Satellite non-coding RNAs: the emerging players in cells, cellular pathways and cancer

Chromosome Research

Volumn 23, Issue 3, 2015, Pages 479-493

  Ferreira, Daniela ^a,b   Meles, Susana ^a,b   Escudeiro, Ana ^a,b   Mendes da Silva, Ana ^a,b   Adega, Filomena ^a,b   Chaves, Raquel ^a,b  

^a UNIVERSITY OF TRÁS OS MONTES AND ALTO DOURO   (Portugal)

^b UNIVERSITY OF LISBON   (Portugal)

Author keywords

Biomarkers; Cancer; Genomic instability; Satellite DNA; Satellite non coding RNA

Indexed keywords

SATELLITE DNA; TUMOR MARKER; UNTRANSLATED RNA; HETEROCHROMATIN;

CANCER DIAGNOSIS; CANCER GENETICS; CANCER PROGNOSIS; CHROMOSOME REARRANGEMENT; CONSTITUTIVE HETEROCHROMATIN; DNA SEQUENCE; GENE EXPRESSION; GENOMIC INSTABILITY; HUMAN; NEXT GENERATION SEQUENCING; OPEN READING FRAME; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; SEQUENCE ANALYSIS; ANIMAL; GENETIC TRANSCRIPTION; GENETICS; GENOME; HETEROCHROMATIN; METABOLISM; NEOPLASM; PHYSIOLOGICAL STRESS; SIGNAL TRANSDUCTION;

ANIMALS; BIOMARKERS, TUMOR; DNA, SATELLITE; GENOME; HETEROCHROMATIN; HUMANS; NEOPLASMS; RNA, UNTRANSLATED; SIGNAL TRANSDUCTION; STRESS, PHYSIOLOGICAL; TRANSCRIPTION, GENETIC;

EID: 84947495774     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-015-9482-8     Document Type: Review

References (87)

1. Adega F, Guedes-Pinto H, Chaves R (2009) Satellite DNA in the karyotype evolution of domestic animals—clinical considerations. Cytogenet Genome Res 126(1-2):12–20
2. Aldrup-Macdonald ME, Sullivan BA (2014) The past, present, and future of human centromere genomics. Genes (Basel) 5(1):33–50
3. Alexiadis V, Ballestas ME, Sanchez C et al (2007) RNAPol-ChIP analysis of transcription from FSHD-linked tandem repeats and satellite DNA. Biochim Biophys Acta 1769(1):29–40
4. Almouzni G, Probst AV (2011) Heterochromatin maintenance and establishment: lessons from the mouse pericentromere. Nucleus 2(5):332–338
5. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS (2011) lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 39(Database issue):D146–151
6. Arutyunyan A, Stoddart S, Yi SJ et al (2012) Expression of cassini, a murine gamma-satellite sequence conserved in evolution, is regulated in normal and malignant hematopoietic cells. BMC Genomics 13:418
7. Bernstein E, Allis CD (2005) RNA meets chromatin. Genes Dev 19(14):1635–1655
8. Bouzinba-Segard H, Guais A, Francastel C (2006) Accumulation of small murine minor satellite transcripts leads to impaired centromeric architecture and function. Proc Natl Acad Sci U S A 103(23):8709–8714
9. Brown JD, Mitchell SE, O’Neill RJ (2012) Making a long story short: noncoding RNAs and chromosome change. Heredity (Edinb) 108(1):42–49
10. Bulut-Karslioglu A, Perrera V, Scaranaro M et al (2012) A transcription factor-based mechanism for mouse heterochromatin formation. Nat Struct Mol Biol 19(10):1023–1030
11. Burgess DJ (2011) Chromosome instability: tumorigenesis via satellite link. Nat Rev Cancer 11(3):158
12. Carone DM, Longo MS, Ferreri GC et al (2009) A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres. Chromosoma 118(1):113–125
13. Chaves R, Louzada S, Meles S, Wienberg J, Adega F (2012) Praomys tullbergi (Muridae, Rodentia) genome architecture decoded by comparative chromosome painting with Mus and Rattus. Chromosome Res 20(6):673–683
14. Chen G, Wang Z, Wang D et al (2013) LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 41(Database issue):D983–986
15. Cohen AK, Huh TY, Helleiner CW (1973) Transcription of satellite DNA in mouse L-cells. Can J Biochem 51(5):529–532
16. Crea F, Watahiki A, Quagliata L et al (2014) Identification of a long non-coding RNA as a novel biomarker and potential therapeutic target for metastatic prostate cancer. Oncotarget 5(3):764–774
17. Da Sacco L, Baldassarre A, Masotti A (2012) Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis. Int J Mol Sci 13(1):97–114
18. De Cecco M, Criscione SW, Peckham EJ et al (2013) Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements. Aging Cell 12(2):247–256
19. Deng G, Sui G (2013) Noncoding RNA in oncogenesis: a new era of identifying key players. Int J Mol Sci 14(9):18319–18349
20. Ehrlich M (2005) DNA methylation and cancer-associated genetic instability. Adv Exp Med Biol 570:363–392
21. Ehrlich M (2009) DNA hypomethylation in cancer cells. Epigenomics 1(2):239–259
22. Enukashvily NI, Donev R, Waisertreiger IS, Podgornaya OI (2007) Human chromosome 1 satellite 3 DNA is decondensed, demethylated and transcribed in senescent cells and in A431 epithelial carcinoma cells. Cytogenet Genome Res 118(1):42–54
23. Enukashvily NI, Ponomartsev NV (2013) Mammalian satellite DNA: a speaking dumb. Adv Protein Chem Struct Biol 90:31–65
24. Eymery A, Callanan M, Vourc’h C (2009) The secret message of heterochromatin: new insights into the mechanisms and function of centromeric and pericentric repeat sequence transcription. Int J Dev Biol 53(2-3):259–268
25. Feldstein O, Nizri T, Doniger T et al (2013) The long non-coding RNA ERIC is regulated by E2F and modulates the cellular response to DNA damage. Mol Cancer 12(1):131
26. Ferri F, Bouzinba-Segard H, Velasco G, Hube F, Francastel C (2009) Non-coding murine centromeric transcripts associate with and potentiate Aurora B kinase. Nucleic Acids Res 37(15):5071–5080
27. Frescas D, Guardavaccaro D, Kuchay SM et al (2008) KDM2A represses transcription of centromeric satellite repeats and maintains the heterochromatic state. Cell Cycle 7(22):3539–3547
28. Gent JI, Dawe RK (2012) RNA as a structural and regulatory component of the centromere. Annu Rev Genet 46:443–453
29. Gutschner T, Diederichs S (2012) The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol 9(6):703–719
30. Harel J, Hanania N, Tapiero H, Harel L (1968) RNA replication by nuclear satellite DNA in different mouse cells. Biochem Biophys Res Commun 33(4):696–701
31. Hauptman N, Glavac D (2013) MicroRNAs and long non-coding RNAs: prospects in diagnostics and therapy of cancer. Radiol Oncol 47(4):311–318
32. Huarte M, Rinn JL (2010) Large non-coding RNAs: missing links in cancer? Hum Mol Genet 19(R2):R152–161
33. Jackson K, Yu MC, Arakawa K et al (2004) DNA hypomethylation is prevalent even in low-grade breast cancers. Cancer Biol Ther 3(12):1225–1231
34. Jenjaroenpun P, Kremenska Y, Nair VM et al (2013) Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing. Peer J 1, e201
35. Jolly C, Metz A, Govin J et al (2004) Stress-induced transcription of satellite III repeats. J Cell Biol 164(1):25–33
36. Kanai Y, Ushijima S, Kondo Y, Nakanishi Y, Hirohashi S (2001) DNA methyltransferase expression and DNA methylation of CPG islands and peri-centromeric satellite regions in human colorectal and stomach cancers. Int J Cancer 91(2):205–212
37. Karapetyan AR, Buiting C, Kuiper RA, Coolen MW (2013) Regulatory roles for long ncRNA and mRNA. Cancers (Basel) 5(2):462–490
38. Kondratova VN, Botezatu IV, Shelepov VP, Likhtenshtein AV (2014) Transcripts of satellite DNA in blood plasma: probable markers of tumor growth. Mol Biol (Mosk) 48(6):999–1007
39. Kononenko AV, Bansal R, Lee NC et al (2014) A portable BRCA1-HAC (human artificial chromosome) module for analysis of BRCA1 tumor suppressor function. Nucleic Acids Res 42(21)
40. Kuhn GC (2015) Satellite DNA transcripts have diverse biological roles in Drosophila. Heredity (Edinb) 115(1):1–2
41. Leonova KI, Brodsky L, Lipchick B et al (2013) p53 cooperates with DNA methylation and a suicidal interferon response to maintain epigenetic silencing of repeats and noncoding RNAs. Proc Natl Acad Sci U S A 110(1):E89–98
42. Li CH, Chen Y (2013) Targeting long non-coding RNAs in cancers: progress and prospects. Int J Biochem Cell Biol 45(8):1895–1910
43. Liu B, Sun L, Song E (2013) Non-coding RNAs regulate tumor cell plasticity. Sci China Life Sci 56(10):886–890
44. Lu J, Gilbert DM (2007) Proliferation-dependent and cell cycle regulated transcription of mouse pericentric heterochromatin. J Cell Biol 179(3):411–421
45. Lu KH, Li W, Liu XH et al (2013) Long non-coding RNA MEG3 inhibits NSCLC cells proliferation and induces apoptosis by affecting p53 expression. BMC Cancer 13:461
46. Maison C, Bailly D, Roche D et al (2011) SUMOylation promotes de novo targeting of HP1alpha to pericentric heterochromatin. Nat Genet 43(3):220–227
47. Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15(1):R17–29
48. McCarthy N (2011) Tumour suppressors: silencing heterochromatin. Nat Rev Cancer 11(11):760
49. Menon DU, Coarfa C, Xiao W, Gunaratne PH, Meller VH (2014) SiRNAs from an X-linked satellite repeat promote X-chromosome recognition in Drosophila melanogaster. Proc Natl Acad Sci U S A 111(46):16460–16465
50. Murphy WJ, Larkin DM, Everts-van der Wind A et al (2005) Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309(5734):613–617
51. Narayan A, Ji W, Zhang XY et al (1998) Hypomethylation of pericentromeric DNA in breast adenocarcinomas. Int J Cancer 77(6):833–838
52. Paco A, Adega F, Mestrovic N, Plohl M, Chaves R (2014) Evolutionary story of a satellite DNA from Phodopus sungorus (Rodentia, Cricetidae). Genome Biol Evol 6(10):2944–2955
53. Plohl M, Luchetti A, Mestrovic N, Mantovani B (2008) Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 409(1-2):72–82
54. Plohl M, Mestrovic N, Mravinac B (2014) Centromere identity from the DNA point of view. Chromosoma 123(4):313–325
55. Probst AV, Okamoto I, Casanova M et al (2010) A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development. Dev Cell 19(4):625–638
56. Pruitt K, Zinn RL, Ohm JE et al (2006) Inhibition of SIRT1 reactivates silenced cancer genes without loss of promoter DNA hypermethylation. PLoS Genet 2(3):e40
57. Qu G, Dubeau L, Narayan A, Yu MC, Ehrlich M (1999a) Satellite DNA hypomethylation vs. overall genomic hypomethylation in ovarian epithelial tumors of different malignant potential. Mutat Res 423(1-2):91–101
58. Qu GZ, Grundy PE, Narayan A, Ehrlich M (1999b) Frequent hypomethylation in Wilms tumors of pericentromeric DNA in chromosomes 1 and 16. Cancer Genet Cytogenet 109(1):34–39
59. Quek XC, Thomson DW, Maag JL et al (2015) lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res 43(Database issue):D168–173
60. Quenet D, Dalal Y (2014) A long non-coding RNA is required for targeting centromeric protein A to the human centromere. Elife 3:e03254
61. Redis RS, Sieuwerts AM, Look MP et al (2013) CCAT2, a novel long non-coding RNA in breast cancer: expression study and clinical correlations. Oncotarget 4(10):1748–1762
62. Renault S, Rouleux-Bonnin F, Periquet G, Bigot Y (1999) Satellite DNA transcription in Diadromus pulchellus (Hymenoptera). Insect Biochem Mol Biol 29(2):103–111
63. Rosic S, Kohler F, Erhardt S (2014) Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division. J Cell Biol 207(3):335–349
64. Saito Y, Kanai Y, Sakamoto M et al (2001) Expression of mRNA for DNA methyltransferases and methyl-CpG-binding proteins and DNA methylation status on CpG islands and pericentromeric satellite regions during human hepatocarcinogenesis. Hepatology 33(3):561–568
65. Saksouk N, Simboeck E, Dejardin J (2015) Constitutive heterochromatin formation and transcription in mammals. Epigenetics Chromatin 8:3
66. Sana J, Faltejskova P, Svoboda M, Slaby O (2012) Novel classes of non-coding RNAs and cancer. J Transl Med 10:103
67. Santos S, Chaves R, Adega F, Bastos E, Guedes-Pinto H (2006) Amplification of the major satellite DNA family (FA-SAT) in a cat fibrosarcoma might be related to chromosomal instability. J Hered 97(2):114–118
68. Scott KC (2013) Transcription and ncRNAs: at the cent(rome)re of kinetochore assembly and maintenance. Chromosome Res 21(6-7):643–651
69. Shapiro JA, von Sternberg R (2005) Why repetitive DNA is essential to genome function. Biol Rev Camb Philos Soc 80(2):227–250
70. Shestakova EA, Mansuroglu Z, Mokrani H, Ghinea N, Bonnefoy E (2004) Transcription factor YY1 associates with pericentromeric gamma-satellite DNA in cycling but not in quiescent (G0) cells. Nucleic Acids Res 32(14):4390–4399
71. Spizzo R, Almeida MI, Colombatti A, Calin GA (2012) Long non-coding RNAs and cancer: a new frontier of translational research? Oncogene 31(43):4577–4587
72. Thanisch K, Schneider K, Morbitzer R et al (2014) Targeting and tracing of specific DNA sequences with dTALEs in living cells. Nucleic Acids Res 42(6):e38
73. Tilman G, Arnoult N, Lenglez S et al (2012) Cancer-linked satellite 2 DNA hypomethylation does not regulate Sat2 non-coding RNA expression and is initiated by heat shock pathway activation. Epigenetics 7(8):903–913
74. Ting DT, Lipson D, Paul S et al (2011) Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 331(6017):593–596
75. Trofimova I, Popova D, Vasilevskaya E, Krasikova A (2014) Non-coding RNA derived from a conservative subtelomeric tandem repeat in chicken and Japanese quail somatic cells. Mol Cytogenet 7(1):102
76. Tsoumani KT, Drosopoulou E, Mavragani-Tsipidou P, Mathiopoulos KD (2013) Molecular characterization and chromosomal distribution of a species-specific transcribed centromeric satellite repeat from the olive fruit fly, Bactrocera oleae. PLoS One 8(11):e79393
77. Ugarkovic D (2005) Functional elements residing within satellite DNAs. EMBO Rep 6(11):1035–1039
78. Usakin L, Abad J, Vagin VV et al (2007) Transcription of the 1.688 satellite DNA family is under the control of RNA interference machinery in Drosophila melanogaster ovaries. Genetics 176(2):1343–1349
79. Valgardsdottir R, Chiodi I, Giordano M et al (2008) Transcription of satellite III non-coding RNAs is a general stress response in human cells. Nucleic Acids Res 36(2):423–434
80. Vieira-da-Silva A, Louzada S, Adega F, Chaves R (2015) A high-resolution comparative chromosome Map of Cricetus Cricetus and Peromyscus eremicus reveals the involvement of constitutive heterochromatin in breakpoint regions. Cytogenet Genome Res 145(1):59–67
81. Vourc’h C, Biamonti G (2011) Transcription of satellite DNAs in mammals. Prog Mol Subcell Biol 51:95–118
82. Walton EL, Francastel C, Velasco G (2014) Dnmt3b prefers germ line genes and centromeric regions: lessons from the ICF syndrome and cancer and implications for diseases. Biology (Basel) 3(3):578–605
83. Widschwendter M, Jiang G, Woods C et al (2004) DNA hypomethylation and ovarian cancer biology. Cancer Res 64(13):4472–4480
84. Wong N, Lam WC, Lai PB et al (2001) Hypomethylation of chromosome 1 heterochromatin DNA correlates with q-arm copy gain in human hepatocellular carcinoma. Am J Pathol 159(2):465–471
85. Wong TN, Sosnick TR, Pan T (2007) Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci U S A 104(46):17995–18000
86. Xie C, Yuan J, Li H et al (2014) NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res 42(Database issue):D98–103
87. Zhu Q, Pao GM, Huynh AM et al (2011) BRCA1 tumour suppression occurs via heterochromatin-mediated silencing. Nature 477(7363):179–184