microRNA expression in patients with non-obstructive azoospermia. Reprod Biol Endocrinol 7, 13, doi:10.1186/1477-7827-7-13 (2009).
32. Liu, H. et al. Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. BMC Syst Biol 4, 51, doi:10.1186/1752-0509-4-51 (2010).
33. Abu-Halima, M. et al. Altered microRNA expression profiles of human spermatozoa in patients with different spermatogenic impairments. Fertil Steril 99, 1249-1255 e1216 doi:10.1016/j.fertnstert.2012.11.054 (2013).
34. Matzuk, M. M., Lamb, D. J. Genetic dissection of mammalian fertility pathways. Nat Cell Biol 4 Suppl, s41-49, doi:10.1038/ncb-nm-fertilityS41 (2002).
35. Szmulewicz, M. N., Ruiz, L. M., Reategui, E. P., Hussini, S., Herrera, R. J. Singlenucleotide variant in multiple copies of a deleted in azoospermia (DAZ) sequence-a human Y chromosome quantitative polymorphism. Hum Hered 53, 8-17, doi:48599 (2002).
36. Vinci, G. et al. A deletion of a novel heat shock gene on the Y chromosome associated with azoospermia. Mol Hum Reprod 11, 295-298, doi:10.1093/molehr/gah153 (2005).
37. Takasaki, N. et al. A heterozygous mutation of GALNTL5 affects male infertility with impairment of sperm motility. Proc Natl Acad Sci USA 111, 1120-1125, doi:10.1073/pnas.1310777111 (2014).
38. Bouhallier, F. et al. Role of miR-34c microRNA in the late steps of spermatogenesis. RNA 16, 720-731, doi:10.1261/rna.1963810 (2010).
39. Liu, Z., Sall, A., Yang, D. MicroRNA: An emerging therapeutic target and intervention tool. Int J Mol Sci 9, 978-999, doi:10.3390/ijms9060978 (2008).