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.

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