Long noncoding RNA associated-competing endogenous RNAs in gastric cancer

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Xia, Tian ^a,b   Liao, Qi ^a   Jiang, Xiaoming ^a   Shao, Yongfu ^a   Xiao, Bingxiu ^a   Xi, Yang ^a   Guo, Junming ^a  

^a NINGBO UNIVERSITY   (China)

^b Yuyao Agricultural and Forestry Bureau   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; MICRORNA; RETINOBLASTOMA PROTEIN; SMALL INTERFERING RNA;

ALGORITHM; BIOSYNTHESIS; CARCINOMA; CELL TRANSFORMATION; CHRONIC LYMPHATIC LEUKEMIA; DNA MICROARRAY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HEAD AND NECK TUMOR; HUMAN; HYPOPHYSIS TUMOR; MALE; OVARY TUMOR; PROSTATE TUMOR; RNA INTERFERENCE; SQUAMOUS CELL CARCINOMA; STOMACH TUMOR; THYROID TUMOR; TUMOR CELL LINE;

ALGORITHMS; CARCINOMA; CARCINOMA, SQUAMOUS CELL; CELL LINE, TUMOR; CELL TRANSFORMATION, NEOPLASTIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HEAD AND NECK NEOPLASMS; HUMANS; LEUKEMIA, LYMPHOCYTIC, CHRONIC, B-CELL; MALE; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OVARIAN NEOPLASMS; PITUITARY NEOPLASMS; PROSTATIC NEOPLASMS; RETINOBLASTOMA PROTEIN; RNA INTERFERENCE; RNA, LONG NONCODING; RNA, SMALL INTERFERING; STOMACH NEOPLASMS; THYROID NEOPLASMS;

EID: 84906241067     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep06088     Document Type: Article

References (43)

1. Pasquinelli, A. E. MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet 13, 271-282 (2012).
2. Thomas, M., Lieberman, J. &Lal, A. Desperately seeking microRNA targets. Nat Struct Mol Biol 17, 1169-1174 (2010).
3. Zhang, H., Li, Y. &Lai, M. The microRNA network and tumor metastasis. Oncogene 29, 937-948 (2010).
4. Gennarino, V. A. et al. Identification of microRNA-regulated gene networks by expression analysis of target genes. Genome Res 22, 1163-1172 (2012).
5. Li, L. et al. 3'UTR shortening identifies high-risk cancers with targeted dysregulation of the ceRNA network. Sci Rep 4, 5406 (2014).
6. Salmena, L., Poliseno, L., Tay, Y., Kats, L. &Pandolfi, P. P. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146, 353-358 (2011).
7. Ebert, M. S., Neilson, J. R. &Sharp, P. A. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4, 721-726 (2007). (Pubitemid 47338166)
8. Poliseno, L. et al.Acoding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033-1038 (2010).
9. Wang, J. et al. CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res 38, 5366-5383 (2010).
10. Lee, D. Y. et al. Expression of versican 3'-untranslated region modulates endogenous microRNA functions. PLoS One 5, e13599 (2010).
11. Jeyapalan, Z. et al. Expression of CD44 3'-untranslated region regulates endogenous microRNA functions in tumorigenesis and angiogenesis. Nucleic Acids Res 39, 3026-3041 (2011).
12. Tay, Y. et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147, 344-357 (2011).
13. Karreth, F. A. et al. In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 147, 382-395 (2011).
14. Sumazin, P. et al. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147, 370-381 (2011).
15. Cesana, M. et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147, 358-369 (2011).
16. Chen, G. et al. LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 41, D983-D986 (2013).
17. Li, Y. et al. HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res 42, D1070-D1074 (2014).
18. Yang, Z. et al. dbDEMC: a database of differentially expressed miRNAs in human cancers. BMC Genomics 11, S5 (2010).
19. Jeggari, A., Marks, D. S. &Larsson, E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics 28, 2062-2063 (2012).
20. Gu, S., Jin, L., Zhang, F., Sarnow, P. &Kay, M. A. Biological basis for restriction of microRNA targets to the3' untranslated region in mammalian mRNAs. Nat Struct Mol Biol 16, 144-150 (2009).
21. Guo, J. et al. Differential expression of microRNA species in human gastric cancer versus non-tumorous tissues. J Gastroenterol Hepatol 24, 652-657 (2009).
22. McKiernan, P. J., Molloy, K., Cryan, S. A., McElvaney, N. G. &Greene, C. M. Long noncoding RNA are aberrantly expressed in vivo in the cystic fibrosis bronchial epithelium. Int J Biochem Cell Biol 52, 184-191 (2014).
23. Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project Genome Res 22, 1760-1774 (2012).
24. Vergoulis, T. et al. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 40, D222-D229 (2012).
25. Volinia, S. et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103, 2257-2261 (2006). (Pubitemid 43271657)
26. Ying, L. et al. Downregulated MEG3 activates autophagy and increases cell proliferation in bladder cancer. Mol Biosyst 9, 407-411 (2013).
27. Tripathi, V. et al. Long noncoding RNA MALAT1 controls cell cycle progression by regulating the expression of oncogenic transcription factor B-MYB. PLoS Genet 9, e1003368 (2013).
28. Wang, Y. et al. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell 25, 69-80 (2013).
29. Kallen, A.N. et al. The imprinted H19 lncRNA antagonizes let-7 microRNAs. Mol Cell 52, 101-112 (2013).
30. Jalali, S., Bhartiya, D., Lalwani, M. K., Sivasubbu, S. &Scaria, V. Systematic transcriptome wide analysis of lncRNA-miRNA interactions. PLoS One 8, e53823 (2013).
31. Khachane, A. N. &Harrison, P. M. Mining mammalian transcript data for functional long non-coding RNAs. PLoS One 5, e10316 (2010).
32. Xiao, B. et al. Detection of miR-106a in gastric carcinoma and its clinical significance. Clin Chim Acta 400, 97-102 (2009).
33. Memczak, S. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333-338 (2013).
34. Hansen, T. B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384-388 (2013).
35. Karreth, F. A. &Pandolfi, P. P. ceRNA cross-talk in cancer: when ce-bling rivalries go awry. Cancer Discov 3, 1113-1121 (2013).
36. Tay, Y., Rinn, J. &Pandolfi, P. P. The multilayered complexity of ceRNA crosstalk and competition. Nature 505, 344-352 (2014).
37. Ala, U. et al. Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments. Proc Natl Acad Sci U S A 110, 7154-7159 (2013).
38. Tang, G. et al. Construction of short tandem target mimic (STTM) to block the functions of plant and animal microRNAs. Methods 58, 118-125 (2012).
39. Liu, K., Yan, Z., Li, Y. &Sun, Z. Linc2GO: a human lincRNA function annotation resource based on ceRNA hypothesis. Bioinformatics 29, 2221-2222 (2013).
40. Li, J.H., Liu, S., Zhou, H., Qu, L. H. &Yang, J.H. starBase v2.0: decodingmiRNAceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res 42, D92-D97 (2014).
41. Almeida, M. I., Reis, R. M. &Calin, G. A. Decoy activity through microRNAs: the therapeutic implications. Expert Opin Biol Ther 12, 1153-1159 (2012).
42. Li, J. et al. Identification of high-quality cancer prognostic markers andmetastasis network modules. Nat Commun 1,34 (2010).
43. Yu, X. et al. Growth inhibitory effects of three miR-129 family members on gastric cancer. Gene 532, 87-93 (2013).