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Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM. The reference genome sequence of Saccharomyces cerevisiae: then and now. G3 (BETHESDA, MD.) 2014; 4:389-98. [PMID: 24374639 PMCID: PMC3962479 DOI: 10.1534/g3.113.008995] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/21/2013] [Indexed: 11/18/2022]
Abstract
The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called "S288C 2010," was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science.
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Affiliation(s)
- Stacia R. Engel
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Fred S. Dietrich
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710
| | - Dianna G. Fisk
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Gail Binkley
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Rama Balakrishnan
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Maria C. Costanzo
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Selina S. Dwight
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Benjamin C. Hitz
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Robert S. Nash
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Shuai Weng
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Edith D. Wong
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Paul Lloyd
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Marek S. Skrzypek
- Department of Genetics, Stanford University, Stanford, California 94305
| | | | - Matt Simison
- Department of Genetics, Stanford University, Stanford, California 94305
| | - J. Michael Cherry
- Department of Genetics, Stanford University, Stanford, California 94305
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Di Rienzi SC, Lindstrom KC, Mann T, Noble WS, Raghuraman MK, Brewer BJ. Maintaining replication origins in the face of genomic change. Genome Res 2012; 22:1940-52. [PMID: 22665441 PMCID: PMC3460189 DOI: 10.1101/gr.138248.112] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Origins of replication present a paradox to evolutionary biologists. As a collection, they are absolutely essential genomic features, but individually are highly redundant and nonessential. It is therefore difficult to predict to what extent and in what regard origins are conserved over evolutionary time. Here, through a comparative genomic analysis of replication origins and chromosomal replication patterns in the budding yeasts Saccharomyces cerevisiae and Lachancea waltii, we assess to what extent replication origins survived genomic change produced from 150 million years of evolution. We find that L. waltii origins exhibit a core consensus sequence and nucleosome occupancy pattern highly similar to those of S. cerevisiae origins. We further observe that the overall progression of chromosomal replication is similar between L. waltii and S. cerevisiae. Nevertheless, few origins show evidence of being conserved in location between the two species. Among the conserved origins are those surrounding centromeres and adjacent to histone genes, suggesting that proximity to an origin may be important for their regulation. We conclude that, over evolutionary time, origins maintain sequence, structure, and regulation, but are continually being created and destroyed, with the result that their locations are generally not conserved.
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Affiliation(s)
- Sara C Di Rienzi
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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Structure, replication efficiency and fragility of yeast ARS elements. Res Microbiol 2012; 163:243-53. [DOI: 10.1016/j.resmic.2012.03.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 01/21/2012] [Indexed: 11/16/2022]
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Nieduszynski CA, Liti G. From sequence to function: Insights from natural variation in budding yeasts. Biochim Biophys Acta Gen Subj 2011; 1810:959-66. [PMID: 21320572 PMCID: PMC3271348 DOI: 10.1016/j.bbagen.2011.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 02/03/2011] [Accepted: 02/08/2011] [Indexed: 12/18/2022]
Abstract
Background Natural variation offers a powerful approach for assigning function to DNA sequence—a pressing challenge in the age of high throughput sequencing technologies. Scope of Review Here we review comparative genomic approaches that are bridging the sequence–function and genotype–phenotype gaps. Reverse genomic approaches aim to analyse sequence to assign function, whereas forward genomic approaches start from a phenotype and aim to identify the underlying genotype responsible. Major Conclusions Comparative genomic approaches, pioneered in budding yeasts, have resulted in dramatic improvements in our understanding of the function of both genes and regulatory sequences. Analogous studies in other systems, including humans, demonstrate the ubiquity of comparative genomic approaches. Recently, forward genomic approaches, exploiting natural variation within yeast populations, have started to offer powerful insights into how genotype influences phenotype and even the ability to predict phenotypes. General Significance Comparative genomic experiments are defining the fundamental rules that govern complex traits in natural populations from yeast to humans. This article is part of a Special Issue entitled Systems Biology of Microorganisms.
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Di Rienzi SC, Collingwood D, Raghuraman MK, Brewer BJ. Fragile genomic sites are associated with origins of replication. Genome Biol Evol 2009; 1:350-63. [PMID: 20333204 PMCID: PMC2817429 DOI: 10.1093/gbe/evp034] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2009] [Indexed: 01/03/2023] Open
Abstract
Genome rearrangements are mediators of evolution and disease. Such rearrangements are frequently bounded by transfer RNAs (tRNAs), transposable elements, and other repeated elements, suggesting a functional role for these elements in creating or repairing breakpoints. Though not well explored, there is evidence that origins of replication also colocalize with breakpoints. To investigate a potential correlation between breakpoints and origins, we analyzed evolutionary breakpoints defined between Saccharomyces cerevisiae and Kluyveromyces waltii and S. cerevisiae and a hypothetical ancestor of both yeasts, as well as breakpoints reported in the experimental literature. We find that origins correlate strongly with both evolutionary breakpoints and those described in the literature. Specifically, we find that origins firing earlier in S phase are more strongly correlated with breakpoints than are later-firing origins. Despite origins being located in genomic regions also bearing tRNAs and Ty elements, the correlation we observe between origins and breakpoints appears to be independent of these genomic features. This study lays the groundwork for understanding the mechanisms by which origins of replication may impact genome architecture and disease.
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Dershowitz A, Snyder M, Sbia M, Skurnick JH, Ong LY, Newlon CS. Linear derivatives of Saccharomyces cerevisiae chromosome III can be maintained in the absence of autonomously replicating sequence elements. Mol Cell Biol 2007; 27:4652-63. [PMID: 17452442 PMCID: PMC1951491 DOI: 10.1128/mcb.01246-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Replication origins in Saccharomyces cerevisiae are spaced at intervals of approximately 40 kb. However, both measurements of replication fork rate and studies of hypomorphic alleles of genes encoding replication initiation proteins suggest the question of whether replication origins are more closely spaced than should be required. We approached this question by systematically deleting replicators from chromosome III. The first significant increase in loss rate detected for the 315-kb full-length chromosome occurred only after all five efficient chromosomal replicators in the left two-thirds of the chromosome (ARS305, ARS306, ARS307, ARS309, and ARS310) had been deleted. The removal of the inefficient replicator ARS308 from this originless region caused little or no additional increase in loss rate. Chromosome fragmentations that removed the normally inactive replicators on the left end of the chromosome or the replicators distal to ARS310 on the right arm showed that both groups of replicators contribute significantly to the maintenance of the originless chromosome. Surprisingly, a 142-kb derivative of chromosome III, lacking all sequences that function as autonomously replicating sequence elements in plasmids, replicated and segregated properly 97% of the time. Both the replication initiation protein ORC and telomeres or a linear topology were required for the maintenance of chromosome fragments lacking replicators.
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Affiliation(s)
- Ann Dershowitz
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, ICPH, 225 Warren St., Newark, NJ 07103, USA
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Abstract
The endmost chromosome I ORF is silenced by a natural telomere position effect. YAR073W/IMD1 was found to be transcribed at much higher levels in sir3 mutants and when its adjacent telomere was removed from it. These results suggest that telomeres play a role in silencing actual genes.
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Affiliation(s)
- Arnold B Barton
- Department of Microbiology and Molecular Genetics, International Center for Public Health, UMDNJ-New Jersey Medical School, Newark, New Jersey 07103, USA
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Barton AB, Su Y, Lamb J, Barber D, Kaback DB. A Function for Subtelomeric DNA in Saccharomyces cerevisiae. Genetics 2003; 165:929-34. [PMID: 14573499 PMCID: PMC1462788 DOI: 10.1093/genetics/165.2.929] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The subtelomeric DNA sequences from chromosome I of Saccharomyces cerevisiae are shown to be inherently poor substrates for meiotic recombination. On the basis of these results and prior observations that crossovers near telomeres do not promote efficient meiosis I segregation, we suggest that subtelomeric sequences evolved to prevent recombination from occurring where it cannot promote efficient segregation.
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Affiliation(s)
- Arnold B Barton
- Department of Microbiology and Molecular Genetics, International Center for Public Health, UMDNJ-New Jersey Medical School, Graduate School of Biomedical Sciences, Newark, New Jersey 07103, USA
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Theis JF, Newlon CS. Two compound replication origins in Saccharomyces cerevisiae contain redundant origin recognition complex binding sites. Mol Cell Biol 2001; 21:2790-801. [PMID: 11283258 PMCID: PMC86909 DOI: 10.1128/mcb.21.8.2790-2801.2001] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While many of the proteins involved in the initiation of DNA replication are conserved between yeasts and metazoans, the structure of the replication origins themselves has appeared to be different. As typified by ARS1, replication origins in Saccharomyces cerevisiae are <150 bp long and have a simple modular structure, consisting of a single binding site for the origin recognition complex, the replication initiator protein, and one or more accessory sequences. DNA replication initiates from a discrete site. While the important sequences are currently less well defined, metazoan origins appear to be different. These origins are large and appear to be composed of multiple, redundant elements, and replication initiates throughout zones as large as 55 kb. In this report, we characterize two S. cerevisiae replication origins, ARS101 and ARS310, which differ from the paradigm. These origins contain multiple, redundant binding sites for the origin recognition complex. Each binding site must be altered to abolish origin function, while the alteration of a single binding site is sufficient to inactivate ARS1. This redundant structure may be similar to that seen in metazoan origins.
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Affiliation(s)
- J F Theis
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, New Jersey 07103, USA
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Theis JF, Yang C, Schaefer CB, Newlon CS. DNA sequence and functional analysis of homologous ARS elements of Saccharomyces cerevisiae and S. carlsbergensis. Genetics 1999; 152:943-52. [PMID: 10388814 PMCID: PMC1460646 DOI: 10.1093/genetics/152.3.943] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
ARS elements of Saccharomyces cerevisiae are the cis-acting sequences required for the initiation of chromosomal DNA replication. Comparisons of the DNA sequences of unrelated ARS elements from different regions of the genome have revealed no significant DNA sequence conservation. We have compared the sequences of seven pairs of homologous ARS elements from two Saccharomyces species, S. cerevisiae and S. carlsbergensis. In all but one case, the ARS308-ARS308(carl) pair, significant blocks of homology were detected. In the cases of ARS305, ARS307, and ARS309, previously identified functional elements were found to be conserved in their S. carlsbergensis homologs. Mutation of the conserved sequences in the S. carlsbergensis ARS elements revealed that the homologous sequences are required for function. These observations suggested that the sequences important for ARS function would be conserved in other ARS elements. Sequence comparisons aided in the identification of the essential matches to the ARS consensus sequence (ACS) of ARS304, ARS306, and ARS310(carl), though not of ARS310.
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Affiliation(s)
- J F Theis
- Department of Microbiology and Molecular Genetics, New Jersey Medical School and Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
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