Analysing the relationship between lncRNA and protein-coding gene and the role of lncRNA as ceRNA in pulmonary fibrosis

Journal of Cellular and Molecular Medicine

Volumn 18, Issue 6, 2014, Pages 991-1003

  Song, Xiaodong ^a   Cao, Guohong ^a,b   Jing, Lili ^a   Lin, Shengcui ^a   Wang, Xiaozhi ^b   Zhang, Jinjin ^a   Wang, Meirong ^a   Liu, Weili ^b   Lv, Changjun ^a,b  

^a BINZHOU MEDICAL UNIVERSITY   (China)

^b Department of Neurology Hospital Affiliated to Binzhou medical University   (China)

Author keywords

CeRNA; LncRNA; MRAK081523; MRAK088388; Pulmonary fibrosis

Indexed keywords

3' UNTRANSLATED REGION; ANTINEOPLASTIC ANTIBIOTIC; BIOLOGICAL MARKER; BLEOMYCIN; LONG UNTRANSLATED RNA; MESSENGER RNA; MICRORNA;

3' UNTRANSLATED REGION; ANIMAL; BINDING COMPETITION; CHEMICALLY INDUCED; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; HUMAN; IN SITU HYBRIDIZATION; LUNG FIBROSIS; METABOLISM; MOUSE; OPEN READING FRAME; PATHOLOGY; RAT; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPRAGUE DAWLEY RAT;

3' UNTRANSLATED REGIONS; ANIMALS; ANTIBIOTICS, ANTINEOPLASTIC; BINDING, COMPETITIVE; BIOLOGICAL MARKERS; BLEOMYCIN; GENE EXPRESSION PROFILING; HUMANS; IN SITU HYBRIDIZATION; MICE; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPEN READING FRAMES; PULMONARY FIBROSIS; RATS; RATS, SPRAGUE-DAWLEY; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, LONG NONCODING; RNA, MESSENGER;

EID: 84904748043     PISSN: 15821838     EISSN: 15824934     Source Type: Journal    
DOI: 10.1111/jcmm.12243     Document Type: Article

References (46)

1. Mattick JS, Makunin IV. Non-coding RNA. Hum Mol Genet. 2006; 15: R17-29.
2. Caley DP, Pink RC, Trujillano D, et al. Long noncoding RNAs, chromatin, and development. Sci World J. 2010; 10: 90-102.
3. Nagano T, Fraser P. No-nonsense functions for long noncoding RNAs. Cell. 2011; 145: 178-81.
4. Lee JT. Epigenetic regulation by long noncoding RNAs. Science. 2012; 338: 1435-9.
5. Paraskevopoulou MD, Georgakilas G, Kostoulas N, et al. DIANA-LncBase: experimentally verified and Computationally predicted microRNA targets on Long non-coding RNAs. Nucleic Acids Res. 2013; 41: D239-45.
6. Mondal T, Rasmussen M, Pandey GK, et al. Characterization of the RNA content of chromatin. Genome Res. 2010; 20: 899-907.
7. Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 2009; 23: 1494-504.
8. Cesana M, Cacchiarelli D, Legnini I, et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011; 147: 358-69.
9. Karreth FA, Pandolfi PP. ceRNA Cross-Talk in cancer: when ce-bling rivalries go awry. Cancer Discovery. 2013; 3: 1113-21.
10. Taulli R, Loretelli C, Pandolfi PP. From pseudo-ceRNAs to circ-ceRNAs: a tale of cross-talk and competition. Nat Struct Mol Biol. 2013; 20: 541-3.
11. Salmena L, Poliseno L, Tay Y, et al. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011; 146: 353-8.
12. Wu SC, Kallin EM, Zhang Y. Role of H3K27 methylation in the regulation of lncRNA expression. Cell Res. 2010; 20: 1109-16.
13. Yang F, Huo XS, Yuan SX, et al. Repression of the long noncoding RNA-LET by histone deacetylase 3 contributes to hypoxia-mediated metastasis. Mol Cell. 2013; 49: 1083-96.
14. Juan L, Wang G, Radovich M, et al. Potential roles of microRNAs in regulating long intergenic noncoding RNAs. BMC Med Genomics. 2013; 6: S7.
15. Liu Q, Huang J, Zhou N, et al. LncRNA loc285194 is a p53-regulated tumor Suppressor. Nucleic Acids Res. 2013; 41: 4976-87.
16. Wapinski O, Chang HY. Long noncoding RNAs and human disease. Trends Cell Biol. 2011; 21: 354-61.
17. Raghu G, Collard HR, Egan JJ, et al. An official ATS/ERS/JRS/ALAT statement: idiopathic pulmonary fibrosis: evidence-based guidelines for diagnosis and management. Am J Respir Crit Care Med. 2011; 183: 788-824.
18. Ding Q, Luckhardt T, Hecker L, et al. New insights into the pathogenesis and treatment of idiopathic pulmonary fibrosis. Drugs. 2011; 71: 981-1001.
19. Cao G, Zhang J, Wang M, et al. Differential expression of long non-coding RNAs in bleomycin-induced lung fibrosis. Int J Mol Med. 2013; 32: 355-64.
20. Song XD, Liu WL, Xie SY, et al. All-transretinoic acid suppresses epithelial-mesenchymal transition by down-regulating the TGF-β1/Smad3 signaling pathway in bleomycin-induced pulmonary fibrosis in rats. Lab Invest. 2013; 93: 1219-31.
21. Wang M, Zhang J, Song X, et al. Astaxanthin ameliorates lung fibrosis in vivo and in vitro by preventing transdifferentiation, inhibiting proliferation, and promoting apoptosis of activated cells. Food Chem Toxicol. 2013; 56: 450-8.
22. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009; 10: 155-9.
23. Guttman M, Donaghey J, Carey BW, et al. LincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 2011; 477: 295-300.
24. Bertani S, Sauer S, Bolotin E, et al. The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. Mol Cell. 2011; 43: 1040-6.
25. He Y, Vogelstein B, Velculescu VE, et al. The antisense transcriptomes of human cells. Science. 2008; 322: 1855-7.
26. Atkinson SR, Marguerat S, Bähler J. Exploring long non-coding RNAs through sequencing. Semin Cell Dev Biol. 2012; 23: 200-5.
27. Schneider DJ, Wu M, Le TT, et al. Cadherin-11 contributes to pulmonary fibrosis: potential role in TGF-β production and epithelial to mesenchymal transition. FASEB J. 2012; 26: 503-12.
28. Gutschner T, Diederichs S. The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol. 2012; 9: 703-19.
29. Schmidt LH, Spieker T, Koschmieder S, et al. The long noncoding MALAT-1 RNA indicates a poor prognosis in non-small cell lung cancer and induces migration and tumor growth. J Thorac Oncol. 2011; 6: 1984-92.
30. Lai MC, Yang Z, Zhou L, et al. Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation. Med Oncol. 2012; 29: 1810-6.
31. Ying L, Chen Q, Wang Y, et al. Upregulated MALAT-1 contributes to bladder cancer cell migration by inducing epithelial-to-mesenchymal transition. Mol BioSyst. 2012; 8: 2289-94.
32. Sui W, Yan Q, Li H, et al. Genome-wide analysis of long noncoding RNA expression in peripheral blood mononuclear cells of uremia patients. J Nephrol. 2013; 26: 731-8.
33. Zhu Z, Gao X, He Y, et al. An insertion/deletion polymorphism within RERT-lncRNA modulates hepatocellular carcinoma risk. Cancer Res. 2012; 72: 6163-72.
34. Lomas NJ, Watts KL, Akram KM, et al. Idiopathic pulmonary fibrosis: immunohistochemical analysis provides fresh insights into lung tissue remodelling with implications for novel prognostic markers. Int J Clin Exp Pathol. 2012; 5: 58-71.
35. Kim KK, Wei Y, Szekeres C, et al. Epithelial cell alpha3beta1 integrin links beta-catenin and Smad signaling to promote myofibroblast formation and pulmonary fibrosis. J Clin Invest. 2009; 119: 213-24.
36. Ramos C, Becerril C, Montaño M, et al. FGF-1 reverts epithelial-mesenchymal transition induced by TGF-{beta}1 through MAPK/ERK kinase pathway. Am J Physiol Lung Cell Mol Physiol. 2010; 299: L222-31.
37. Wang Y, Xu Z, Jiang J, et al. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell. 2013; 25: 69-80.
38. Wang J, Liu X, Wu H, et al. CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res. 2010; 38: 5366-83.
39. Johnsson P, Ackley A, Vidarsdottir L, et al. A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat Struct Mol Biol. 2013; 20: 440-6.
40. Dharap A, Nakka VP, Vemuganti R. Effect of focal ischemia on long noncoding RNAs. Stroke. 2012; 43: 2800-2.
41. Zheng MZ, Qin HD, Yu XJ, et al. Haplotype of gene Nedd4 binding protein 2 associated with sporadic nasopharyngeal carcinoma in the Southern Chinese population. J Transl Med. 2007; 5: 36.
42. Vancheri C. Idiopathic pulmonary fibrosis: an altered fibroblast proliferation linked to cancer biology. Proc Am Thorac Soc. 2012; 9: 153-7.
43. Cushing L, Kuang PP, Qian J, et al. miR-29 is a major regulator of genes associated with pulmonary fibrosis. Am J Respir Cell Mol Biol. 2011; 45: 287-94.
44. Kigel B, Rabinowicz N, Varshavsky A, et al. Plexin-A4 promotes tumor progression and tumor angiogenesis by enhancement of VEGF and bFGF signaling. Blood. 2011; 118: 4285-96.
45. Wan YY, Tian GY, Guo HS, et al. Endostatin, an angiogenesis inhibitor, ameliorates bleomycin-induced pulmonary fibrosis in rats. Respir Res. 2013; 14: 56.
46. Pandit KV, Corcoran D, Yousef H, et al. Inhibition and role of let-7d in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2010; 182: 220-9.