The Effect of Replication Initiation on Gene Amplification in the rDNA and Its Relationship to Aging

Molecular Cell

Volumn 35, Issue 5, 2009, Pages 683-693

  Ganley, Austen R D ^a,b,c   Ide, Satoru ^a   Saka, Kimiko ^a   Kobayashi, Takehiko ^a,b  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^c MASSEY UNIVERSITY   (New Zealand)

Author keywords

DNA

Indexed keywords

EXTRACHROMOSOMAL DNA; RIBOSOME DNA;

AGING; ARTICLE; CONTROLLED STUDY; DNA REPLICATION; EPISOME; GENE ACTIVITY; GENE AMPLIFICATION; GENETIC STABILITY; GENOMIC INSTABILITY; LIFESPAN; NONHUMAN; YEAST;

AGING; CELL DIVISION; DNA REPLICATION; DNA, CIRCULAR; DNA, RIBOSOMAL; DNA-BINDING PROTEINS; GENE AMPLIFICATION; GENE EXPRESSION REGULATION, FUNGAL; GENOMIC INSTABILITY; KINETICS; MUTATION; PLASMIDS; RECOMBINATION, GENETIC; REPLICATION ORIGIN; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SISTER CHROMATID EXCHANGE;

EUKARYOTA;

EID: 69749092718     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2009.07.012     Document Type: Article

References (52)

1. Aguilaniu H., Gustafsson L., Rigoulet M., and Nyström T. Asymmetric inheritance of oxidatively damaged proteins during cytokinesis. Science 299 (2003) 1751-1753
2. Andersen J.S., Lam Y.W., Leung A.K.L., Ong S.-E., Lyon C.E., Lamond A.I., and Mann M. Nucleolar proteome dynamics. Nature 433 (2005) 77-83
3. Andersson D.I., Slechta E.S., and Roth J.R. Evidence that gene amplification underlies adaptive mutability of the bacterial lac operon. Science 282 (1998) 1133-1135
4. Bell S.P., and Stillman B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357 (1992) 128-134
5. Brewer B.J., and Fangman W.L. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51 (1987) 463-471
6. Brewer B.J., and Fangman W.L. Mapping replication origins in yeast chromosomes. Bioessays 13 (1991) 317-322
7. Burkhalter M.D., and Sogo J.M. rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replication. Mol. Cell 15 (2004) 409-421
8. Caburet S., Conti C., Schurra C., Lebofsky R., Edelstein S.J., and Bensimon A. Human ribosomal RNA gene arrays display a broad range of palindromic structures. Genome Res. 15 (2005) 1079-1085
9. Chindamporn A., Iwagichi S.-I., Nakagawa Y., Homma M., and Tanaka K. Clonal size-variation of rDNA cluster region on chromosome XII of Saccharomyces cerevisiae. J. Gen. Microbiol. 139 (1993) 1409-1415
10. Conti C., Herrick J., and Bensimon A. Unscheduled DNA replication origin activation at inserted HPV 18 sequences in a HPV-18/MYC amplicon. Genes Chromosomes Cancer 46 (2007) 724-734
11. Defossez P.A., Prusty R., Kaeberlein M., Lin S.J., Ferrigno P., Silver P.A., Keil R.L., and Guarente L. Elimination of replication fork block protein Fob1 extends the life span of yeast mother cells. Mol. Cell 3 (1999) 447-455
12. Dijkwel P.A., and Hamlin J.L. Initiation of DNA replication in the dihydrofolate reductase locus is confined to the early S period in CHO cells synchronized with the plant amino acid mimosine. Mol. Cell. Biol. 12 (1992) 3715-3722
13. Ellis N.A., Groden J., Ye T.Z., Straughen J., Lennon D.J., Ciocci S., Proytcheva M., and German J. The Bloom's syndrome gene product is homologous to RecQ helicases. Cell 83 (1995) 655-666
14. Falcón A.A., and Aris J.P. Plasmid accumulation reduced life span in Saccharomyces cerevisiae. J. Biol. Chem. 278 (2003) 41607-41617
15. Falcón A.A., Rios N., and Aris J.P. 2-micron plasmids do not reduce yeast life span. FEMS Microbiol. Lett. 250 (2005) 245-251
16. Fangman W.L., and Brewer B.J. Activation of replication origins within yeast chromosomes. Annu. Rev. Cell Biol. 7 (1991) 375-402
17. Gietz R.D., and Sugino A. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74 (1988) 527-534
18. Haber J.E., and Debatisse M. Gene amplification: yeast takes a turn. Cell 125 (2006) 1237-1240
19. Hawley R.S., and Marcus C.H. Recombinational controls of rDNA redundancy in Drosophila. Annu. Rev. Genet. 23 (1989) 87-120
20. Heo S.J., Tatebayashi K., Ohsugi I., Shimamoto A., Furuichi Y., and Ikeda H. Bloom's syndrome gene suppresses premature ageing caused by Sgs1 deficiency in yeast. Genes Cells 4 (1999) 619-625
21. Hoopes L.L., Budd M., Choe W., Weitao T., and Campbell J.L. Mutations in DNA replication genes reduce yeast life span. Mol. Cell. Biol. 22 (2002) 4136-4146
22. Ide S., Watanabe K., Watanabe H., Shirahige K., Kobayashi T., and Maki H. Abnormality in initiation program of DNA replication is monitored by the highly repetitive rRNA gene array on chromosome XII in budding yeast. Mol. Cell. Biol. 27 (2007) 568-578
23. Kaiser C., Michaelis S., and Mitchell A. Methods in yeast genetics (1994), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
24. Kaeberlein M., McVey M., and Guarente L. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev. 13 (1999) 2570-2580
25. Kennedy B.K., Austriaco Jr. N.R., and Guarente L. Daughter cells of Saccharomyces cerevisiae from old mothers display a reduced life span. J. Cell Biol. 127 (1994) 1985-1993
26. Kim S., Benguria A., Lai C.-Y., and Jazwinski S.M. Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae. Mol. Biol. Cell 10 (1999) 3125-3136
27. Kobayashi T. Strategies to maintain the stability of the ribosomal RNA gene repeats. Genes Genet. Syst. 81 (2006) 155-161
28. Kobayashi T. A new role of the rDNA and nucleolus in the nucleus-rDNA instability maintains genome integrity. Bioessays 30 (2008) 267-272
29. Kobayashi T., and Horiuchi T. A yeast gene product, Fob1 protein, required for both replication fork blocking and recombinational hotspot activities. Genes Cells 1 (1996) 465-474
30. Kobayashi T., and Ganley A.R.D. Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science 309 (2005) 1581-1584
31. Kobayashi T., Heck D.J., Nomura M., and Horiuchi T. Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev. 12 (1998) 3821-3830
32. Kobayashi T., Nomura M., and Horiuchi T. Identification of DNA cis elements essential for expansion of ribosomal DNA repeats in Saccharomyces cerevisiae. Mol. Cell. Biol. 21 (2001) 136-147
33. Kobayashi T., Horiuchi T., Tongaonkar P., Vu L., and Nomura M. SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast. Cell 117 (2004) 441-453
34. Lesur I., and Campbell J.L. The transcriptome of prematurely aging yeast cells is similar to that of telomerase-deficient cells. Mol. Biol. Cell 15 (2004) 1297-1312
35. Little C.D., Nau M.M., Carney D.N., Gazdar A.F., and Minna J.D. Amplification and expression of the c-myc oncogene in human lung cancer cell lines. Nature 306 (1983) 194-196
36. Marahrens Y., and Stillman B. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255 (1992) 817-823
37. Merker R.J., and Klein H.L. hpr1 affects ribosomal DNA recombination and cell life span in Saccharomyces cerevisiae. Mol. Cell. Biol. 22 (2002) 421-429
38. Miller C.A., and Kowalski D. cis-acting components in the replication origin from ribosomal DNA of Saccharomyces cerevisiae. Mol. Cell. Biol. 13 (1993) 5360-5369
39. Oakes M., Aris J.P., Brockenbrough J.S., Wai H., Vu L., and Nomura M. Mutational analysis of the structure and localization of the nucleolus in the yeast Saccharomyces cerevisiae. J. Cell Biol. 143 (1998) 23-34
40. Park P.U., Defossez P.A., and Guarente L. Effects of mutations in DNA repair genes on formation of ribosomal DNA circles and life span in Saccharomyces cerevisiae. Mol. Cell. Biol. 19 (1999) 3848-3856
41. Ritossa F.M. Unstable redundancy of genes of ribosomal RNA. Proc. Natl. Acad. Sci. USA 60 (1968) 509-516
42. Rustchenko E.P., Curran T.M., and Sherman F. Variations in the number of ribosomal DNA units in morphological mutants and normal strains of Candida albicans and in normal strains of Saccharomyces cerevisiae. J. Bacteriol. 175 (1993) 7189-7199
43. Schimke R.T. Gene amplification in cultured animal cells. Cell 37 (1984) 705-713
44. Shirahige K., Iwasaki T., Rashid M.B., Ogasawara N., and Yoshikawa H. Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae. Mol. Cell. Biol. 13 (1993) 5043-5056
45. Sinclair D.A., and Guarente L. Extrachromosomal rDNA circles-a cause of aging in yeast. Cell 91 (1997) 1033-1042
46. Stults D.M., Killen M.W., Pierce H.H., and Pierce A.J. Genomic architecture and inheritance of human ribosomal RNA gene clusters. Genome Res. 18 (2008) 13-18
47. Takeuchi Y., Horiuchi T., and Kobayashi T. Transcription-dependent recombination and the role of fork collision in yeast rDNA. Genes Dev. 17 (2003) 1497-1506
48. Tartof K.D. Unequal mitotic sister chromatin exchange as the mechanism of ribosomal RNA gene magnification. Proc. Natl. Acad. Sci. USA 71 (1974) 1272-1276
49. Vassilev L., and Johnson E.M. An initiation zone of chromosomal DNA replication located upstream of the c-myc gene in proliferating HeLa cells. Mol. Cell. Biol. 10 (1990) 4899-4904
50. Yu C.E., Oshima J., Fu Y.H., Wijsman E.M., Hisama F., Alisch R., Matthews S., Nakura J., Miki T., Ouais S., et al. Positional cloning of the Werner's syndrome gene. Science 272 (1996) 258-262
51. Wai H., Johzuka K., Vu L., Eliason K., Kobayashi T., Horiuchi T., and Nomura M. Yeast RNA polymerase I enhancer is dispensable for transcription of the chromosomal rRNA gene and cell growth, and its apparent transcription enhancement from ectopic promoters requires Fob1 protein. Mol. Cell. Biol. 21 (2001) 5541-5553
52. Weir B.A., Woo M.S., Getz G., Perner S., Ding L., Beroukhim R., Lin W.M., Province M.A., Kraja A., Johnson L.A., et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 450 (2007) 893-898