The long non-coding RNA ERIC is regulated by E2F and modulates the cellular response to DNA damage

Molecular Cancer

Volumn 12, Issue 1, 2013, Pages

  Feldstein, Orit ^a   Nizri, Tal ^a   Doniger, Tirza ^a   Jacob, Jasmine ^b,c   Rechavi, Gideon ^b,c   Ginsberg, Doron ^a  

^a BAR ILAN UNIVERSITY   (Israel)

^b SHEBA MEDICAL CENTER   (Israel)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

Apoptosis; E2F1; Long non coding RNA

Indexed keywords

ETOPOSIDE; LONG UNTRANSLATED RNA; TRANSCRIPTION FACTOR E2F1; TRANSCRIPTION FACTOR E2F3;

APOPTOSIS; ARTICLE; CELL CYCLE; CELL DEATH; CONTROLLED STUDY; DNA DAMAGE; HUMAN; NEGATIVE FEEDBACK; UPREGULATION;

APOPTOSIS; CELL CYCLE CHECKPOINTS; CELL LINE, TUMOR; DNA DAMAGE; E2F1 TRANSCRIPTION FACTOR; GENE EXPRESSION REGULATION; HUMANS; RNA, LONG NONCODING; TRANSCRIPTION, GENETIC; UP-REGULATION;

EID: 84886404516     PISSN: None     EISSN: 14764598     Source Type: Journal    
DOI: 10.1186/1476-4598-12-131     Document Type: Article

References (58)

1. Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem 2012, 81:145-166.
2. Amaral PP, Mattick JS. Noncoding RNA in development. Mamm Genome 2008, 19:454-492.
3. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458:223-227.
4. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011, 477:295-300.
5. Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P, et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet 2011, 43:621-629.
6. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 2009, 106:11667-11672.
7. Loewer S, Cabili MN, Guttman M, Loh YH, Thomas K, Park IH, Garber M, Curran M, Onder T, Agarwal S, et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet 2010, 42:1113-1117.
8. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010, 329:689-693.
9. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011, 472:120-124.
10. Gibb EA, Brown CJ, Lam WL. The functional role of long non-coding RNA in human carcinomas. Mol Cancer 2011, 10:38.
11. Liu Q, Huang J, Zhou N, Zhang Z, Zhang A, Lu Z, Wu F, Mo YY. LncRNA loc285194 is a p53-regulated tumor suppressor. Nucleic Acids Res 2013, 41:4976-4987.
12. Gibb EA, Vucic EA, Enfield KS, Stewart GL, Lonergan KM, Kennett JY, Becker-Santos DD, MacAulay CE, Lam S, Brown CJ, Lam WL. Human cancer long non-coding RNA transcriptomes. PLoS One 2011, 6:e25915.
13. Gutschner T, Hammerle M, Diederichs S. MALAT1 - a paradigm for long noncoding RNA function in cancer. J Mol Med 2013, 91:791-801.
14. Gutschner T, Diederichs S. The Hallmarks of Cancer: a long non-coding RNA point of view. RNA Biol 2012, 9:703-719.
15. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464:1071-1076.
16. Wang KC, Chang HY. Molecular Mechanisms of Long Noncoding RNAs. Mol Cell 2011, 43:904-914.
17. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007, 129:1311-1323.
18. Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 2008, 322:1717-1720.
19. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008, 322:750-756.
20. Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010, 143:46-58.
21. Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, Xiong Y. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene 2011, 30:1956-1962.
22. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010, 142:409-419.
23. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Solda G, Simons C, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008, 18:1433-1445.
24. Chen LL, Carmichael GG. Long noncoding RNAs in mammalian cells: what, where, and why?. Wiley Interdiscip Rev RNA 2010, 1:2-21.
25. Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. Non-coding RNAs: regulators of disease. J Pathol 2010, 220:126-139.
26. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 2004, 116:499-509.
27. Polager S, Ginsberg D. E2F - at the crossroads of life and death. Trends Cell Biol 2008, 18:528-535.
28. Sherr CJ, McCormick F. The RB and p53 pathways in cancer. Canc Cell 2002, 2:103-112.
29. Dimova DK, Stevaux O, Frolov MV, Dyson NJ. Cell cycle-dependent and cell cycle-independent control of transcription by the Drosophila E2F/RB pathway. Genes Dev 2003, 17:2308-2320.
30. van den Heuvel S, Dyson NJ. Conserved functions of the pRB and E2F families. Nat Rev Mol Cell Biol 2008, 9:713-724.
31. Hallstrom TC, Nevins JR. Balancing the decision of cell proliferation and cell fate. Cell Cycle 2009, 8:532-535.
32. Tracy K, Dibling BC, Spike BT, Knabb JR, Schumacker P, Macleod KF. BNIP3 is an RB/E2F target gene required for hypoxia-induced autophagy. Mol Cell Biol 2007, 27:6229-6242.
33. Polager S, Ofir M, Ginsberg D. E2F1 regulates autophagy and the transcription of autophagy genes. Oncogene 2008, 27:4860-4864.
34. Kusama Y, Sato K, Kimura N, Mitamura J, Ohdaira H, Yoshida K. Comprehensive analysis of expression pattern and promoter regulation of human autophagy-related genes. Apoptosis 2009, 14:1165-1175.
35. Iaquinta PJ, Lees JA. Life and death decisions by the E2F transcription factors. Curr Opin Cell Biol 2007, 19:649-657.
36. Johnson DG, Degregori J. Putting the Oncogenic and Tumor Suppressive Activities of E2F into Context. Curr Mol Med 2006, 6:731-738.
37. Vigo E, Muller H, Prosperini E, Hateboer G, Cartwright P, Moroni MC, Helin K. CDC25A phosphatase is a target of E2F and is required for efficient E2F-induced S phase. Mol Cell Biol 1999, 19:6379-6395.
38. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011, 25:1915-1927.
39. Polager S, Ginsberg D. p53 and E2f: partners in life and death. Nat Rev Canc 2009, 9:738-748.
40. Lize M, Pilarski S, Dobbelstein M. E2F1-inducible microRNA 449a/b suppresses cell proliferation and promotes apoptosis. Cell Death Differ 2009, 17:452-458.
41. Yang X, Feng M, Jiang X, Wu Z, Li Z, Aau M, Yu Q. miR-449a and miR-449b are direct transcriptional targets of E2F1 and negatively regulate pRb-E2F1 activity through a feedback loop by targeting CDK6 and CDC25A. Genes Dev 2009, 23:2388-2393.
42. Ofir M, Hacohen D, Ginsberg D. miR-15 and miR-16 Are direct transcriptional targets of E2F1 that limit E2F-induced proliferation by targeting cyclin E. Mol Canc Res 2011, 9:440-447.
43. Wapinski O, Chang HY. Long noncoding RNAs and human disease. Trends Cell Biol 2011, 21:354-361.
44. Ozgur E, Mert U, Isin M, Okutan M, Dalay N, Gezer U. Differential expression of long non-coding RNAs during genotoxic stress-induced apoptosis in HeLa and MCF-7 cells. Clin Exp Med 2012, 13:119-126.
45. Berteaux N, Lottin S, Monte D, Pinte S, Quatannens B, Coll J, Hondermarck H, Curgy JJ, Dugimont T, Adriaenssens E. H19 mRNA-like noncoding RNA promotes breast cancer cell proliferation through positive control by E2F1. J Biol Chem 2005, 280:29625-29636.
46. Wan G, Mathur R, Hu X, Liu Y, Zhang X, Peng G, Lu X. Long non-coding RNA ANRIL (CDKN2B-AS) is induced by the ATM-E2F1 signaling pathway. Cell Signal 2013, 25:1086-1095.
47. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012, 22:1775-1789.
48. Chaussepied M, Ginsberg D. Transcriptional Regulation of AKT Activation by E2F. Mol Cell 2004, 16:831-837.
49. Bueno MJ, Gomez De Cedron M, Laresgoiti U, Fernandez-Piqueras J, Zubiaga AM, Malumbres M. Multiple E2F-induced microRNAs prevent replicative stress in response to mitogenic signaling. Mol Cell Biol 2010, 30:2983-2995.
50. Hallstrom TC, Nevins JR. Specificity in the activation and control of transcription factor E2F-dependent apoptosis. Proc Natl Acad Sci USA 2003, 100:10848-10853.
51. Ben Shachar B, Feldstein O, Hacohen D, Ginsberg D. The tumor suppressor maspin mediates E2F1-induced sensitivity of cancer cells to chemotherapy. Mol Canc Res 2010, 8:363-372.
52. Elliott MJ, Farmer MR, Atienza C, Stilwell A, Dong YB, Yang HL, Wong SL, McMasters KM. E2F-1 gene therapy induces apoptosis and increases chemosensitivity in human pancreatic carcinoma cells. Tumour Biol 2002, 23:76-86.
53. Dong YB, Yang HL, McMasters KM. E2F-1 overexpression sensitizes colorectal cancer cells to camptothecin. Canc Gene Ther 2003, 10:168-178.
54. Putzer BM, Engelmann D. E2F1 apoptosis counterattacked: evil strikes back. Trends Mol Med 2013, 19:89-98.
55. Berkovich E, Ginsberg D. ATM is a target for positive regulation by E2F-1. Oncogene 2003, 22:161-167.
56. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25.
57. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
58. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010, 11:R106.