Publications

1994
Lin, JJ, and VA Zakian. “Isolation and characterization of two Saccharomyces cerevisiae genes that encode proteins that bind to (TG1-3)n single strand telomeric DNA in vitro.”. Nucleic Acids Res 22.23 (1994): , 22, 23, 4906-13. Print.Abstract
By screening lambda gt11 libraries with a radiolabeled (TG1-3)n oligonucleotide, two Saccharomyces cerevisiae genes were identified that encode polypeptides that recognize the single-stranded telomeric repeat sequence (TG1-3)n. The first gene, NSR1, a previously identified gene, encodes a protein involved in ribosomal RNA maturation and possibly in transport of proteins into the nucleus. The second gene, GBP2 (G-strand Binding Protein), is an anonymous open reading frame from chromosome III. These two genes contain RNA recognition motifs (RRMs) that are found in proteins that interact with RNA. Both Nsr1p and Gbp2p bind specifically to yeast single strand (TG1-3)n DNA in vitro. To test whether these two proteins associate with telomeres in vivo, strains were constructed in which one or both of these genes were either disrupted or overexpressed. None of these alterations affected telomere length or telomere position effect. The potential role of these two (TG1-3)n binding proteins is discussed.
Schulz, VP, and VA Zakian. “The saccharomyces PIF1 DNA helicase inhibits telomere elongation and de novo telomere formation.”. Cell 76.1 (1994): , 76, 1, 145-55. Print.Abstract
A screen to detect yeast mutants that frequently lost expression of subtelomeric genes identified two mutations in PIF1, a gene known to encode a 5' to 3' DNA helicase. The loss of expression of subtelomeric genes in pif1 cells was due to deletion of the subtelomeric regions of the chromosomes and the generation of new telomeres at proximal sites. In pif1 mutants, de novo telomere formation usually occurred at sites with very little homology to telomeric DNA. De novo telomere formation after HO-induced chromosome breakage also occurred at elevated frequencies in pif1 cells. Moreover, mutations in PIF1 caused all telomeres to lengthen. These results suggest that the PIF1 helicase is an inhibitor of both de novo telomere formation and telomere elongation.
Sandell, LL, DE Gottschling, and VA Zakian. “Transcription of a yeast telomere alleviates telomere position effect without affecting chromosome stability.”. Proc Natl Acad Sci U S A 91.25 (1994): , 91, 25, 12061-5. Print.Abstract
Telomeres are required for the stable maintenance of chromosomes in the yeast Saccharomyces cerevisiae. Telomeres also repress the expression of genes in their vicinity, a phenomenon known as telomere position effect. In an attempt to construct a conditional telomere, an inducible promoter was introduced adjacent to a single telomere of a chromosome such that transcription could be induced toward the end of the chromosome. Transcription toward two other essential chromosomal elements, centromeres and origins of replication, eliminates their function. In contrast, transcription toward a telomere did not affect the stability function of the telomere as measured by the loss rate of the transcribed chromosome. Transcription proceeded through the entire length of the telomeric tract and caused a modest reduction in the average length of the transcribed telomere. Transcription of the telomere substantially reduced the frequency of cells in which an adjacent URA3 gene was subject to telomere position effect. These results indicate that telomere position effect can be alleviated without compromising chromosome stability.
1993
Sandell, LL, and VA Zakian. “Loss of a yeast telomere: arrest, recovery, and chromosome loss.”. Cell 75.4 (1993): , 75, 4, 729-39. Print.Abstract
Yeast strains were constructed in which a single telomere could be eliminated from the end of a dispensable chromosome. In wild-type cells, elimination of a telomere caused a RAD9-mediated cell cycle arrest, indicating that telomeres help cells to distinguish intact chromosomes from damaged DNA. However, many cells recovered from the arrest without repairing the damaged chromosome, replicating and segregating it for as many as ten cell divisions prior to its eventual loss. Telomere elimination caused a dramatic increase in loss of the chromosome in all strains examined, demonstrating that yeast telomeres are also essential for maintaining chromosome stability. Thus, in spite of checkpoint and DNA damage repair systems, many chromosomes that lose a telomere are themselves destined for loss.
Wellinger, RJ, AJ Wolf, and VA Zakian. “Origin activation and formation of single-strand TG1-3 tails occur sequentially in late S phase on a yeast linear plasmid.”. Mol Cell Biol 13.7 (1993): , 13, 7, 4057-65. Print.Abstract
In order to understand the mechanisms leading to the complete duplication of linear eukaryotic chromosomes, the temporal order of the events involved in replication of a 7.5-kb Saccharomyces cerevisiae linear plasmid called YLpFAT10 was determined. Two-dimensional agarose gel electrophoresis was used to map the position of the replication origin and the direction of replication fork movement through the plasmid. Replication began near the center of YLpFAT10 at the site in the 2 microns sequences that corresponds to the 2 microns origin of DNA replication. Replication forks proceeded bidirectionally from the origin to the ends of YLpFAT10. Thus, yeast telomeres do not themselves act as origins of DNA replication. The time of origin utilization on YLpFAT10 and on circular 2 microns DNA in the same cells was determined both by two-dimensional gel electrophoresis and by density transfer experiments. As expected, 2 microns DNA replicated in early S phase. However, replication of YLpFAT10 occurred in late S phase. Thus, the time of activation of the 2 microns origin depended upon its physical context. Density transfer experiments established that the acquisition of telomeric TG1-3 single-strand tails, a predicted intermediate in telomere replication, occurred immediately after the replication forks approached the ends of YLpFAT10. Thus, telomere replication may be the very last step in S phase.
Runge, KW, and VA Zakian. “Saccharomyces cerevisiae linear chromosome stability (lcs) mutants increase the loss rate of artificial and natural linear chromosomes.”. Chromosoma 102.3 (1993): , 102, 3, 207-17. Print.Abstract
We isolated mutants of Saccharomyces cerevisiae that lose a 100 kb linear yeast artificial chromosome (YAC) at elevated rates. Mutations in two of these LCS (linear chromosome stability) genes had little or no effect on the loss rate of a circular YAC that had the same centromere and origin of replication as present on the linear YAC. Moreover, mutations in these LCS genes also increased the loss rate of an authentic linear yeast chromosome, chromosome III, but had only small effects on the loss rate of a circular derivative of chromosome III. As these mutants preferentially destabilize linear chromosomes, they may affect chromosome stability through interactions at telomeres. Telomeres are thought to be essential for the protection and complete replication of chromosome ends. The cytological properties of telomeres suggest that these structures may play additional roles in chromosome function. The lengths of the terminal C1-3A repeats at the ends of yeast chromosomes were unaltered in the linear preferential lcs mutants, suggesting that these mutants do not affect the replication or protection of telomeric DNA. Thus, the linear-preferential lcs mutants may identify a role for telomeres in chromosome stability that is distinct from their function in the replication and protection of chromosomal termini.
Wellinger, RJ, AJ Wolf, and VA Zakian. “Saccharomyces telomeres acquire single-strand TG1-3 tails late in S phase.”. Cell 72.1 (1993): , 72, 1, 51-60. Print.Abstract
Saccharomyces telomeres consist of approximately 300 bp of C1-3A/TG1-3 DNA. Nondenaturing Southern hybridization, capable of detecting approximately 60 to approximately 300 bases of TG1-3 DNA, revealed that yeast telomeres acquired and lost TG1-3 tails, the predicted intermediate in telomere replication, in a cell cycle-dependent manner. TG1-3 tails were also detected on the ends of a linear plasmid isolated from late S phase cells. In addition, a nonlinear form of this plasmid was detected: this structure migrated in two-dimensional agarose gels like a nicked circle of the same size as the linear plasmid, but had considerably more single-stranded character than a conventional nicked circle. The evidence indicates that these circles were formed by telomere-telomere interactions involving the TG1-3 tails. These data provide evidence for a cell cycle-dependent change in telomere structure and demonstrate that TG1-3 tails, generated during replication of a linear plasmid in vivo, are capable of mediating telomere-telomere interactions.
Wellinger, RJ, AJ Wolf, and VA Zakian. “Structural and temporal analysis of telomere replication in yeast.”. Cold Spring Harb Symp Quant Biol 58 (1993): , 58, 725-32. Print.
1992
Wellinger, RJ, AJ Wolf, and VA Zakian. “Use of non-denaturing Southern hybridization and two dimensional agarose gels to detect putative intermediates in telomere replication in Saccharomyces cerevisiae.”. Chromosoma 102.1 Suppl (1992): , 102, 1 Suppl, S150-6. Print.Abstract
Telomeres are required for the complete duplication of the ends of linear chromosomes. Saccharomyces telomeres bear approximately 350 bps of C1-3A/TG1-3 sequences. Previous work using non-denaturing Southern blotting has demonstrated the cell cycle controlled appearance of single stranded TG1-3 tails on chromosomal and plasmid telomeres (Wellinger et al. submitted). Furthermore it was shown that short linear plasmids carrying an origin of replication derived from 2 microns DNA can circularize at the time of telomere replication (Wellinger et al. submitted). Here we demonstrate that those loci previously shown to acquire single stranded tails are indeed telomeres and that single stranded TG1-3 cannot be observed in non-telomeric C1-3A/TG1-3-tracts. Moreover, we demonstrate that the formation of circular DNA by short linear plasmids is not restricted to plasmids containing a 2 microns origin of replication but can also be detected for plasmids containing ARS1.
Wright, JH, DE Gottschling, and VA Zakian. “Saccharomyces telomeres assume a non-nucleosomal chromatin structure.”. Genes Dev 62 (1992): , 6, 2, 197-210. Print.Abstract
The chromatin structures of the telomeric and subtelomeric regions on chromosomal DNA molecules in Saccharomyces cerevisiae were analyzed using micrococcal nuclease and DNAse I. The subtelomeric repeats X and Y' were assembled in nucleosomes. However, the terminal tracts of C1-3A repeats were protein protected in a particle larger than a nucleosome herein called a telosome. The proximal boundary of the telosome was a DNase I hypersensitive site. This boundary between the telosome and adjacent nucleosomes was completely accessible to Escherichia coli dam methylase when this enzyme was expressed in yeast, whereas a site 250 bp internal to the telomeric repeats was relatively inaccessible. Telosomes could be cleaved from chromosome ends with nuclease and solubilized as protein-DNA complexes. Immunoprecipitation of chromosomal telosomes with antiserum to the RAP1 protein indicated that RAP1 was one component of isolated telosomes. Thus, the termini of chromosomal DNA molecules in yeast are assembled in a non-nucleosomal structure encompassing the entire terminal C1-3A tract. This structure is separated from adjacent nucleosomes by a region of DNA that is highly accessible to enzymes.
Sandell, LL, and VA Zakian. “Telomeric position effect in yeast.”. Trends Cell Biol 21 (1992): , 2, 1, 10-4. Print.Abstract
Telomeres are the physical ends of chromosomes. In yeast, when a gene is placed near a telomere, its transcription is repressed. Genes under the influence of this telomeric position effects switch between a repressed state and a transcriptionally active state, each of which is stable for many cell generations. Telomeric position effect may provide a model system for the study of heritable gene regulation in other, more complex organisms.
1991
Runge, KW, RJ Wellinger, and VA Zakian. “Effects of excess centromeres and excess telomeres on chromosome loss rates.”. Mol Cell Biol 11.6 (1991): , 11, 6, 2919-28. Print.Abstract
The linear chromosomes of eukaryotes contain specialized structures to ensure their faithful replication and segregation to daughter cells. Two of these structures, centromeres and telomeres, are limited, respectively, to one and two copies per chromosome. It is possible that the proteins that interact with centromere and telomere DNA sequences are present in limiting amounts and could be competed away from the chromosomal copies of these elements by additional copies introduced on plasmids. We have introduced excess centromeres and telomeres into Saccharomyces cerevisiae and quantitated their effects on the rates of loss of chromosome III and chromosome VII by fluctuation analysis. We show that (i) 600 new telomeres have no effect on chromosome loss; (ii) an average of 25 extra centromere DNA sequences increase the rate of chromosome III loss from 0.4 x 10(-4) events per cell division to 1.3 x 10(-3) events per cell division; (iii) centromere DNA (CEN) sequences on circular vectors destabilize chromosomes more effectively than do CEN sequences on 15-kb linear vectors, and transcribed CEN sequences have no effect on chromosome stability. We discuss the different effects of extra centromere and telomere DNA sequences on chromosome stability in terms of how the cell recognizes these two chromosomal structures.
1990
Zakian, VA, K Runge, and SS Wang. “How does the end begin? Formation and maintenance of telomeres in ciliates and yeast.”. Trends Genet 61 (1990): , 6, 1, 12-6. Print.Abstract
Current models of telomere formation and replication involve either telomerase, a novel ribonucleoprotein, or recombination between the ends of DNA molecules. However, present models will have to be modified to explain recent data on telomere formation in yeast. An understanding of the mechanisms of telomere maintenance in yeast may reveal how other organisms with heterogeneous telomeric repeats replicate their chromosomal termini.
Gottschling, DE, et al.Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription.”. Cell 63.4 (1990): , 63, 4, 751-62. Print.Abstract
S. cerevisiae chromosomes end with the telomeric repeat (TG1-3)n. When any of four Pol II genes was placed immediately adjacent to the telomeric repeats, expression of the gene was reversibly repressed as demonstrated by phenotype and mRNA analyses. For example, cells bearing a telomere-linked copy of ADE2 produced predominantly red colonies (a phenotype characteristic of ade2- cells) containing white sectors (characteristic of ADE2+ cells). Repression was due to proximity to the telomere itself since an 81 bp tract of (TG1-3)n positioned downstream of URA3 when URA3 was approximately 20 kb from the end of chromosome VII did not alter expression of the gene. However, this internal tract of (TG1-3)n could spontaneously become telomeric, in which case expression of the URA3 gene was repressed. These data demonstrate that yeast telomeres exert a position effect on the transcription of nearby genes, an effect that is under epigenetic control.
Runge, KW, and VA Zakian. “Properties of the transcriptional enhancer in Saccharomyces cerevisiae telomeres.”. Nucleic Acids Res 18.7 (1990): , 18, 7, 1783-7. Print.Abstract
Saccharomyces cerevisiae chromosomes end with the sequence C2-3A(CA)1-4, commonly abbreviated as C1-3A. These sequences can function as upstream activators of transcription (UAS's) when placed in front of a CYC1-lacZ fusion gene. When C1-3A sequences are placed between the GAL1,10 UAS and the CYC1-lacZ fusion, the C1-3A UAS still functions and the amount of beta-galactosidase produced in cells grown on glucose is as much or more than that for cells grown on either glycerol medium, or cells grown on glucose medium containing a plasmid with just the C1-3A UAS. These data indicate that the UAS is immune from glucose repression from the upstream GAL1,10 UAS. Because C1-3A sequences are bound in vitro by the transcription factor RAP1, the UAS activity of yeast telomere sequences was compared with that of a similar UAS from the tightly regulated ribosomal protein gene RP39A, which also contains a RAP1 binding site. While transcription from the ribosomal protein gene UAS was responsive to cell density, the amount of transcription from the C1-3A UAS was nearly the same at all cell densities tested. These data show that the transcriptional activation by C1-3A sequences is not regulated by cell density.
Conrad, MN, et al.RAP1 protein interacts with yeast telomeres in vivo: overproduction alters telomere structure and decreases chromosome stability.”. Cell 63.4 (1990): , 63, 4, 739-50. Print.Abstract
The protein encoded by the RAP1 gene of S. cerevisiae binds in vitro to a consensus sequence occurring at a number of sites in the yeast genome, including the repeated sequence C2-3A(CA)1-6 found at yeast telomeres. We present two lines of evidence for the in vivo binding of RAP1 protein at telomeres: first, RAP1 is present in telomeric chromatin and second, alterations in the level of RAP1 protein affect telomere length. The length changes seen with under- and overexpression of RAP1 are consistent with the interpretation that RAP1 binding to telomeres protects them from degradation. Unexpectedly, overproduction of the RAP1 protein was also shown to decrease greatly chromosome stability, suggesting that RAP1 mediates interactions that have a more global effect on chromosome behavior than simply protecting telomeres from degradation. Such interactions may involve telomere associations both with other telomeres and/or with structural elements of the nucleus.
Wang, SS, and VA Zakian. “Sequencing of Saccharomyces telomeres cloned using T4 DNA polymerase reveals two domains.”. Mol Cell Biol 10.8 (1990): , 10, 8, 4415-9. Print.Abstract
By using T4 DNA polymerase rather than S1 or Bal31 nuclease to clone yeast telomeres, very little telomeric DNA is lost. These clones were used to determine the DNA sequence of virtually the entire telomeric tract. Our results demonstrated that a slightly modified version, C2-3A(CA)1-6, of the consensus derived from sequence analysis of more-internal regions (J. Shampay, J. W. Szostak, and E. H. Blackburn, Nature [London] 310:154-157, 1984) extends to the very end of the chromosome. The sequence analysis also suggests that yeast telomeres consist of two domains: the proximal 120 to 150 base pairs, which appear to be protected from processes such as recombination, degradation, and elongation, and the distal portion of the telomere, which is more susceptible to these events.
Wang, SS, and VA Zakian. “Telomere-telomere recombination provides an express pathway for telomere acquisition.”. Nature 345.6274 (1990): , 345, 6274, 456-8. Web.Abstract
DNA termini from Tetrahymena and Oxytricha, which bear C4A2 and C4A4 repeats respectively, can support telomere formation in Saccharomyces cerevisiae by serving as substrates for the addition of yeast telomeric C1-3A repeats. Previously, we showed that linear plasmids with 108 base pairs of C4A4 DNA (YLp108CA) efficiently acquired telomeres, whereas plasmids containing 28-64 base pairs of C4A4 DNA also promoted telomere formation, but with reduced efficiency. Although many of the C4A4 termini on these plasmids underwent recombination with a C4A2 terminus, the mechanism of telomere-telomere recombination was not established. We now report the sequence of the C4A4 ends from the linear plasmids. The results provide strong evidence for a novel recombination process involving a gene conversion event that requires little homology, occurs at or near the boundary of telomeric and nontelomeric DNA, and resembles the recombination process involved in bacteriophage T4 DNA replication.
1989
Wang, SS, AF Pluta, and VA Zakian. “DNA sequence analysis of newly formed telomeres in yeast.”. Prog Clin Biol Res 318 (1989): , 318, 81-9. Print.Abstract
A plasmid can be maintained in linear form in baker's yeast if it bears telomeric sequences at each end. Linear plasmids bearing cloned telomeric C4A4 repeats at one end (test end) and a natural DNA terminus with approximately 300 bps of C4A2 repeats at the other or control end were introduced by transformation into yeast. Test-end termini of 28 to 112 bps supported telomere formation. During telomere formation, C4A2 repeats were often transferred to test-end termini. To determine in greater detail the fate of test-end sequences on these plasmids after propagation in yeast, test-end telomeres were subcloned into E. coli and sequenced. DNA sequencing established a number of points about the molecular events involved in telomere formation in yeast. The results suggest that there are at least two mechanisms for telomere formation in yeast. One is mediated by a recombination event that requires neither a long stretch of homology nor the RAD52 gene product. The other mechanism is by addition of C1-3A repeats to the termini of linear DNA molecules. The telomeric sequence required to support C1-3A addition need not be at the very end of a molecule for telomere formation.
Runge, KW, and VA Zakian. “Introduction of extra telomeric DNA sequences into Saccharomyces cerevisiae results in telomere elongation.”. Mol Cell Biol 94 (1989): , 9, 4, 1488-97. Print.Abstract
The termini of Saccharomyces cerevisiae chromosomes consist of tracts of C1-3A (one to three cytosine and one adenine residue) sequences of approximately 450 base pairs in length. To gain insights into trans-acting factors at telomeres, high-copy-number linear and circular plasmids containing tracts of C1-3A sequences were introduced into S. cerevisiae. We devised a novel system to distinguish by color colonies that maintained the vector at 1 to 5, 20 to 50, and 100 to 400 copies per cell and used it to change the amount of telomeric DNA sequences per cell. An increase in the number of C1-3A sequences caused an increase in the length of telomeric C1-3A repeats that was proportional to plasmid copy number. Our data suggest that telomere growth is inhibited by a limiting factor(s) that specifically recognizes C1-3A sequences and that this factor can be effectively competed for by long tracts of C1-3A sequences at telomeres or on circular plasmids. Telomeres without this factor are exposed to processes that serve to lengthen chromosome ends.
Wellinger, RJ, and VA Zakian. “Lack of positional requirements for autonomously replicating sequence elements on artificial yeast chromosomes.”. Proc Natl Acad Sci U S A 86.3 (1989): , 86, 3, 973-7. Print.Abstract
In the yeast Saccharomyces cerevisiae, origins of replication (autonomously replicating sequences; ARSs), centromeres, and telomeres have been isolated and characterized. The identification of these structures allows the construction of artificial chromosomes in which the architecture of eukaryotic chromosomes may be studied. A common feature of most, and possibly all, natural yeast chromosomes is that they have an ARS within 2 kilobases of their physical ends. To study the effects of such telomeric ARSs on chromosome maintenance, we introduced artificial chromosomes of approximately 15 and 60 kilobases into yeast cells and analyzed the requirements for telomeric ARSs and the effects of ARS-free chromosomal arms on the stability of these molecules. We find that terminal blocks of telomeric repeats are sufficient to be recognized as telomeres. Moreover, artificial chromosomes containing telomere-associated Y' sequences and telomeric ARSs were no more stable during both mitosis and meiosis than artificial chromosomes lacking terminal ARSs, indicating that yeast-specific blocks of telomeric sequences are the only cis-acting requirement for a functional telomere during both mitotic growth and meiosis. The results also show that there is no requirement for an origin of replication on each arm of the artificial chromosomes, indicating that a replication fork may efficiently move through a functional centromere region.
Pluta, AF, and VA Zakian. “Recombination occurs during telomere formation in yeast.”. Nature 337.6206 (1989): , 337, 6206, 429-33. Web.Abstract
Short stretches of cloned telomeric sequences are necessary and sufficient for telomere formation in yeast as long as the sequences are present in the same orientation as they are found in vivo. During telomere formation, DNA termini usually undergo RAD52-independent recombination with other DNA termini as would be predicted by models of recombination-mediated telomere replication.
Zakian, VA. “Structure and function of telomeres.”. Annu Rev Genet 23 (1989): , 23, 579-604. Web.
Sweeney, R, and VA Zakian. “Extrachromosomal elements cause a reduced division potential in nib 1 strains of Saccharomyces cerevisiae.”. Genetics 122.4 (1989): , 122, 4, 749-57. Print.Abstract
The nib 1 allele of yeast confers a sensitivity to an endogenous plasmid, 2 mu DNA, in that nib 1 strains bearing 2 mu DNA (cir+) exhibit a reduction in division potential. In the present study, the reduction in division potential characteristic of nib 1 cir+ strains is shown to be dependent on the simultaneous presence of both the A and the D open reading frames of 2 mu DNA as well as on the presence of an unidentified extrachromosomal element other than 2 mu DNA. Furthermore, in nib 1 strains, an uncharacterized extrachromosomal element can cause a less severe reduction of division potential in the absence of intact 2 mu DNA. Thus, the nib 1 allele may confer a generalized sensitivity to extrachromosomal elements.
Zakian, VA, and AF Pluta. “Telomere formation in yeast.”. Nature 338.6215 (1989): , 338, 6215, 468. Web.
1988
Zakian, VA, and HM Blanton. “Distribution of telomere-associated sequences on natural chromosomes in Saccharomyces cerevisiae.”. Mol Cell Biol 85 (1988): , 8, 5, 2257-60. Print.Abstract
Pulsed-field gel electrophoresis was used to examine the distribution of telomere-associated sequences on individual chromosomes in four strains of Saccharomyces cerevisiae. The pattern of X and Y' distribution was different for each strain. At least one chromosome in each strain lacked Y', and in some strains, chromosome I, the smallest yeast chromosome, lacked detectable amounts of both X and Y'.
Conrad, MN, and VA Zakian. “Plasmid associations with residual nuclear structures in Saccharomyces cerevisiae.”. Curr Genet 13.4 (1988): , 13, 4, 291-7. Print.Abstract
Acentric yeast plasmids are mitotically unstable, apparently because they cannot freely diffuse after replicating and therefore are not included in the daughter nucleus. This behavior could result if plasmids remain attached to structural elements of the nucleus after replicating. Since DNA replication is believed to take place on the nuclear matrix, we tested whether there was a correlation between the mitotic stability of a given plasmid and the extent to which it was found associated with residual nuclear structures. Residual nuclei were prepared from yeast nuclei by extraction with either high salt, 2 M NaCl, or low salt, 10 mM lithium diiodosalicylate (LIS). Hybridization analysis was used to estimate the fraction of plasmid molecules remaining after nuclei were extracted. We examined the extent of matrix association of three ARS1 plasmids, Trp1-RI circle (1.45 kb), YRp7 (5.7 kb) and p lambda BAT (45.1 kb) with mitotic loss rates ranging from 3-25%. In addition we examined the matrix binding of the endogenous 2 micron plasmid and the 2 micron-derived YEp13 which is relatively stable in the presence of 2 micron and less stable in cir degree strains. Among the ARS1 plasmids we observed a negative correlation between stability and matrix association, consistent with models in which binding to the nuclear matrix prevents passive segregation of ARS1 plasmid molecules. No such correlation was observed among the 2 micron plasmids. Among all plasmids examined there is a positive correlation between size and matrix association.
1987
Zakian, VA. “Ciliates: the molecular biology of ciliated protozoa.”. Science 237.4812 (1987): , 237, 4812, 306. Web.
1986
Zakian, VA, HM Blanton, and L Wetzel. “Distribution of telomere-associated sequences in yeast.”. Basic Life Sci 40 (1986): , 40, 493-8. Print.Abstract
Two middle repetitive DNA sequences called X and Y' are found near the telomeres of many chromosomes in Saccharomyces cerevisiae. Orthogonal field gel electrophoresis (OFAGE) was used to examine the distribution of X and Y' on different yeast chromosomes. Although the distribution of X and Y' varies among different laboratory strains of yeast, most yeast chromosomes in four different strains carry both X and Y'. However, at least one chromosome in each strain lacks the Y' element. This result indicates that Y' is not essential for replication or segregation of at least some yeast chromosomes.
Zakian, VA, et al.Size threshold for Saccharomyces cerevisiae chromosomes: generation of telocentric chromosomes from an unstable minichromosome.”. Mol Cell Biol 63 (1986): , 6, 3, 925-32. Print.Abstract
A 9-kilobase pair CEN4 linear minichromosome constructed in vitro transformed Saccharomyces cerevisiae with high frequency but duplicated or segregated inefficiently in most cells. Stable transformants were only produced by events which fundamentally altered the structure of the minichromosome: elimination of telomeres, alteration of the centromere, or an increase of fivefold or greater in its size. Half of the stable transformants arose via homologous recombination between an intact chromosome IV and the CEN4 minichromosome. This event generated a new chromosome from each arm of chromosome IV. The other "arm" of each new chromosome was identical to one "arm" of the unstable minichromosome. Unlike natural yeast chromosomes, these new chromosomes were telocentric: their centromeres were either 3.9 or 5.4 kilobases from one end of the chromosome. The mitotic stability of the telocentric chromosome derived from the right arm of chromosome IV was determined by a visual assay and found to be comparable to that of natural yeast chromosomes. Both new chromosomes duplicated, paired, and segregated properly in meiosis. Moreover, their structure, as deduced from mobilities in orthogonal field gels, did not change with continued mitotic growth or after passage through meiosis, indicating that they did not give rise to isochromosomes or suffer large deletions or additions. Thus, in S. cerevisiae the close spacing of centromeres and telomeres on a DNA molecule of chromosomal size does not markedly alter the efficiency with which it is maintained. Taken together these data suggest that there is a size threshold below which stable propagation of linear chromosomes is no longer possible.
Gottschling, DE, and VA Zakian. “Telomere proteins: specific recognition and protection of the natural termini of Oxytricha macronuclear DNA.”. Cell 47.2 (1986): , 47, 2, 195-205. Print.Abstract
The macronuclear DNA in the ciliated protozoan O. nova consists of integral of 10(7) gene-sized DNA molecules, all of which terminate with 20 bp of C4A4 repeats followed by a 3' (G4T4)2 single-stranded tail. Two immunologically distinct proteins of 55 and 26 kd, which are tenaciously, but noncovalently associated with Oxytricha macronuclear DNA termini, have been purified. These proteins protect DNA termini from degradation by the exonuclease Bal31. They also facilitate retention of natural and synthetic telomeric DNAs onto nitrocellulose. The Oxytricha proteins are not simply C4A4-binding proteins. Rather, their efficient binding requires both the 3' single-stranded (G4T4)2 tail and the adjacent duplex region. Thus, these proteins require both the sequence and the structure of natural DNA termini for efficient binding. As such they represent the first described example of telomeric-specific proteins.
1985
Zakian, VA, HM Blanton, and GM Dani. “Formation and stability of linear plasmids in a recombination deficient strain of yeast.”. Curr Genet 96 (1985): , 9, 6, 441-5. Print.Abstract
Natural termini from macronuclear DNA of the ciliated protozoans Tetrahymena thermophila and Oxytricha fallax can support telomere formation yeast. However, plasmids carrying these ciliate termini are modified by the addition of DNA which hybridizes to the synthetic oligonucleotide poly [d(C-A]), a sequence which also hybridizes to terminal restriction fragments from yeast chromosomes but not to Tetrahymena or Oxytricha macronuclear DNAs. Thus, in yeast, the creation of new telomeres on ciliate termini involves the acquisition of yeast-specific terminal sequences presumably by either recombination or non-templated DNA synthesis. The RAD52 gene is required for the majority of yeast mitotic and meiotic recombination events. Moreover, the absence of an active RAD52 gene product results in high rates of chromosome loss. Here we demonstrate that terminal restriction fragments from Tetrahymena macronuclear ribosomal DNA (rDNA) support the formation of modified telomeres in a yeast strain carrying a defect in the RAD52 gene. Moreover, linear plasmids bearing these modified ciliate termini are stably propagated in rad52- cells.
Zakian, VA. “Nuclear structure. Taken with a grain of salt.”. Nature 314.6008 (1985): , 314, 6008, 223-4. Print.
1984
Zakian, VA. “Architecture of interphase nuclei.”. Nature 308.5958 (1984): , 308, 5958, 406. Print.
Pluta, AF, et al.Elaboration of telomeres in yeast: recognition and modification of termini from Oxytricha macronuclear DNA.”. Proc Natl Acad Sci U S A 81.5 (1984): , 81, 5, 1475-9. Print.Abstract
The termini of macronuclear DNA molecules from the protozoan Oxytricha fallax share a common sequence and structure, both of which differ markedly from those deduced for yeast telomeres. Despite these differences, terminal restriction fragments from O. fallax macronuclear DNA can support telomere formation in yeasts. Two linear plasmids (LYX-1 and LYX-2) constructed by ligating BamHI-digested total Oxytricha macronuclear DNA to a yeast vector were analyzed. One end of LYX-1 and both ends of LYX-2 are derived from the Oxytricha DNA that encodes rRNA (rDNA) whereas the other end of LYX-1 is from an Oxytricha fragment other than rDNA. After propagation in yeast, both ends of LYX-1 and LYX-2 retain the C4A4 repeat characteristic of the O. fallax terminal sequence. In addition, both ends of both plasmids acquire 300-1000 base pairs of DNA containing the sequence (C-A)n, a sequence found near the termini of yeast chromosomes. Thus, at least two different Oxytricha termini display distinctive properties in yeast cells in that linear plasmids containing them are not degraded nor are they integrated into chromosomal DNA. These Oxytricha termini may act directly as telomeres in yeast; alternatively, the Oxytricha DNA may serve as a signal that results in the elaboration of a yeast telomere on the ciliate DNA.
1983
Zakian, VA. “Control of chromosome behaviour in yeast.”. Nature 305.5932 (1983): , 305, 5932, 275. Print.
Roth, GE, et al.Isolation and characterization of sequences from mouse chromosomal DNA with ARS function in yeasts.”. Mol Cell Biol 311 (1983): , 3, 11, 1898-908. Print.Abstract
Fragments of chromosomal DNA from a variety of eucaryotes can act as ARSs (autonomously replicating sequence) in yeasts. ARSs enable plasmids to be maintained in extrachromosomal form, presumably because they function as initiation sites for DNA replication. We isolated eight different sequences from mouse chromosomal DNA which function as ARSs in Saccharomyces cerevisiae (bakers' yeast). Although the replication efficiency of the different mouse ARSs in yeasts appears to vary widely, about one-half of them functions as well as the yeast chromosomal sequence ARS1. Moreover, five of the ARSs also promote self replication of plasmids in Schizosaccharomyces pombe (fission yeast). Each of the ARSs was cloned into plasmids suitable for transformation of mouse tissue culture cells. Plasmids were introduced into thymidine kinase (TK)-deficient mouse L cells by the calcium phosphate precipitation technique in the absence of carrier DNA. In some experiments, the ARS plasmid contained the herpes simplex virus type 1 TK gene; in other experiments (cotransformations), the TK gene was carried on a separate plasmid used in the same transformation. In contrast to their behavior in yeasts, none of the ARS plasmids displayed a significant increase in transformation frequency in mouse cells compared with control plasmids. Moreover, only 1 of over 100 cell lines contained the original plasmid in extrachromosomal form. The majority of cell lines produced by transformation with an ARS TK plasmid contained multiple copies of plasmid integrated into chromosomal DNA. In most cases, results with plasmids used in cotransformations were similar to those for plasmids carrying TK. However, cell lines produced by cotransformations with plasmids containing any one of three of the ARSs (m24, m25, or m26) often contained extrachromosomal DNAs.
Dani, GM, and VA Zakian. “Mitotic and meiotic stability of linear plasmids in yeast.”. Proc Natl Acad Sci U S A 80.11 (1983): , 80, 11, 3406-10. Print.Abstract
Circular recombinant DNA plasmids that contain autonomously replicating sequences (ARSs) are maintained in extrachromosomal form in transformed yeast cells. However, these plasmids are unstable, being rapidly lost from cells growing without selection. Although the stability of such a plasmid can be increased by the presence of yeast centromere DNA (CEN), even CEN plasmids are lost at a high rate compared to a bona fide yeast chromosome. Natural yeast chromosomes are linear molecules; therefore, we have asked if linearization can improve the stability of recombinant DNA plasmids. Linear plasmids with and without yeast CENs were constructed in vitro by using termini from the extrachromosomal ribosomal DNA (rDNA) of the ciliated protozoan Tetrahymena thermophila as "telomeres." These linear plasmids transformed yeast at high frequency and were maintained as linear extrachromosomal molecules during mitotic growth. Moreover, linear plasmids containing CENs were also transmitted through meiosis: these plasmids segregate predominantly 2+:2- at the first meiotic division, indicating that Tetrahymena rDNA termini can provide telomere function during yeast meiosis. Linear plasmids without CENs were about as stable in mitosis as the comparable circular plasmid. Thus, the Tetrahymena rDNA termini have no marked positive or negative effect on the mitotic stability of ARS plasmids. However, linear plasmids containing CENs are three to four times less stable in mitotic cells than circular CEN plasmids. This decrease in stability is not due to a functional change in the centromere itself; rather, linearization of a CEN plasmid has a direct detrimental effect on its mitotic stability. These results may reflect the existence of spatial constraints on the positions of centromeres and telomeres, constraints which must be satisfied to achieve stable segregation of chromosomes during mitosis.
1982
Zakian, VA, and JF Scott. “Construction, replication, and chromatin structure of TRP1 RI circle, a multiple-copy synthetic plasmid derived from Saccharomyces cerevisiae chromosomal DNA.”. Mol Cell Biol 23 (1982): , 2, 3, 221-32. Print.Abstract
Transformation studies with Saccharomyces cerevisiae (bakers' yeast) have identified DNA sequences which permit extrachromosomal maintenance of recombinant DNA plasmids in transformed cells. It has been hypothesized that such sequences (called ARS for autonomously replicating sequence) serve as initiation sites for DNA replication in recombinant DNA plasmids and that they represent the normal sites for initiation of replication in yeast chromosomal DNA. We have constructed a novel plasmid called TRP1 R1 Circle which consists solely of 1,453 base pairs of yeast chromosomal DNA. TRP1 RI Circle contains both the TRP1 gene and a sequence called ARS1. This plasmid is found in 100 to 200 copies per cell and is relatively stable during both mitotic and meiotic cell cycles. Replication of TRP1 RI Circle requires the products of the same genes (CDC28, CDC4, CDC7, and CDC8) required for replication of chromosomaL DNA. Like chromosomal DNA, its replication does not occur in cells arrested in the B1 phase of the cell cycle by incubation with the yeast pheromone alpha-factor. In addition, TRP1 RI Circle DNA is organized into nucleosomes whose size and spacing are indistinguishable from that of bulk yeast chromatin. These results indicate that TRP1 RI Circle has the replicative and structural properties expected for an origin of replication from yeast chromosomal DNA. Thus, this plasmid is a suitable model for further studies of yeast DNA replication in both cells and cell-free extracts.
Zakian, VA, and DM Kupfer. “Replication and segregation of an unstable plasmid in yeast.”. Plasmid 81 (1982): , 8, 1, 15-28. Print.
1981
Zakian, VA. “Origin of replication from Xenopus laevis mitochondrial DNA promotes high-frequency transformation of yeast.”. Proc Natl Acad Sci U S A 78.5 (1981): , 78, 5, 3128-32. Print.Abstract
A specific fraction of chromosomal DNA from both yeast and a wide variety of other eukaryotes, but not from Escherichia coli, promotes high-frequency transformation in yeast. The plasmids containing these sequences are maintained as extra-chromosomal molecules in transformed cells. These results suggest that similar or identical sequences are used for the initiation of DNA replication in eukaryotes. To test this hypothesis, several foreign eukaryotic DNAs implicated directly or indirectly in the initiation of DNA replication have been examined for their ability to promote autonomous, extrachromosomal replication in yeast. Simian virus 40 DNA, amplified Xenopus laevis ribosomal DNA, X. laevis 5S ribosomal DNA, X. laevis mtDNA, and five different members of the Alu I family of human middle repetitive DNAs were cloned into the vector YIp5 and used to transform yeast. Of these DNAs, only Xenopus mtDNA promoted high-frequency transformation and extrachromosomal maintenance of YIp5 DNA. A 2.2-kilobase EcoRI fragment from the 17.4-kilobase mtDNA molecule was responsible for these activities. This fragment contains the sequence used for the initiation of replication in Xenopus mitochondria.
Rabek, JP, VA Zakian, and AJ Levine. “The SV40 A gene product suppresses the adenovirus H5ts125 defect in DNA replication.”. Virology 109.2 (1981): , 109, 2, 290-302. Print.
Zakian, VA, DW Wagner, and WL Fangman. “Yeast L double-stranded ribonucleic acid is synthesized during the G1 phase but not the S phase of the cell cycle.”. Mol Cell Biol 18 (1981): , 1, 8, 673-9. Print.Abstract
The cytoplasm of Saccharomyces cerevisiae contains two major classes of protein-encapsulated double-stranded ribonucleic acids (dsRNA's), L and M. Replication of L and M dsRNA's was examined in cells arrested in the G1 phase by either alpha-factor, a yeast mating pheromone, or the restrictive temperature for a cell cycle mutant (cdc7). [3H]uracil was added during the arrest periods to cells prelabeled with [14C]uracil, and replication was monitored by determining the ratio of 3H/14C for purified dsRNA's. Like mitochondrial deoxyribonucleic acid, both L and M dsRNA's were synthesized in the G1 arrested cells. The replication of L dsRNA was also examined during the S phase, using cells synchronized in two different ways. Cells containing the cdc7 mutation, treated sequentially with alpha-factor and then the restrictive temperature, enter a synchronous S phase when transferred to permissive temperature. When cells entered the S phase, synthesis of L dsRNA ceased, and little or no synthesis was detected throughout the S phase. Synthesis of L dsRNA was also observed in G1 phase cells isolated from asynchronous cultures by velocity centrifugation. Again, synthesis ceased when cells entered the S phase. These results indicate that L dsRNA replication is under cell cycle control. The control differs from that of mitochondrial deoxyribonucleic acid, which replicates in all phases of the cell cycle, and from that of 2-micron DNA, a multiple-copy plasmid whose replication is confined to the S phase.
1980
Brewer, BJ, VA Zakian, and WL Fangman. “Replication and meiotic transmission of yeast ribosomal RNA genes.”. Proc Natl Acad Sci U S A 77.11 (1980): , 77, 11, 6739-43. Print.Abstract
The yeast Saccharomyces cerevisiae has approximately 120 genes for the ribosomal RNAs (rDNA) which are organized in tandem within chromosomal DNA. These multiple-copy genes are homogeneous in sequence but can undergo changes in copy number and topology. To determine if these changes reflect unusual features of rDNA metabolism, we have examined both the replication of rDNA in the mitotic cell cycle and the inheritance of rDNA during meiosis. The results indicate that rDNA behaves identically to chromosomal DNA: each rDNA unit is replicated once during the S phase of each cell cycle and each unit is conserved through meiosis. Therefore, the flexibility in copy number and topology of rDNA does not arise from the selective replication of units in each S phase nor by the selective inheritance of units in meiosis.
1979
Zakian, VA, BJ Brewer, and WL Fangman. “Replication of each copy of the yeast 2 micron DNA plasmid occurs during the S phase.”. Cell 17.4 (1979): , 17, 4, 923-34. Print.Abstract
Saccharomyces cerevisiae contains 50-100 copies per cell of a circular plasmid called 2 micron DNA. Replication of this DNA was studied in two ways. The distribution of replication events among 2 micron DNA molecules was examined by density transfer experiments with asynchronous cultures. The data show that 2 micron DNA replication is similar to chromosomal DNA replication: essentially all 2 micron duplexes were of hybrid density at one cell doubling after the density transfer, with the majority having one fully dense strand and one fully light strand. The results show that replication of 2 micron DNA occurs by a semiconservative mechanism where each of the plasmid molecules replicates once each cell cycle. 2 micron DNA is the only known example of a multiple-copy, extrachromosomal DNA in which every molecule replicates in each cell cycle. Quantitative analysis of the data indicates that 2 micron DNA replication is limited to a fraction of the cell cycle. The period in the cell cycle when 2 micron DNA replicates was examined directly with synchronous cell cultures. Synchronization was accomplished by sequentially arresting cells in G1 phase using the yeast pheromone alpha-factor and incubating at the restrictive temperature for a cell cycle (cdc 7) mutant. Replication was monitored by adding 3H-uracil to cells previously labeled with 14C-uracil, and determining the 3H/14C ratio for purified DNA species. 2 micron DNA replication did not occur during the G1 arrest periods. However, the population of 2 micron DNA doubled during the synchronous S phase at the permissive temperature, with most of the replication occurring in the first third of S phase. Our results indicate that a mechanism exists which insures that the origin of replication of each 2 micron DNA molecule is activated each S phase. As with chromosomal DNA, further activation is prevented until the next cell cycle. We propose that the mechanism which controls the replication initiation of each 2 micron DNA molecule is identical to that which controls the initiation of chromosomal DNA.
1976
Zakian, VA. “Electron microscopic analysis of DNA replication in main band and satellite DNAs of Drosophila virilis.”. J Mol Biol 108.2 (1976): , 108, 2, 305-31. Print.

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