Nucleic Acids Research, 1993, Vol. 21, No. 3 555-560
© 1993
MOLECULAR BIOLOGY |
Ease of DNA unwinding is a conserved property of yeast replication origins
Molecular and Cellular Biology Department, Roswell Park Cancer lnstftute Buffalo, NY 14263, USA
*To whom correspondence should be addressed
Received October 16, 1992. Revised December 18, 1992. Accepted December 18, 1992.
Autonomously replicating sequence (ARS) elements function as plasmid replication origins. Our studies of the H4 ARS and ARS3O7 have established the requirement for a DNA unwinding element (DUE), a broad easily-unwound sequence 3' to the essential consensus that likely facilitates opening of the origin. in this report, we examine the intrinsic ease of unwinding a variety of ARS elements using (1) a single-strand-specific nuclease to probe for DNA unwinding in a negatively-supercoiled piasmid, and (2) a computer program that calculates DNA helical stability from the nucleotide sequence. ARS elements that are associated with replication origins on chromosome III are nuclease hypersensitive, and the helical stability minima correctly predict the location and hierarchy of the hypersensitive sites. All well-studied ARS elements in which the essential consensus sequence has been identified by mutational analysis contain a 100-bp region of low helical stability immediately 3' to the consensus, as do ARS elements created by mutation within the prokaryotic M13 vector. The level of helical stability is, in all cases, below that of ARS3O7 derivatives inactivated by mutations in the DUE. Our findings indicate that the ease of DNA unwinding at the broad region directly 3' to the ARS consensus is a conserved property of yeast replication origins.
+Present address: Biology Department, University of Virginia, Charlottesville VA 22903, USA
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Kemp, B. Bae, J. P. Yu, M. Ghosh, M. Leffak, and S. K. Nair Structure and Function of the c-myc DNA-unwinding Element-binding Protein DUE-B J. Biol. Chem., April 6, 2007; 282(14): 10441 - 10448. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. A. Nieduszynski, S.-i. Hiraga, P. Ak, C. J. Benham, and A. D. Donaldson OriDB: a DNA replication origin database Nucleic Acids Res., January 12, 2007; 35(suppl_1): D40 - D46. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. A. Nieduszynski, Y. Knox, and A. D. Donaldson Genome-wide identification of replication origins in yeast by comparative genomics Genes & Dev., July 15, 2006; 20(14): 1874 - 1879. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Ghosh, M. Kemp, G. Liu, M. Ritzi, A. Schepers, and M. Leffak Differential Binding of Replication Proteins across the Human c-myc Replicator. Mol. Cell. Biol., July 1, 2006; 26(14): 5270 - 5283. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. M. Rommens, O. Bougri, H. Yan, J. M. Humara, J. Owen, K. Swords, and J. Ye Plant-Derived Transfer DNAs Plant Physiology, November 1, 2005; 139(3): 1338 - 1349. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Casper, M. G. Kemp, M. Ghosh, G. M. Randall, A. Vaillant, and M. Leffak The c-myc DNA-unwinding Element-binding Protein Modulates the Assembly of DNA Replication Complexes in Vitro J. Biol. Chem., April 1, 2005; 280(13): 13071 - 13083. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Boucher, F. McNicoll, M. Laverdiere, A. Rochette, M.-N. Chou, and B. Papadopoulou The ribosomal RNA gene promoter and adjacent cis-acting DNA sequences govern plasmid DNA partitioning and stable inheritance in the parasitic protozoan Leishmania Nucleic Acids Res., May 25, 2004; 32(9): 2925 - 2936. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Huang and D. Kowalski WEB-THERMODYN: sequence analysis software for profiling DNA helical stability Nucleic Acids Res., July 1, 2003; 31(13): 3819 - 3821. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Tamaru and E. U. Selker Synthesis of Signals for De Novo DNA Methylation in Neurospora crassa Mol. Cell. Biol., April 1, 2003; 23(7): 2379 - 2394. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Liu, M. Malott, and M. Leffak Multiple Functional Elements Comprise a Mammalian Chromosomal Replicator Mol. Cell. Biol., March 1, 2003; 23(5): 1832 - 1842. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Christensen and P. Tattersall Parvovirus Initiator Protein NS1 and RPA Coordinate Replication Fork Progression in a Reconstituted DNA Replication System J. Virol., June 5, 2002; 76(13): 6518 - 6531. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. M. Wilmes and S. P. Bell The B2 element of the Saccharomyces cerevisiaeARS1 origin of replication requires specific sequences to facilitate pre-RC formation PNAS, December 21, 2001; (2001) 12578499. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. M. Fullerton, J. Bond, J. A. Schneider, B. Hamilton, R. M. Harding, A. J. Boyce, and J. B. Clegg Polymorphism and Divergence in the {beta}-Globin Replication Origin Initiation Region Mol. Biol. Evol., January 1, 2000; 17(1): 179 - 188. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. A. Miller, R. M. Umek, and D. Kowalski The inefficient replication origin from yeast ribosomal DNA is naturally impaired in the ARS consensus sequence and in DNA unwinding Nucleic Acids Res., October 1, 1999; 27(19): 3921 - 3930. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Vujcic, C. A. Miller, and D. Kowalski Activation of Silent Replication Origins at Autonomously Replicating Sequence Elements near the HML Locus in Budding Yeast Mol. Cell. Biol., September 1, 1999; 19(9): 6098 - 6109. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. van Brabant, W. L. Fangman, and B. J. Brewer Active Role of a Human Genomic Insert in Replication of a Yeast Artificial Chromosome Mol. Cell. Biol., June 1, 1999; 19(6): 4231 - 4240. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Vernis, M. Chasles, P. Pasero, A. Lepingle, C. Gaillardin, and P. Fournier Short DNA Fragments without Sequence Similarity Are Initiation Sites for Replication in the Chromosome of the Yeast Yarrowia lipolytica Mol. Biol. Cell, March 1, 1999; 10(3): 757 - 769. [Abstract] [Full Text]
|
|
|
|
|
|
S. T. Hurst and D. H. Rivier Identification of a Compound Origin of Replication at the HMR-E Locus in Saccharomyces cerevisiae J. Biol. Chem., February 12, 1999; 274(7): 4155 - 4159. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-M. Kim and J. A. Huberman Multiple Orientation-Dependent, Synergistically Interacting, Similar Domains in the Ribosomal DNA Replication Origin of the Fission Yeast, Schizosaccharomyces pombe Mol. Cell. Biol., December 1, 1998; 18(12): 7294 - 7303. [Abstract] [Full Text]
|
|
|
|
|
|
K L Friedman, J D Diller, B M Ferguson, S V Nyland, B J Brewer, and W L Fangman Multiple determinants controlling activation of yeast replication origins late in S phase. Genes & Dev., July 1, 1996; 10(13): 1595 - 1607. [Abstract] [PDF]
|
|
|
|
|
|
M. Gencheva, B. Anachkova, and G. Russev Mapping the Sites of Initiation of DNA Replication in Rat and Human rRNA Genes J. Biol. Chem., February 2, 1996; 271(5): 2608 - 2614. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Charron, J.-P. Julien, and V. Bibor-Hardy Neuron Specificity of the Neurofilament Light Promoter in Transgenic Mice Requires the Presence of DNA Unwinding Elements J. Biol. Chem., October 27, 1995; 270(43): 25739 - 25745. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. M. Wilmes and S. P. Bell The B2 element of the Saccharomyces cerevisiaeARS1 origin of replication requires specific sequences to facilitate pre-RC formation PNAS, January 8, 2002; 99(1): 101 - 106. [Abstract] [Full Text] [PDF]
|
|