High-resolution analysis of four efficient yeast replication origins reveals new insights into the ORC and putative MCM binding elements

Nucleic Acids Research

Volumn 39, Issue 15, 2011, Pages 6523-6535

  Chang, Fu Jung ^a   May, Caitlin D ^a   Hoggard, Timothy ^b   Miller, Jeremy ^a   Fox, Catherine A ^b   Weinreich, Michael ^a  

^a VAN ANDEL RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MINICHROMOSOME MAINTENANCE PROTEIN; ORIGIN RECOGNITION COMPLEX; SILENT INFORMATION REGULATOR PROTEIN 2; HELICASE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CONTROLLED STUDY; DNA REPLICATION ORIGIN; FUNGAL GENOME; GENE SEQUENCE; MUTAGENESIS; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; BINDING SITE; CONSENSUS SEQUENCE; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

EUKARYOTA; SACCHAROMYCETALES;

BASE SEQUENCE; BINDING SITES; CONSENSUS SEQUENCE; DNA HELICASES; MOLECULAR SEQUENCE DATA; NUCLEOSOMES; ORIGIN RECOGNITION COMPLEX; REPLICATION ORIGIN; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ALIGNMENT;

EID: 80055087240     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr301     Document Type: Article

References (52)

1. Bell, S.P. (2002) The origin recognition complex: from simple origins to complex functions. Genes Dev., 16, 659-672. (Pubitemid 34274034)
2. DePamphilis, M.L. (2003) The 'ORC cycle': a novel pathway for regulating eukaryotic DNA replication. Gene, 310, 1-15.
3. Remus, D. and Diffley, J.F. (2009) Eukaryotic DNA replication control: lock and load, then fire. Curr. Opin. Cell Biol., 21, 771-777.
4. Broach, J.R., Li, Y.Y., Feldman, J., Jayaram, M., Abraham, J., Nasmyth, K.A. and Hicks, J.B. (1983) Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harbor Symp. Quant. Biol., 47, 1165-1173.
5. Marahrens, Y. and Stillman, B. (1992) A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science, 255, 817-823.
6. Palzkill, T.G., Oliver, S.G. and Newlon, C.S. (1986) DNA sequence analysis of ARS elements from chromosome III of Saccharomyces cerevisiae: identification of a new conserved sequence. Nucleic Acids Res., 14, 6247-6264.
7. Chang, F., Theis, J.F., Miller, J., Nieduszynski, C.A., Newlon, C.S. and Weinreich, M. (2008) Analysis of chromosome III replicators reveals an unusual structure for the ARS318 silencer origin and a conserved WTW sequence within the origin recognition complex binding site. Mol. Cell. Biol., 28, 5071-5081.
8. Rao, H., Marahrens, Y. and Stillman, B. (1994) Functional conservation of multiple elements in yeast chromosomal replicators. Mol. Cell. Biol., 14, 7643-7651. (Pubitemid 24326430)
9. Shirahige, K., Iwasaki, T., Rashid, M.B., Ogasawara, N. and Yoshikawa, H. (1993) Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae. Mol. Cell. Biol., 13, 5043-5056. (Pubitemid 23220408)
10. Theis, J.F. and Newlon, C.S. (1994) Domain B of ARS307 contains two functional elements and contributes to chromosomal replication origin function. Mol. Cell. Biol., 14, 7652-7659. (Pubitemid 24326431)
11. Newlon, C.S. and Theis, J.F. (1993) The structure and function of yeast ARS elements. Curr. Opin. Genet. Dev., 3, 752-758. (Pubitemid 23305048)
12. Rao, H. and Stillman, B. (1995) The origin recognition complex interacts with a bipartite DNA binding site within yeast replicators. Proc. Natl Acad. Sci. USA, 92, 2224-2228.
13. Rowley, A., Cocker, J.H., Harwood, J. and Diffley, J.F. (1995) Initiation complex assembly at budding yeast replication origins begins with the recognition of a bipartite sequence by limiting amounts of the initiator, ORC. EMBO J., 14, 2631-2641.
14. Theis, J.F. and Newlon, C.S. (1997) The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence. Proc. Natl Acad. Sci. USA, 94, 10786-10791. (Pubitemid 27430812)
15. Xu, W., Aparicio, J.G., Aparicio, O.M. and Tavare, S. (2006) Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics, 7, 276.
16. Nieduszynski, C.A., Knox, Y. and Donaldson, A.D. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev., 20, 1874-1879. (Pubitemid 44079324)
17. Chang, V.K., Donato, J.J., Chan, C.S. and Tye, B.K. (2004) Mcm1 promotes replication initiation by binding specific elements at replication origins. Mol. Cell. Biol., 24, 6514-6524. (Pubitemid 38891149)
18. Irlbacher, H., Franke, J., Manke, T., Vingron, M. and Ehrenhofer-Murray, A.E. (2005) Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression. Genes Dev., 19, 1811-1822. (Pubitemid 41126920)
19. Walker, S.S., Francesconi, S.C. and Eisenberg, S. (1990) A DNA replication enhancer in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 87, 4665-4669.
20. Wilmes, G.M. and Bell, S.P. (2002) The B2 element of the Saccharomyces cerevisiae ARS1 origin of replication requires specific sequences to facilitate pre-RC formation. Proc. Natl Acad. Sci. USA, 99, 101-106. (Pubitemid 34060323)
21. Zou, L. and Stillman, B. (2000) Assembly of a complex containing Cdc45p, replication protein A, and Mcm2p at replication origins controlled by S-phase cyclin-dependent kinases and Cdc7p-Dbf4p kinase. Mol. Cell. Biol., 20, 3086-3096. (Pubitemid 30215021)
22. Crampton, A., Chang, F., Pappas, D.L. Jr, Frisch, R.L. and Weinreich, M. (2008) An ARS element inhibits DNA replication through a SIR2-dependent mechanism. Mol. Cell, 30, 156-166. (Pubitemid 351626680)
23. Rashid, M.B., Shirahige, K., Ogasawara, N. and Yoshikawa, H. (1994) Anatomy of the stimulative sequences flanking the ARS consensus sequence of chromosome VI in Saccharomyces cerevisiae. Gene, 150, 213-220.
24. Thomas, B.J. and Rothstein, R. (1989) Elevated recombination rates in transcriptionally active DNA. Cell, 56, 619-630.
25. Pappas, D.L. Jr, Frisch, R. and Weinreich, M. (2004) The NAD(+)- dependent Sir2p histone deacetylase is a negative regulator of chromosomal DNA replication. Genes Dev., 18, 769-781. (Pubitemid 38480889)
26. Bell, S.P., Mitchell, J., Leber, J., Kobayashi, R. and Stillman, B. (1995) The multidomain structure of Orc1p reveals similarity to regulators of DNA replication and transcriptional silencing. Cell, 83, 563-568.
27. Bolon, Y.T. and Bielinsky, A.K. (2006) The spatial arrangement of ORC binding modules determines the functionality of replication origins in budding yeast. Nucleic Acids Res., 34, 5069-5080.
28. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. (Pubitemid 350162903)
29. Van Houten, J.V. and Newlon, C.S. (1990) Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Mol. Cell. Biol., 10, 3917-3925.
30. Bell, S.P. and Stillman, B. (1992) ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature, 357, 128-134.
31. Breier, A.M., Chatterji, S. and Cozzarelli, N.R. (2004) Prediction of Saccharomyces cerevisiae replication origins. Genome Biol., 5, R22.
32. Friedman, K.L., Brewer, B.J. and Fangman, W.L. (1997) Replication profile of Saccharomyces cerevisiae chromosome VI. Genes Cells, 2, 667-678. (Pubitemid 127688612)
33. Yamashita, M., Hori, Y., Shinomiya, T., Obuse, C., Tsurimoto, T., Yoshikawa, H. and Shirahige, K. (1997) The efficiency and timing of initiation of replication of multiple replicons of Saccharomyces cerevisiae chromosome VI. Genes Cells, 2, 655-665. (Pubitemid 127688611)
34. Diffley, J.F., Cocker, J.H., Dowell, S.J. and Rowley, A. (1994) Two steps in the assembly of complexes at yeast replication origins in vivo. Cell, 78, 303-316. (Pubitemid 24241097)
35. Albert, I., Mavrich, T.N., Tomsho, L.P., Qi, J., Zanton, S.J., Schuster, S.C. and Pugh, B.F. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature, 446, 572-576. (Pubitemid 46514724)
36. Eaton, M.L., Galani, K., Kang, S., Bell, S.P. and MacAlpine, D.M. (2010) Conserved nucleosome positioning defines replication origins. Genes Dev., 24, 748-753.
37. Field, Y., Kaplan, N., Fondufe-Mittendorf, Y., Moore, I.K., Sharon, E., Lubling, Y., Widom, J. and Segal, E. (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput. Biol., 4, e1000216.
38. Berbenetz, N.M., Nislow, C. and Brown, G.W. (2010) Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure. PLoS Genet., 6, e1001092.
39. Muller, P., Park, S., Shor, E., Huebert, D.J., Warren, C.L., Ansari, A.Z., Weinreich, M., Eaton, M.L., MacAlpine, D.M. and Fox, C.A. (2010) The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin. Genes Dev., 24, 1418-1433.
40. Lee, W., Tillo, D., Bray, N., Morse, R.H., Davis, R.W., Hughes, T.R. and Nislow, C. (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet., 39, 1235-1244. (Pubitemid 47482684)
41. Mavrich, T.N., Ioshikhes, I.P., Venters, B.J., Jiang, C., Tomsho, L.P., Qi, J., Schuster, S.C., Albert, I. and Pugh, B.F. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res., 18, 1073-1083. (Pubitemid 351931158)
42. Shivaswamy, S., Bhinge, A., Zhao, Y., Jones, S., Hirst, M. and Iyer, V.R. (2008) Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol., 6, e65.
43. Whitehouse, I., Rando, O.J., Delrow, J. and Tsukiyama, T. (2007) Chromatin remodelling at promoters suppresses antisense transcription. Nature, 450, 1031-1035. (Pubitemid 350273613)
44. Yuan, G.C., Liu, Y.J., Dion, M.F., Slack, M.D., Wu, L.F., Altschuler, S.J. and Rando, O.J. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science, 309, 626-630. (Pubitemid 41033649)
45. Jiang, C. and Pugh, B.F. (2009) A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol., 10, R109.
46. Lipford, J.R. and Bell, S.P. (2001) Nucleosomes positioned by ORC facilitate the initiation of DNA replication. Mol. Cell, 7, 21-30. (Pubitemid 32162896)
47. Poloumienko, A., Dershowitz, A., De, J. and Newlon, C.S. (2001) Completion of replication map of Saccharomyces cerevisiae chromosome III. Mol. Biol. Cell, 12, 3317-3327. (Pubitemid 33108467)
48. Speck, C., Chen, Z., Li, H. and Stillman, B. (2005) ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA. Nat. Struct. Mol. Biol., 12, 965-971.
49. Lee, D.G. and Bell, S.P. (1997) Architecture of the yeast origin recognition complex bound to origins of DNA replication. Mol. Cell. Biol., 17, 7159-7168. (Pubitemid 27505946)
50. Stevenson, J.B. and Gottschling, D.E. (1999) Telomeric chromatin modulates replication timing near chromosome ends. Genes Dev., 13, 146-151. (Pubitemid 29061944)
51. Cosgrove, A.J., Nieduszynski, C.A. and Donaldson, A.D. (2002) Ku complex controls the replication time of DNA in telomere regions. Genes Dev., 16, 2485-2490.
52. Huang, R.Y. and Kowalski, D. (1996) Multiple DNA elements in ARS305 determine replication origin activity in a yeast chromosome. Nucleic Acids Res., 24, 816-823. (Pubitemid 26076184)