A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres

Chromosoma

Volumn 118, Issue 1, 2009, Pages 113-125

  Carone, Dawn M ^a   Longo, Mark S ^a   Ferreri, Gianni C ^a   Hall, Laura ^a   Harris, Melissa ^a   Shook, Nicole ^a   Bulazel, Kira V ^a   Carone, Benjamin R ^a   Obergfell, Craig ^a   O'Neill, Michael J ^a   O'Neill, Rachel J ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

ARTICLE; CELLULAR DISTRIBUTION; CENTROMERE; CHROMOSOME SATELLITE; CONTROLLED STUDY; EUKARYOTE EVOLUTION; GENE LOCATION; GENETIC CONSERVATION; NONHUMAN; NUCLEOTIDE SEQUENCE; RETROVIRUS; RNA ANALYSIS; RNA PROCESSING; VIRUS IDENTIFICATION;

ANIMALS; CELLS, CULTURED; CENTROMERE; CHROMOSOMES; CHROMOSOMES, ARTIFICIAL, BACTERIAL; FIBROBLASTS; IN SITU HYBRIDIZATION, FLUORESCENCE; MAMMALS; MICE; RETROELEMENTS; RETROVIRIDAE; RNA, SATELLITE; TRANSCRIPTION, GENETIC;

EUKARYOTA; MACROPUS EUGENII; MAMMALIA; SACCHAROMYCETALES; VERTEBRATA;

EID: 58349099600     PISSN: 00095915     EISSN: 14320886     Source Type: Journal    
DOI: 10.1007/s00412-008-0181-5     Document Type: Article

References (53)

1. Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ (2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316:744-747
2. Blower MD, Sullivan BA, Karpen GH (2002) Conserved organization of centromeric chromatin in flies and humans. Developmental Cell 2:319-330
3. 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 103:8709-8714
4. Boyd KE, Farnham PJ (1999) Coexamination of site-specific transcription factor binding and promoter activity in living cells. Mol Cell Biol 19:8393-8399
5. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128:1089-1103
6. Bulazel K, Metcalfe C, Ferreri GC, Yu J, Eldridge MD, O'Neill RJ (2006) Cytogenetic and molecular evaluation of centromere-associated DNA sequences from a marsupial (Macropodidae: Macropus rufogriseus) X chromosome. Genetics 172:1129-1137
7. Bulazel K, Ferreri GC, Eldridge MD, O'Neill RJ (2007) Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages. Genome Biol 8:R170
8. Cheng Z, Dong F, Langdon T, Ouyang S, Buell CR, Gu M, Blattner FR, Jiang J (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691-1704
9. Choo K (1997) The centromere. Oxford University Press, Oxford
10. Dalby B, Cates S, Harris A, Ohki EC, Tilkins ML, Price PJ, Ciccarone VC (2004) Advanced transfection with Lipofectamine 2000 reagent: Primary neurons, siRNA, and high-throughput applications. Methods 33:95-103
11. Diaz MO, Barsacchi-Pilone G, Mahon KA, Gall JG (1981) Transcripts from both strands of a satellite DNA occur on lampbrush chromosome loops of the newt Notophthalmus. Cell 24:649-659
12. Dunn CA, Romanish MT, Gutierrez LE, van de Lagemaat LN, Mager DL (2006) Transcription of two human genes from a bidirectional endogenous retrovirus promoter. Gene 366:335-342
13. Earnshaw WC, Rothfield N (1985) Identification of a family of human centromere proteins using autoimmune sera from patients with scleroderma. Chromosoma 91:313-321
14. Ferreri GC, Marzelli M, Rens W, O'Neill RJ (2004) A centromere-specific retroviral element associated with breaks of synteny in macropodine marsupials. Cytogenet Genome Res 107:115-118
15. Ferreri GC, Liscinsky DM, Mack JA, Eldridge MD, O'Neill RJ (2005) Retention of latent centromeres in the Mammalian genome. J Hered 96:217-224
16. Fukagawa T, Nogami M, Yoshikawa M, Ikeno M, Okazaki T, Takami Y, Nakayama T, Oshimura M (2004) Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nat Cell Biol 6:784-791
17. Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293-296
18. Hartig JV, Tomari Y, Forstemann K (2007) piRNAs - the ancient hunters of genome invaders. Genes Dev 21:1707-1713
19. Hayman DL (1977) Chromosome number-constancy and variation. In: Gilmore D (ed) The biology of marsupials. Macmillan, London
20. Hayman DL (1990) Marsupial cytogenetics. In: Cooper DW (ed) Mammals from pouches and eggs: Genetics, breeding and evolution of marsupials and monotremes. CSIRO, Melbourne
21. Hudson DF, Fowler KJ, Earle E, Saffery R, Kalitsis P, Trowell H, Hill J, Wreford NG, de Kretser DM, Cancilla MR, Howman E, Hii L, Cutts SM, Irvine DV, Choo KH (1998) Centromere protein B null mice are mitotically and meiotically normal but have lower body and testis weights. J Cell Biol 141:309-319
22. Jiang J, Birchler JA, Parrott WA, Dawe RK (2003) A molecular view of plant centromeres. Trends Plant Sci 8:570-575
23. Josse T, Teysset L, Todeschini A-L, Sidor CM, Anxolabehere D, Ronsseray S (2007) Telomeric trans-silencing: An epigenetic repression combining RNA silencing and heterochromatin formation. PLOS Genet 3:e158
24. Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, Livingston DM, Rajewsky K (2005) Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19:489-501
25. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316:1484-1488
26. Kim VN (2006) Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev 20:1993-1997
27. Kuznetsova I, Podgornaya O, Ferguson-Smith MA (2006) High-resolution organization of mouse centromeric and pericentromeric DNA. Cytogenet Genome Res 112:248-255
28. Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP, Kingston RE (2006) Characterization of the piRNA complex from rat testes. Science 313:363-367
29. Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002) MicroRNA maturation: stepwise processing and subcellular localization. Embo J 21:4663-4670
30. Lee HR, Neumann P, Macas J, Jiang J (2006) Transcription and evolutionary dynamics of the centromeric satellite repeat CentO in rice. Mol Biol Evol 23:2505-2520
31. Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC (1988) Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Human Genet 80:224-234
32. May BP, Lippman ZB, Fang Y, Spector DL, Martienssen RA (2005) Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet 1:e79
33. Murchison EP, Partridge JF, Tam OH, Cheloufi S, Hannon GJ (2005) Characterization of dicer-deficient murine embryonic stem cells. Proc Natl Acad Sci U S A 102:12135-12140
34. Nagaki K, Cheng Z, Ouyang S, Talbert PB, Kim M, Jones KM, Henikoff S, Buell CR, Jiang J (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36:138-145
35. Neumann P, Yan H, Jiang J (2007) The centromeric retrotransposons of rice are transcribed and differentially processed by RNA interference. Genetics 176:749-761
36. Ohzeki J, Nakano M, Okada T, Masumoto H (2002) CENP-B box is required for de novo centromere chromatin assembly on human alphoid DNA. J Cell Biol 159:765-775
37. Okada T, Ohzeki J, Nakano M, Yoda K, Brinkley WR, Larionov V, Masumoto H (2007) CENP-B controls centromere formation depending on the chromatin context. Cell 131:1287-1300
38. O'Neill RJ, O'Neill MJ, Graves JA (1998) Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 393:68-72
39. Pal-Bhadra M, Leibovitch BA, Gandhi SG, Rao M, Bhadra U, Birchler JA, Elgin SC (2004) Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303:669-672
40. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45
41. Reinhart BJ, Bartel DP (2002) Small RNAs correspond to centromere heterochromatic repeats. Science 297:1831
42. Rice JC, Briggs SD, Ueberheide B, Barber CM, Shabanowitz J, Hunt DF, Shinkai Y, Allis CD (2003) Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol Cell 12:1591-1598
43. Sambrook J, Fritsch EF, Maniatis T (2001) Molecular cloning. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
44. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF (2001) Genomic and genetic definition of a functional human centromere. Science 294:109-115
45. Topp CN, Zhong CX, Dawe RK (2004) Centromere-encoded RNAs are integral components of the maize kinetochore. Proc Natl Acad Sci U S A 101:15986-15991
46. Ugarkovic D (2005) Functional elements residing within satellite DNAs. EMBO Rep 6:1035-1039
47. Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, Zamore PD (2006) A distinct small RNA pathway silences selfish genetic elements in the germ line. Science 313:320-324
48. Valgardsdottir R, Chiodi I, Giordano M, Cobianchi F, Riva S, Biamonti G (2005) Structural and functional characterization of noncoding repetitive RNAs transcribed in stressed human cells. Mol Biol Cell 16:2597-2604
49. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303:672-676
50. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833-1837
51. Volpe T, Schramke V, Hamilton GL, White SA, Teng G, Martienssen RA, Allshire RC (2003) RNA interference is required for normal centromere function in fission yeast. Chromosome Res 11:137-146
52. White SA, Allshire RC (2004) Loss of dicer fowls up centromeres. Nat Cell Biol 6:696-697
53. Wong LH, Brettingham-Moore KH, Chan L, Quach JM, Anderson MA, Northrop EL, Hannan R, Saffery R, Shaw ML, Williams E, Choo KH (2007) Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere. Genome Res 17:1146-1160