DIANA-LncBase: Experimentally verified and computationally predicted microRNA targets on long non-coding RNAs

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Paraskevopoulou, Maria D ^a,b   Georgakilas, Georgios ^a,c   Kostoulas, Nikos ^d   Reczko, Martin ^a,e   Maragkakis, Manolis ^a,f   Dalamagas, Theodore M ^d,g   Hatzigeorgiou, Artemis G ^a,c  

^a BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING   (Greece)

^b UNIVERSITY OF ATHENS   (Greece)

^c UNIVERSITY OF THESSALY   (Greece)

^d INSTITUTE FOR THE MANAGEMENT OF INFORMATION SYSTEMS   (Greece)

^e Synaptic Ltd   (Greece)

^f UNIVERSITY OF PENNSYLVANIA   (United States)

^g NATIONAL TECHNICAL UNIVERSITY OF ATHENS   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; MICRORNA; RNA BINDING PROTEIN;

5' UNTRANSLATED REGION; ARTICLE; BINDING SITE; COMPUTER MODEL; CONTROLLED STUDY; DATA BASE; GENE SEQUENCE; GENETIC CONSERVATION; HUMAN; IMMUNOPRECIPITATION; INTRON; MOLECULAR GENETICS; MOUSE; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CROSS LINKING; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; RNA SEQUENCE;

ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; MICE; MICRORNAS; RNA, LONG UNTRANSLATED; SEQUENCE ANALYSIS, RNA;

EID: 84876523096     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1246     Document Type: Article

References (30)

1. Wang, K.C. and Chang, H.Y. (2011) Molecular mechanisms of long noncoding RNAs. Mol. Cell, 43, 904-914.
2. Ponting, C.P., Oliver, P.L. and Reik, W. (2009) Evolution and functions of long noncoding RNAs. Cell, 136, 629-641.
3. Gibb, E.A., Brown, C.J. and Lam, W.L. (2011) The functional role of long non-coding RNA in human carcinomas. Mol. Cancer, 10, 38.
4. Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
5. Khalil, A.M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B.E., van Oudenaarden, A. et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl Acad. Sci. USA, 106, 11667-11672.
6. Guttman, M., Donaghey, J., Carey, B.W., Garber, M., Grenier, J.K., Munson, G., Young, G., Lucas, A.B., Ach, R., Bruhn, L. et al. (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature, 477, 295-300.
7. Ponjavic, J., Ponting, C.P. and Lunter, G. (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res., 17, 556-565.
8. Espinoza, C.A., Goodrich, J.A. and Kugel, J.F. (2007) Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA, 13, 583-596.
9. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
10. Kim, V.N., Han, J. and Siomi, M.C. (2009) Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol., 10, 126-139.
11. Friedman, R.C., Farh, K.K., Burge, C.B. and Bartel, D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
12. Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M. Jr, Jungkamp, A.C., Munschauer, M. et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 141, 129-141.
13. 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.
14. Cesana, M., Cacchiarelli, D., Legnini, I., Santini, T., Sthandier, O., Chinappi, M., Tramontano, A. and Bozzoni, I. (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell, 147, 358-369.
15. Wang, J., Liu, X., Wu, H., Ni, P., Gu, Z., Qiao, Y., Chen, N., Sun, F. and Fan, Q. (2010) CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res., 38, 5366-5383.
16. Cai, X. and Cullen, B.R. (2007) The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA, 13, 313-316.
17. Mercer, T.R., Qureshi, I.A., Gokhan, S., Dinger, M.E., Li, G., Mattick, J.S. and Mehler, M.F. (2010) Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci., 11, 14.
18. Klein, U., Lia, M., Crespo, M., Siegel, R., Shen, Q., Mo, T., Ambesi-Impiombato, A., Califano, A., Migliazza, A., Bhagat, G. et al. (2010) The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell, 17, 28-40.
19. Jeggari, A., Marks, D.S. and Larsson, E. (2012) miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics, 28, 2062-2063.
20. Chi, S.W., Zang, J.B., Mele, A. and Darnell, R.B. (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature, 460, 479-486.
21. Reczko, M., Maragkakis, M., Alexiou, P., Grosse, I. and Hatzigeorgiou, A.G. (2012) Functional microRNA targets in protein coding sequences. Bioinformatics, 28, 771-776.
22. Harrow, J., Frankish, A., Gonzalez, J.M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B.L., Barrell, D., Zadissa, A., Searle, S. et al. (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res., 22, 1760-1774.
23. Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. and Rinn, J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
24. Bu, D., Yu, K., Sun, S., Xie, C., Skogerbo, G., Miao, R., Xiao, H., Liao, Q., Luo, H., Zhao, G. et al. (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res., 40, D210-D215.
25. Rehmsmeier, M., Steffen, P., Hochsmann, M. and Giegerich, R. (2004) Fast and effective prediction of microRNA/target duplexes. RNA, 10, 1507-1517.
26. Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
27. Gibb, E.A., Vucic, E.A., Enfield, K.S., Stewart, G.L., Lonergan, K.M., Kennett, J.Y., Becker-Santos, D.D., MacAulay, C.E., Lam, S., Brown, C.J. et al. (2011) Human cancer long non-coding RNA transcriptomes. PLoS One, 6, e25915.
28. Bono, H., Yagi, K., Kasukawa, T., Nikaido, I., Tominaga, N., Miki, R., Mizuno, Y., Tomaru, Y., Goto, H., Nitanda, H. et al. (2003) Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res., 13, 1318-1323.
29. Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84-D90.
30. Garber, M., Guttman, M., Clamp, M., Zody, M.C., Friedman, N. and Xie, X. (2009) Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics, 25, i54-i62.