Long non-coding RNAs: Challenges for diagnosis and therapies

Nucleic Acid Therapeutics

Volumn 23, Issue 1, 2013, Pages 15-20

  Sánchez, Yolanda ^a   Huarte, Maite ^a  

^a UNIVERSITY OF NAVARRA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; MESSENGER RNA; MICRORNA;

ARTICLE; CARDIOVASCULAR DISEASE; DEGENERATIVE DISEASE; DIABETES MELLITUS; DIAGNOSTIC TEST; HUMAN; NEOPLASM; NONHUMAN; PRIORITY JOURNAL; PROSTATE CANCER; PSORIASIS; RNA SPLICING; SCHIZOPHRENIA; SPINOCEREBELLAR DEGENERATION;

BIOLOGICAL MARKERS; GENETIC THERAPY; HUMANS; MENTAL DISORDERS; NEOPLASMS; NEURODEGENERATIVE DISEASES; RNA INTERFERENCE; RNA, LONG UNTRANSLATED; RNA, NEOPLASM;

EID: 84873668884     PISSN: 21593337     EISSN: None     Source Type: Journal    
DOI: 10.1089/nat.2012.0414     Document Type: Article

References (54)

1. ANNILO, T., KEPP, K., and LAAN, M. (2009). Natural antisense transcript of natriuretic peptide precursor A (NPPA): Structural organization and modulation of NPPA expression. BMC Mol. Biol. 10, 81
2. BELTRAN, M., PUIG, I., PENA, C., GARCIA, J.M., ALVAREZ, A.B., PENA, R., BONILLA, F., and DE HERREROS, A.G. (2008). A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev. 22, 756-769
3. CABIANCA, D. S., CASA, V., and GABELLINI, D. (2012). A novel molecular mechanism in human genetic disease: A DNA repeat-derived lncRNA point-of-view. RNA Biol. 9, 1211- 1217
4. CARRIERI, C., CIMATTI, L., BIAGIOLI, M., BEUGNET, A., ZUCCHELLI, S., FEDELE, S., PESCE, E., FERRER, I., COLLAVIN, L., SANTORO, C., et al. (2012). Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491, 454-457
5. CHEN, W. L., LIN, J. W., HUANG, H. J., WANG, S. M., SU, M. T., LEE-CHEN, G. J., CHEN, C. M., and HSIEH-LI, H. M. (2008). SCA8 mRNA expression suggests an antisense regulation of KLHL1 and correlates to SCA8 pathology. Brain Res. 1233, 176-184
6. CHUBB, J.E., BRADSHAW, N.J., SOARES, D.C., PORTEOUS, D.J., and MILLAR, J.K. (2008). The DISC locus in psychiatric illness. Mol. Psychiatry 13, 36-64
7. COLLEY, S.M., and LEEDMAN, P.J. (2009). SRA and its binding partners: An expanding role for RNA-binding coregulators in nuclear receptor-mediated gene regulation. Crit. Rev. Biochem. Mol. Biol. 44, 25-33
8. CUNNINGTON, M S., SANTIBANEZ KOREF, M., MAYOSI, B. M., BURN, J., and KEAVNEY, B. (2010). Chromosome 9p21
9. SNPs associated with multiple disease phenotypes correlate with ANRIL expression. PLoS Genet 6, e1000899
10. DINGER, M.E., PANG, K.C., MERCER, T.R., and MATTICK, J.S. (2008). Differentiating protein-coding and noncoding RNA: Challenges and ambiguities. PLoS Comput. Biol. 4, e1000176
11. DJEBALI, S., DAVIS, C.A., MERKEL, A., DOBIN, A., ASSMANN, T., MORTAZAVI, A., TANZER, A., LAGARDE, J., LIN, W., SCHLESINGER, F., et al. (2012). Landscape of ranscription in human cells. Nature 489, 101-108
12. DUNHAM, I., KUNDAJE, A., ALDRED, S.F., COLLINS, P.J., DAVIS, C.A., DOYLE, F., EPSTEIN, C.B., FRIETZE, S., HARROW, J., KAUL, R., et al. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74
13. EIßMANN, M., Gutschner, T., HÄMMERLE, M., GÜNTHER, S., Caudron-Herger, M., Groß, M., Schirmacher, P., Rippe, K., Braun, T., Zö rnig, M., and Diederichs, S. (2012). Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol. 9, 1076-1087
14. ESTELLER, M. (2011). Non-coding RNAs in human disease. Nat. Rev. Genet. 12, 861-874
15. FAGHIHI, M.A., MODARRESI, F., KHALIL, A.M., WOOD, D.E., SAHAGAN, B.G., MORGAN, T.E., FINCH, C.E., ST LAURENT, G., 3rd, KENNY, P.J., and WAHLESTEDT, C. (2008). Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat. Med. 14, 723-730
16. GIBB, E.A., ENFIELD, K.S., STEWART, G.L., LONERGAN, K.M., CHARI, R., NG, R.T., ZHANG, L., MACAULAY, C.E., ROSIN, M.P., and LAM, W.L. (2011). Long non-coding RNAs are expressed in oral mucosa and altered in oral premalignant lesions. Oral Oncol. 47, 1055-1061
17. GUPTA, R.A., SHAH, N., WANG, K.C., KIM, J., HORLINGS, H.M., WONG, D.J., TSAI, M.C., HUNG, T., ARGANI, P., RINN, J.L., et al. (2010). Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-1076
18. GUTSCHNER, T., BAAS, M., and DIEDERICHS, S. (2011). Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases. Genome Res. 21, 1944-1954
19. GUTTMAN, M., and RINN, J.L. (2012). Modular regulatory principles of large non-coding RNAs. Nature 482, 339-346
20. HAN, L., ZHANG, K., SHI, Z., ZHANG, J., ZHU, J., ZHU, S., ZHANG, A., JIA, Z., WANG, G., YU, S., et al. (2012). LncRNA pro fi le of glioblastoma reveals the potential role of lncRNAs in contributing to glioblastoma pathogenesis. Int. J. Oncol. 40, 2004-2012
21. HUARTE, M., GUTTMAN, M., FELDSER, D., GARBER, M., KOZIOL, M.J., KENZELMANN-BROZ, D., KHALIL, A.M., ZUK, O., AMIT, I., RABANI, M., et al. (2010). A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409-419
22. HUDSON, T.J., ANDERSON, W., ARTEZ, A., BARKER, A.D., BELL, C., BERNABE, R.R., BHAN, M.K., CALVO, F., EEROLA, I., GERHARD, D.S., et al. (2010). International network of cancer genome projects. Nature 464, 993-998
23. HUNG, T., WANG, Y., LIN, M.F., KOEGEL, A.K., KOTAKE, Y., GRANT, G.D., HORLINGS, H.M., SHAH, N., UMBRICHT, C., WANG, P., et al. (2011). Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat. Genet. 43, 621-629
24. ISHII, N., OZAKI, K., SATO, H., MIZUNO, H., SAITO, S., TAKAHASHI, A., MIYAMOTO, Y., IKEGAWA, S., KAMATANI, N., HORI, M., et al. (2006). Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J. Hum Genet. 51, 1087-1099
25. JI, P., DIEDERICHS, S., WANG, W., BOING, S., METZGER, R., SCHNEIDER, P.M., TIDOW, N., BRANDT, B., BUERGER, H., BULK, E., et al. (2003). MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in earlystage non-small cell lung cancer. Oncogene 22, 8031-8041
26. JOHNSON, R. (2012). Long non-coding RNAs in Huntington's disease neurodegeneration. Neurobiol. Dis. 46, 245-254
27. KHALIL, A. M., FAGHIHI, M. A., MODARRESI, F., BROTHERS, S. P., and WAHLESTEDT, C. (2008). A novel RNA transcript with antiapoptotic function is silenced in fragile X syndrome. PLoS One 3, e1486
28. KINO, T., HURT, D.E., ICHIJO, T., NADER, N., and CHROUSOS, G.P. (2010). Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal 3, ra8
29. KOGO, R., SHIMAMURA, T., MIMORI, K., KAWAHARA, K., IMOTO, S., SUDO, T., TANAKA, F., SHIBATA, K., SUZUKI, A., KOMUNE, S., et al. (2011). Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 71, 6320-6326
30. LEE, G.L., DOBI, A., and SRIVASTAVA, S. (2011). Prostate cancer: Diagnostic performance of the PCA3 urine test. Nat. Rev. Urol. 8, 123-124
31. LI, X., ISONO, K., YAMADA, D., ENDO, T.A., ENDOH, M., SHINGA, J., MIZUTANI-KOSEKI, Y., OTTE, A.P., CASANOVA, M., et al is a novel regulatory component of PRC2 that can differentially modulate polycomb activity both at the Hox gene cluster and at Cdkn2a genes. Mol. Cell Biol. 31, 351-364
32. LIN, R., MAEDA, S., LIU, C., KARIN, M., and EDGINGTON, T.S. (2007). A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 26, 851-858
33. LOTTIN, S., ADRIAENSSENS, E., DUPRESSOIR, T., BERTEAUX, N., MONTPELLIER, C., COLL, J., DUGIMONT, T., and CURGY, J.J. (2002). Overexpression of an ectopic H19 gene enhances the tumorigenic properties of breast cancer cells. Carcinogenesis 23, 1885-1895
34. MAASS, P.G., RUMP, A., SCHULZ, H., STRICKER, S., SCHULZE, L., PLATZER, K., AYDIN, A., TINSCHERT, S., GOLDRING, M.B., LUFT, F.C., and BAHRING, S. (2012). A misplaced lncRNA causes brachydactyly in humans. J. Clin. Invest. 122, 3990-4002
35. MATOUK, I. J., DEGROOT, N., MEZAN, S., AYESH, S., ABULAIL, R., HOCHBERG, A., and GALUN, E. (2007). The H19 non-coding RNA is essential for human tumor growth. PLoS One 2, e845
36. MERCER, T.R., DINGER, M.E., and MATTICK, J.S. (2009). Long non-coding RNAs: Insights into functions. Nat. Rev. Genet. 10, 155-159
37. MIZRAHI, A., CZERNIAK, A., LEVY, T., AMIUR, S., GALLULA, J., MATOUK, I., ABU-LAIL, R., SORIN, V., BIRMAN, T., DE GROOT, N., et al. (2009). Development of targeted therapy for ovarian cancer mediated by a plasmid expressing diphtheria toxin under the control of H19 regulatory sequences. J. Transl. Med. 7, 69
38. PENG, X., GRALINSKI, L., ARMOUR, C. D., FERRIS, M. T., THOMAS, M. J., PROLL, S., BRADEL-TRETHEWAY, B. G., KORTH, M. J., CASTLE, J. C., BIERY, M. C., et al. (2010). Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling. MBio 1, DOI: 10.1128/mBio.00206-00210
39. RINN, J.L., and CHANG, H.Y. (2012). Genome Regulation by Long Noncoding RNAs. Annu. Rev. Biochem. 81, 145-166
40. SCHEELE, C., NIELSEN, A. R., WALDEN, T. B., SEWELL, D. A., FISCHER, C. P., BROGAN, R. J., PETROVIC, N., LARSSON, O., TESCH, P. A., WENNMALM, K., et al. (2007). Altered regulation of the PINK1 locus: A link between type 2 diabetes and neurodegeneration Faseb J 21, 3653-3665
41. SEIM, I., COLLET, C., HERINGTON, A.C., and CHOPIN, L.K. (2007). Revised genomic structure of the human ghrelin gene and identification of novel exons, alternative splice variants and natural antisense transcripts. BMC Genomics 8, 298
42. SONKOLY, E., BATA-CSORGO, Z., PIVARCSI, A., POLYANKA, H., KENDERESSY-SZABO, A., MOLNAR, G., SZENTPALI, K., BARI, L., MEGYERI, K., MANDI, Y., et al. (2005). Identification and characterization of a novel, psoriasis susceptibility-related noncoding RNA gene, PRINS. J. Biol. Chem. 280, 24159-24167
43. SUI, W., YAN, Q., LI, H., LIU, J., CHEN, J., LI, L., and DAI, Y. (2012). Genome-wide analysis of long noncoding RNA expression in peripheral blood mononuclear cells of uremia patients. J Nephrol, DOI: 10.5301/jn.5000201
44. TAHIRA, A.C., KUBRUSLY, M.S., FARIA.M.F., DAZZANI, B., FONSECA, R.S., MARACAJA-COUTINHO, V., VERJOVSKIALMEIDA, S., MACHADO, M.C., and REIS, E.M. (2011). Long noncoding intronic RNAs are differentially xpressed in primary and metastatic pancreatic cancer. Mol. Cancer 10, 141
45. TAMURA, Y., KUNUGI, H., OHASHI, J., and HOHJOH, H. (2007). Epigenetic aberration of the human REELIN gene in psychiatric disorders. Mol Psychiatry 12, 593-600
46. TRIPATHI, V., ELLIS, J.D., SHEN, Z., SONG, D.Y., PAN, Q., WATT, A.T., FREIER, S.M., BENNETT, C.F., SHARMA, A., BUBULYA, P.A., et al. (2010). The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 39, 925-938
47. TSAI, M.C., SPITALE, R.C., and CHANG, H.Y. (2011). Long intergenic noncoding RNAs: New links in cancer progression. Cancer Res. 71, 3-7
48. TUFARELLI, C., STANLEY, J.A., GARRICK, D., SHARPE, J.A., AYYUB, H., WOOD, W.G., and HIGGS, D.R. (2003). Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat. Genet 34, 157-165
49. WANG, K.C., and CHANG, H.Y. (2011). Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904-914
50. WAPINSKI, O., and CHANG, H.Y. (2011). Long noncoding RNAs and human disease. Trends Cell Biol. 21, 354-356
51. YANG, Z., ZHOU, L., WU, L.M., LAI, M.C., XIE, H.Y., ZHANG, F., and ZHENG, S.S. (2011). Overexpression of long noncoding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation. Ann. Surg. Oncol. 18, 1243-1250
52. YOON, J. H., ABDELMOHSEN, K., SRIKANTAN, S., YANG, X., MARTINDALE, J. L., DE, S., HUARTE, M., ZHAN, M., BECKER, K. G., and GOROSPE, M. (2012). LincRNA-p21 Suppresses Target mRNA Translation. Mol Cell 47, 648-655
53. ZHANG, W., CHEN, Y., LIU, P., CHEN, J., SONG, L., TANG, Y., WANG, Y., LIU, J., HU, F.B., and HUI, R. (2012). Variants on chromosome 9p21.3 correlated with ANRIL expression contribute to stroke risk and recurrence in a large prospective stroke population. Stroke 43, 14-21
54. ZIATS, M. N., and RENNERT, O. M. (2012). Aberrant Expression of Long Noncoding RNAs in Autistic Brain. J Mol Neurosci, DOI: 10.1007/s12031-12012- 19880-12038