SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer

RNA

Volumn 17, Issue 5, 2011, Pages 878-891

  Askarian Amiri, Marjan E ^a   Crawford, Joanna ^a   French, Juliet D ^a   Smart, Chanel E ^a,c   Smith, Martin A ^a   Clark, Michael B ^a   Ru, Kelin ^a   Mercer, Tim R ^a   Thompson, Ella R ^b   Lakhani, Sunil R ^a,c,d   Vargas, Ana C ^c   Campbell, Ian G ^b,e   Brown, Melissa A ^a   Dinger, Marcel E ^a   Mattick, John S ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b PETER MACCALLUM CANCER CENTRE   (Australia)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d ROYAL BRISBANE AND WOMEN'S HOSPITAL   (Australia)

^e UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Noncoding RNA; SnoRNA; Tumor suppressor

Indexed keywords

GENE PRODUCT; PROTEIN SNORD; UNCLASSIFIED DRUG;

5' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; BREAST CANCER; BREAST DEVELOPMENT; BREAST EPITHELIUM; CELL DIFFERENTIATION; CELL PROLIFERATION; DOWN REGULATION; FEMALE; GENE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE LOCATION; GENETIC CONSERVATION; HALF LIFE TIME; IN VIVO STUDY; MARKER GENE; MOUSE; NONHUMAN; PRIORITY JOURNAL; SNORD12 GENE; SNORD12B GENE; SNORD12C GENE; TUMOR SUPPRESSOR GENE; ZFAS1 GENE;

ALTERNATIVE SPLICING; ANIMALS; BETA CATENIN; BREAST NEOPLASMS; CELL LINE; FEMALE; GENE EXPRESSION REGULATION; HUMANS; MAMMARY GLANDS, ANIMAL; MAMMARY GLANDS, HUMAN; MICE; RNA, SMALL NUCLEOLAR; RNA, UNTRANSLATED; TRANSCRIPTION, GENETIC; TUMOR MARKERS, BIOLOGICAL;

EID: 79955005458     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2528811     Document Type: Article

References (67)

1. Al-Shahrour F, Minguez P, Tárraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J. 2006. BABELOMICS: A systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res 34: W472-W476. (Pubitemid 44529816)
2. Amaral PP, Mattick JS. 2008. Noncoding RNA in development. Mamm Genome 19: 454-492.
3. Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC, Mattick JS. 2009. Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA 15: 2013-2027.
4. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. 2010. lncRNAdb: A reference database for long noncoding RNAs. Nucleic Acids Res 39: D146-D151.
5. Babak T, Blencowe BJ, Hughes TR. 2005. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics 6: 104. doi: 10.1186/1471-2164-6-104. (Pubitemid 41372172)
6. Badger JH, Olsen GJ. 1999. CRITICA: Coding region identification tool invoking comparative analysis. Mol Biol Evol 16: 512-524. (Pubitemid 29190958)
7. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. 2004. Ultraconserved elements in the human genome. Science 304: 1321-1325. (Pubitemid 38697428)
8. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816. (Pubitemid 46920138)
9. Brosius J. 2005. Waste not, want not-transcript excess in multicellular eukaryotes. Trends Genet 21: 287-288. (Pubitemid 40558934)
10. Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R, Sevignani C, Fabbri M, Cimmino A, Lee EJ, Wojcik SE, et al. 2007. Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12: 215-229. (Pubitemid 47333418)
11. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
12. Dieci G, Preti M, Montanini B. 2009. Eukaryotic snoRNAs: A paradigm for gene expression flexibility. Genomics 94: 83-88.
13. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Solda G, Simons C, et al. 2008a. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18: 1433-1445.
14. Dinger ME, Pang KC, Mercer TR, Mattick JS. 2008b. Differentiating protein-coding and noncoding RNA: Challenges and ambiguities. PLoS Comput Biol 4: E1000176. doi: 10.1371/journal.pcbi.1000176.
15. Dinger ME, Amaral PP, Mercer TR, Mattick JS. 2009. Pervasive transcription of the eukaryotic genome: Functional indices and conceptual implications. Brief Funct Genomics Proteomics 8: 407-423.
16. Dong XY, Guo P, Boyd J, Sun X, Li Q, Zhou W, Dong JT. 2009. Implication of snoRNA U50 in human breast cancer. J Genet Genomics 36: 447-454.
17. Dunphy EJ, McNeel DG. 2005. Antigen-specific IgG elicited in subjects with prostate cancer treated with flt3 ligand. J Immunother 28: 268-275. (Pubitemid 40593993)
18. Eis PS, Tam W, Sun L, Chadburn A, Li Z, Gomez MF, Lund E, Dahlberg JE. 2005. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc Natl Acad Sci 102: 3627-3632. (Pubitemid 40354662)
19. Ender C, Krek A, Friedlander MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G. 2008. A human snoRNA with microRNA-like functions. Mol Cell 32: 519-528.
20. Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, et al. 2006. Complex loci in human and mouse genomes. PLoS Genet 2: E47. doi: 10.1371/ journal.pgen.0020047.
21. Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD. 2006. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20: 1470-1484. (Pubitemid 43830654)
22. Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furuno M, Bult CJ, Quackenbush J, et al. 2006. Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol 3: 40-48.
23. Gabory A, Jammes H, Dandolo L. 2010. The H19 locus: Role of an imprinted non-coding RNA in growth and development. Bioessays 32: 473-480.
24. Georgopoulou N, Hurel C, Politis PK, Gaitanou M, Matsas R, Thomaidou D. 2006. BM88 is a dual function molecule inducing cell cycle exit and neuronal differentiation of neuroblastoma cells via cyclin D1 down-regulation and retinoblastoma protein hypophosphorylation. J Biol Chem 281: 33606-33620. (Pubitemid 46036741)
25. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
26. Hennighausen L, Robinson GW. 1998. Think globally, act locally: The making of a mouse mammary gland. Genes Dev 12: 449-455. (Pubitemid 28101007)
27. Hennighausen L, Robinson GW. 2001. Signaling pathways in mammary gland development. Dev Cell 1: 467-475. (Pubitemid 33586099)
28. Hernandez A, Garcia B, Obregon MJ. 2007. Gene expression from the imprinted Dio3 locus is associated with cell proliferation of cultured brown adipocytes. Endocrinology 148: 3968-3976. (Pubitemid 47105881)
29. Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH. 2005. Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs. RNA 11: 1303-1316. (Pubitemid 41132401)
30. Huarte M, Rinn JL. 2010. Large non-coding RNAs: Missing links in cancer? Hum Mol Genet 19: R152-R161.
31. Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H, Bachellerie JP, Brosius J. 2001. RNomics: An experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J 20: 2943-2953. (Pubitemid 32938577)
32. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR. 2002. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296: 916-919. (Pubitemid 34464898)
33. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, et al. 2007a. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316: 1484-1488. (Pubitemid 46906616)
34. Kapranov P, Willingham AT, Gingeras TR. 2007b. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8: 413-423. (Pubitemid 46789245)
35. Keydar I, Chen L, Karby S, Weiss FR, Delarea J, Radu M, Chaitcik S, Brenner HJ. 1979. Establishment and characterization of a cell line of human breast carcinoma origin. Eur J Cancer 15: 659-670. (Pubitemid 9198534)
36. Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP. 2010. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 3: Ra8. doi: 10.11126/ scisignal.2000568.
37. Lasfargues EY, Coutinho WG, Dion AS. 1979. A human breast tumor cell line (BT-474) that supports mouse mammary tumor virus replication. In Vitro 15: 723-729. (Pubitemid 10168122)
38. Master SR, Hartman JL, D'Cruz CM, Moody SE, Keiper EA, Ha SI, Cox JD, Belka GK, Chodosh LA. 2002. Functional microarray analysis of mammary organogenesis reveals a developmental role in adaptive thermogenesis. Mol Endocrinol 16: 1185-1203. (Pubitemid 34621068)
39. Mazar J, Sinha S, Dinger ME, Mattick JS, Perera RJ. 2010. Proteincoding and non-coding gene expression analysis in differentiating human keratinocytes using a three-dimensional epidermal equivalent. Mol Genet Genomics 284: 1-9.
40. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. 2008. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci 105: 716-721. (Pubitemid 351171774)
41. Mercer TR, Dinger ME, Mattick JS. 2009. Long noncoding RNAs: Insights into function. Nat Rev Genet 10: 155-159.
42. Mercer TR, Qureshi IA, Gokhan S, Dinger ME, Li G, Mattick JS, Mehler MF. 2010. Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci 11: 14. doi: 10.1186/1471-2202-11-14.
43. Metcalfe AD, Gilmore A, Klinowska T, Oliver J, Valentijn AJ, Brown R, Ross A, MacGregor G, Hickman JA, Streuli CH. 1999. Developmental regulation of Bcl-2 family protein expression in the involuting mammary gland. J Cell Sci 112: 1771-1783. (Pubitemid 29295053)
44. Mosmann T. 1983. Rapid colorimetric assay for cellular growth and survival: Application to proliferation and cytotoxicity assays. J Immunol Methods 65: 55-63. (Pubitemid 14203433)
45. Mourtada-Maarabouni M, Pickard MR, Hedge VL, Farzaneh F, Williams GT. 2009. GAS5, a non-protein-coding RNA, controls apoptosis and is down-regulated in breast cancer. Oncogene 28: 195-208.
46. Naylor MJ, Oakes SR, Gardiner-Garden M, Harris J, Blazek K, Ho TW, Li FC, Wynick D, Walker AM, Ormandy CJ. 2005. Transcriptional changes underlying the secretory activation phase of mammary gland development. Mol Endocrinol 19: 1868-1883. (Pubitemid 41007898)
47. Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, Mattick JS. 2009. Genome-wide identification of long noncoding RNAs in CD8+ T cells. J Immunol 182: 7738-7748.
48. Pelczar P, Filipowicz W. 1998. The host gene for intronic U17 small nucleolar RNAs in mammals has no protein-coding potential and is a member of the 59-terminal oligopyrimidine gene family. Mol Cell Biol 18: 4509-4518. (Pubitemid 28343035)
49. Ponjavic J, Ponting CP, Lunter G. 2007. Functionality or transcriptional noisě Evidence for selection within long noncoding RNAs. Genome Res 17: 556-565. (Pubitemid 46715505)
50. Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M, Okunishi R, Fukuda S, Ru K, Frith MC, Gongora MM, et al. 2006. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res 16: 11-19. (Pubitemid 43048929)
51. Robinson GW, McKnight RA, Smith GH, Hennighausen L. 1995. Mammary epithelial cells undergo secretory differentiation in cycling virgins but require pregnancy for the establishment of terminal differentiation. Development 121: 2079-2090.
52. Song Z, Krishna S, Thanos D, Strominger JL, Ono SJ. 1994. A novel cysteine-rich sequence-specific DNA-binding protein interacts with the conserved X-box motif of the human major histocompatibility complex class II genes via a repeated Cys-His domain and functions as a transcriptional repressor. J Exp Med 180: 1763-1774.
53. Soule HD, Vazguez J, Long A, Albert S, Brennan M. 1973. A human cell line from a pleural effusion derived from a breast carcinoma. J Natl Cancer Inst 51: 1409-1416.
54. Struhl K. 2007. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol 14: 103-105.
55. Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL. 2009. MEN varepsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19: 347-359.
56. Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, Mattick JS. 2009. Small RNAs derived from snoRNAs. RNA 15: 1233-1240.
57. Tan-Wong SM, French JD, Proudfoot NJ, Brown MA. 2008. Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc Natl Acad Sci 105: 5160-5165. (Pubitemid 351738527)
58. Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, Myers RM. 2004. An abundance of bidirectional promoters in the human genome. Genome Res 14: 62-66. (Pubitemid 38088526)
59. Troester MA, Hoadley KA, Sorlie T, Herbert BS, Borresen-Dale AL, Lonning PE, Shay JW, Kaufmann WK, Perou CM. 2004. Cell-typespecific responses to chemotherapeutics in breast cancer. Cancer Res 64: 4218-4226. (Pubitemid 38802426)
60. Vizcaino JA, Cote R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L. 2009. A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 9: 4276-4283.
61. Wang H, Iacoangeli A, Lin D, Williams K, Denman RB, Hellen CU, Tiedge H. 2005. Dendritic BC1 RNA in translational control mechanisms. J Cell Biol 171: 811-821. (Pubitemid 41746583)
62. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, et al. 2008. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903. (Pubitemid 351913645)
63. Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF. 2005. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol 23: 1383-1390. (Pubitemid 41679390)
64. Wilusz JE, Sunwoo H, Spector DL. 2009. Long noncoding RNAs: Functional surprises from the RNA world. Genes Dev 23: 1494-1504.
65. Yan MD, Hong CC, Lai GM, Cheng AL, Lin YW, Chuang SE. 2005. Identification and characterization of a novel gene Saf transcribed from the opposite strand of Fas. Hum Mol Genet 14: 1465-1474.
66. Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH. 2006. snoSeeker: An advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res 34: 5112-5123. (Pubitemid 44742476)
67. Zucchi I, Bini L, Albani D, Valaperta R, Liberatori S, Raggiaschi R, Montagna C, Susani L, Barbieri O, Pallini V, et al. 2002. Dome formation in cell cultures as expression of an early stage of lactogenic differentiation of the mammary gland. Proc Natl Acad Sci 99: 8660-8665. (Pubitemid 34693616)