Faculty & Research
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Molecular Biology Faculty

Virginia A. Zakian

Harry C. Wiess Professor in the Life Sciences
Professor of Molecular Biology

Virginia Zakian

Phone (609) 258-6770
locationLewis Thomas Lab, 103
Phone Lab (609) 258-2723
Faculty Assistant
william mercado
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Phone (609) 258-1694

Research Focus

DNA replication and chromosome structure in yeast; telomeres; trinucleotide repeats

Research in the Zakian lab focuses on structures and processes that ensure the faithful maintenance of eukaryotic chromosomes, mainly using the yeast Saccharomyces cerevisiae as a model system. A major goal is to understand how telomeres, the physical ends of chromosomes, contribute to chromosome stability. Yeast chromosomes end in ~350 bps of C1-3A/TG1-3 DNA and the many proteins that associate with this DNA. Telomeres are essential for the stable maintenance of yeast chromosomes (Sandell and Zakian, 1993): they protect the end of the chromosome against degradation, help the cell distinguish intact from broken DNA, and promote replication of the very end of the chromosome. In addition, yeast telomeres are specialized sites for gene expression: genes placed near yeast telomeres are transcriptionally repressed, a phenomenon called telomere position effect (TPE) (Gottschling et al., 1990). In most eukaryotes, telomeric DNA is synthesized by a telomere specific reverse transcriptase called telomerase, but recombination provides an alternative mechanism for lengthening telomeric tracts in both yeast (Teng et al., 2000) and mammals.

Our lab uses a combination of genetic, biochemical, and cell biological approaches to identify proteins that affect telomeres and to determine their mechanism of action. For example, using a genetic strategy, we identified the Pif1p DNA helicase as an inhibitor of telomere lengthening and especially of telomere formation (Schulz and Zakian, 1994). Mutations that eliminate the helicase activity of Pif1p in vitro fail to inhibit telomerase mediated telomere lengthening in vivo (Zhou et al., 2000). Thus, Pif1p is a catalytic inhibitor of telomerase. Because Pif1p is telomere associated in vivo, it likely affects telomere replication directly. We also study other proteins that inhibit (for example, the Rif proteins; Teng et al., 2000) or promote (eg., Cdc13p; Qi and Zakian, 2000) the telomerase pathway.

Using a combination of database searches and gene isolation strategies, we found that Pif1p is the prototype member of a helicase subfamily, conserved from yeast to humans (Zhou et al., 2000). Saccharomyces has a second Pif1-like protein, called Rrm3p. Although Rrm3p also affects replication of telomeric DNA, it has an additional and very important role in replication of ribosomal DNA (rDNA). By virtue of its helicase activity, Rrm3p promotes fork progression throughout the rDNA and is especially important to resolve the converging replication forks that accumulate at the end of rDNA replication (Ivessa et al., 2000). Again, because Rrm3p is rDNA associated in vivo, it probably affects replication directly. Rrm3p has the appropriate properties to be the replicative helicase for rDNA.

The lab also uses yeast as a model system to study trinucleotide repeats. Expansion of trinucleotide repeats is the causative mutation in ~20 human genetic diseases. In many of these diseases, the expanded repeat array is a preferred site of chromosome breakage, a so-called "fragile site." Remarkably, both CTG (Freudenreich et al., 1998) and CGG (Balakumaran et al., 2000) tracts are length-dependent fragile sites in yeast, a behavior that provides the basis for genetic assays to identify genes affecting repeat expansion.


Selected Publications

Bochman ML, Paeschke K, Chan A, Zakian VA. (2014) Hrq1, a homolog of the human RecQ4 helicase, acts catalytically and structurally to promote genome integrity. Cell Rep. 6: 346-56. Pubmed

Webb CJ, Wu Y, Zakian VA. (2013) DNA repair at telomeres: keeping the ends intact. Cold Spring Harb Perspect Biol. 5. pii: a012666. Pubmed

Paeschke K, Bochman ML, Garcia PD, ..., Zakian VA. (2013) Pif1 family helicases suppress genome instability at G-quadruplex motifs. Nature. 497: 458-62. Pubmed

Di Domenico EG, Mattarocci S, Cimino-Reale G, ..., Zakian VA, Ascenzioni F. (2013) Tel1 and Rad51 are involved in the maintenance of telomeres with capping deficiency. Nucleic Acids Res. 41: 6490-500. Pubmed

Wu Y, Dimaggio PA Jr, Perlman DH, Zakian VA, Garcia BA. (2013) Novel phosphorylation sites in the S. cerevisiae Cdc13 protein reveal new targets for telomere length regulation. J Proteome Res. 12: 316-27. Pubmed

Bochman ML, Paeschke K, Zakian VA. (2012) DNA secondary structures: stability and function of G-quadruplex structures. Nat Rev Genet. 13: 770-80. Pubmed

Zakian VA. (2012) Telomeres: the beginnings and ends of eukaryotic chromosomes. Exp Cell Res. 318: 1456-1460. Pubmed

Sabouri N, McDonald KR, Webb CJ, Cristea IM, Zakian VA. (2012) DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase. Genes Dev. 26: 581-93. PubMed

Webb CJ, Zakian VA. (2012) Schizosaccharomyces pombe Ccq1 and TER1 bind the 14-3-3-like domain of Est1, which promotes and stabilizes telomerase-telomere association. Genes Dev. 26: 82-91. PubMed

Wu Y, Zakian VA. (2011) The telomeric Cdc13 protein interacts directly with the telomerase subunit Est1 to bring it to telomeric DNA ends in vitro. Proc Natl Acad Sci. 108: 20362-69. PubMed

Paeschke K, Capra JA, Zakian VA. (2011) DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell. 145: 678-91. PubMed

Tuzon CT, Wu Y, Chan A, Zakian VA. (2011) The Saccharomyces cerevisiae telomerase subunit Est3 binds telomeres in a cell cycle- and Est1-dependent manner and interacts directly with Est1 in vitro. PLoS Genet. 7: e1002060. PubMed

Bochman ML, Judge CP, Zakian VA. (2011) The Pif1 family in prokaryotes: what are our helicases doing in your bacteria? Mol Biol Cell. 22: 1955-59. PubMed

McGee JS, Phillips JA, Chan A, Sabourin M, Paeschke K, Zakian VA. (2010) Reduced Rif2 and lack of Mec1 target short telomeres for elongation rather than double-strand break repair. Nat Struct Mol Biol. 17: 1438-45. PubMed

Capra JA, Paeschke K, Singh M, Zakian VA. (20101) G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae. PLoS Comput Biol. 6: e1000861. PubMed

Paeschke K, McDonald KR, Zakian VA. (2010) Telomeres: Structures in need of unwinding. FEBS Lett. 584: 3760-72. PubMed

Boulé JB, Zakian VA. (2010) Characterization of the helicase activity and anti-telomerase properties of yeast Pif1p in vitro. Methods Mol Biol. 587: 359-76. PubMed

Bochman ML, Sabouri N, Zakian VA. (2010) Unwinding the functions of the Pif1 family helicases. DNA Repair (Amst). 9: 237-49. PubMed

Zakian VA (2009) The ends have arrived. Cell 139: 1038-1040. PubMed

Wu Y, Zakian VA. (2009) Identity crisis when telomeres left unprotected. J Mol Cell Biol. 2: 14-16. PubMed

Azvolinsky A, Giresi PG, Lieb JD, Zakian VA. (2009) Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae. Mol Cell. 34: 722-34. PubMed

Chan A, Boule JB, Zakian VA. (2008). Two pathways recruit telomerase to S. cerevisiae telomeres. PLoS Genet. 4: e1000236. PubMed

Pinter S, Aubert S, Zakian VA. (2008) The S. pombe Pfh1p DNA helicase is essential for the maintenance of nuclear and mitochondrial DNA. Mol Cell Biol. 28: 6594–608. PubMed

Sabourin M, Zakian VA. (2008) ATM-like kinases and regulation of telomerase: lessons from yeast and mammals. Trends Cell Biol. 18: 337-46. PubMed

Webb CJ, Zakian VA. (2008) Identification and characterization of the Schizosaccharomyces pombe TER1 telomerase RNA. Nat Struct Mol Biol. 15: 34-42. PubMed

Mondoux MA, Scaife JG, Zakian VA. (2007) Differential nuclear localization does not determine the silencing status of Saccharomyces cerevisiae telomeres. Genetics. 177: 2019-29. PubMed

Mondoux MA, Zakian VA. (2007) Subtelomeric elements influence but do not determine silencing levels at Saccharomyces cerevisiae telomeres. Genetics. 177: 2541-46. PubMed

Boulé JB, Zakian VA. (2007) The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates. Nucleic Acids Res. 35: 5809-18. PubMed

Sabourin M, Tuzon CT, Zakian VA. (2007) Telomerase and Tel1p preferentially associate with short telomeres in S. cerevisiae. Mol Cell. 27: 550-61. PubMed

Vega LR, Phillips J, Thornton BR, ..., Zakian VA. (2007) Sensitivity of yeast strains with long G-tails to levels of telomere-bound telomerase. PLoS Genet. 3: e105. PubMed

Bhasakara V, Dupre A, Lengsfeld B, ..., Zakian VA, Paull TT. (2007) Rad50 Adenylate kinase activity regulates DNA tethering activities of Mre11/Rad50 complexes. Mol Cell. 25: 647-61. PubMed

Sabourin M, Tuzon CT, Fisher TS, Zakian VA. (2007) A flexible protein linker improves the function of epitope tagged protein in S. cerevisiae. Yeast. 24: 39-45. PubMed.

Snow BE, Mateyak M, Paderova J, ..., Zakian V, et al. (2007) Murine Pif1 interacts with telomerase and is dispensable for telomere function in vivo. Mol Cell Biol. 27: 1017-26. PubMed

Sabourin M, Tuzon CT, Fisher TS, Zakian VA. (2006) A flexible protein linker improves the function of epitope tagged protein in S. cerevisiae. Yeast. 24: 39-45. PubMed

Azvolinsky A, Dunaway S, Torres JZ, Bessler JB, and Zakian VA. (2006) The S. cerevisiae Rrm3p DNA helicase moves with the replication fork and affects replication of all yeast chromosomes. Genes Dev 20: 3104-3116. PubMed

Mateyak MK, Zakian VA. (2006) Human PIF helicase is cell cycle regulated and associates with telomerase. Cell Cycle. 5: 2796-804. PubMed

Goudsouzian LK, Tuzon CT, Zakian VA. (2006) S. cerevisiae Tel1p and Mre11p are required for normal levels of Est1p and Est2p telomere association. Mol Cell. 24: 603-10. PubMed

Boule JB, Zakian VA. (2006) Roles of Pif1-like helicases in the maintenance of genomic stability. Nucl Acids Res. 34: 4147-53. PubMed

Boule JB, Vega LR, Zakian VA. (2005) The yeast Pif1p helicase removes telomerase from telomeric DNA. Nature. 438: 57-61. PubMed

Fisher TS, Zakian VA. (2005) Ku: a multifunctional protein involved in telomere maintenance. DNA Repair (Amst). 4: 1215-26. PubMed

Fisher TS, Taggart AKP, Zakian VA. (2004) Cell cycle-dependent regulation of yeast telomerase by Ku. Nat Struct Mol Biol. 11: 1198-205. PubMed

Bessler JB, Zakian VA. (2004) The amino terminus of the Saccharomyces cerevisiae DNA helicase Rrm3p modulates protein function altering replication and checkpoint activity. Genetics. 168: 1205-18. PubMed

Torres JZ, Schnakenberg SL, Zakian VA. (2004) Saccharomyces cerevisiae Rrm3p DNA helicase promotes genome integrity by preventing replication fork stalling: viability of rrm3 cells requires the intra-S-phase checkpoint and fork restart activities. Mol Cell Biol. 24: 3198-212. PubMed

Torres JZ, Bessler JB, Zakian VA. (2004) Local chromatin structure at the ribosomal DNA causes replication fork pausing and genome instability in the absence of the S. cerevisiae DNA helicase Rrm3p. Genes Dev. 18: 498-503. PubMed

Ivessa AS, Lenzmeier BA, Bessler JB, ..., Zakian VA. (2003) The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes. Mol Cell. 12: 1525-36. PubMed

Vega LR, Mateyak MK, Zakian VA. (2003) Getting to the end: telomerase access in yeast and humans. Nat Rev Mol Cell Biol. 4: 948-59. PubMed

Callahan JL, Andrews KJ, Zakian VA, Freudenreich CH. (2003) Mutations in yeast replication proteins that increase CAG/CTG expansions also increase repeat fragility. Mol Cell Biol. 23: 7849-60. PubMed

Taggart AK, Zakian VA. (2003) Telomerase: what are the Est proteins doing? Curr Opin Cell Biol. 15: 275-80. PubMed

Alexander MK, Zakian VA. (2003) Rap1p telomere association is not required for mitotic stability of a C(3)TA(2) telomere in yeast. Embo J. 22: 1688-96. PubMed

Ivessa AS, Zakian VA. (2002) To fire or not to fire: origin activation in Saccharomyces cerevisiae ribosomal DNA. Genes Dev. 16: 2459-64. PubMed

Taggart AK, Teng SC, Zakian VA. (2002) Est1p as a cell cycle-regulated activator of telomere-bound telomerase. Science. 297: 1023-26. PubMed

Tham WH, Zakian VA. (2002) Transcriptional silencing at Saccharomyces telomeres: implications for other organisms. Oncogene. 21: 512-21. PubMed

Zhou J-Q, Qi H, Schulz VP, Mateyak MK, Monson EK, Zakian VA (2002). Schizosaccharomyces pombe pfh1+ encodes an essential 5' to 3' DNA helicase that is a member of the PIF1 subfamily of DNA helicases. Mol Biol Cell. 13: 2180-91. PubMed

Ivessa AS, Zhou JQ, Schulz VP, Monson EK, Zakian VA. (2002) Saccharomyces Rrm3p, a 5' to 3' DNA helicase that promotes replication fork progression through telomeric and subtelomeric DNA. Genes Dev. 16: 1383-96. PubMed

Mangahas JL, Alexander MK, Sandell LL, Zakian VA. (2001) Repair of chromosome ends after telomere loss in Saccharomyces. Mol Biol Cell. 12: 4078-89. PubMed

Tsukamoto Y, Taggart AKP, Zakian VA. (2001) The role of the Mre11-Rad50-Xrs2 complex in telomerase mediated lengthening of Saccharomyces telomeres. Curr Biol. 11: 1328-35. PubMed

Tham W-H, Wyithe JSB, Ko Ferrigno P, Silver PA, Zakian VA. (2001). Localization of yeast telomeres to the nuclear periphery is separable from transcriptional repression and telomere stability functions. Mol Cell. 8: 189-99. PubMed

Bessler JB, Torres JZ, Zakian VA. (2001) The Pif1p subfamily of helicases: region specific DNA helicases? Trends Cell Biol. 11: 60-65. PubMed

Teng S-C, Chang J, McCowan B, Zakian VA. (2000) Telomerase-independent lengthening of yeast telomeres occurs by an abrupt Rad50p-dependent, Rif-inhibited recombinational process. Mol Cell. 6: 947-52. PubMed

de Bruin D, Kantrow SM, Liberatore RA, Zakian VA. (2000) Chromatin remodeling and transcriptional reactivation of a telomere-linked gene independent of DNA replication. Mol Cell Biol. 20: 7991-8000. PubMed

Tham W-H, Zakian VA. (2000) Telomeric tethers. Nature. 403: 34-35. PubMed

Balakumaran BS, Freudenreich CH, Zakian VA. (2000). CGG/CCG repeats exhibit orientation dependent instability and orientation independent fragility in Saccharomyces cerevisiae. Hum Mol Genet. 9: 93-100. PubMed

Zhou J-Q, Monson EK, Teng S-C, Schulz VP, Zakian VA. (2000) Pif1p helicase, a catalytic inhibitor of telomerase in yeast. Science. 289: 771-74. PubMed

Qi H, Zakian VA. (2000). The Saccharomyces telomere binding protein Cdc13p interacts with both the catalytic subunit of DNA polymerase a and the telomerase associated Est1 protein. Genes Dev. 14: 1777-88. PubMed

Ivessa AS, Zhou J-Q, Zakian VA. (2000). The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA. Cell. 100: 479-89. PubMed

Teng SC. Zakian VA (1999). Telomere-telomere recombination is an efficient bypass pathway for telomere maintenance in Saccharomyces cerevisiae. Mol Cell Biol. 19: 8083-93. PubMed

Stavenhagen JB, Zakian VA. (1998). Yeast telomeres exert a position effect on recombination between internal tracts of yeast telomeric DNA. Genes Dev. 12: 3044-58. PubMed

Bourns BB, Alexander MK, Smith AM, Zakian VA. (1998) Sir proteins, Rif proteins, and Cdc13p bind Saccharomyces telomeres in vivo. Mol Cell Biol. 18: 5600-08. PubMed

Freudenreich CH, Kantrow SM, Zakian VA. (1998) Expansion and length-dependent fragility of CTG repeats in yeast. Science. 279: 853-56. PubMed

Monson EK, DeBriun D, Zakian VA. (1997). The yeast Cac1 protein is required for the stable inheritance of transcriptionally repressed chromatin at telomeres. Proc Natl Acad Sci. 94: 13081-86. PubMed

Zakian VA. (1997) Life and cancer without telomerase. Cell. 91: 1-3. PubMed

Freudenreich CH, Stavenhagen JB, Zakian VA. (1997) Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome. Mol Cell Biol. 17: 2090-98. PubMed

Lin JJ, Zakian VA. (1996) The Saccharomyces CDC13 protein is a single-strand TG1-3 telomeric DNA binding protein in vitro that affects telomere behavior in vivo. Proc Natl Acad Sci. 93: 13760-65. PubMed

Zakian VA. (1996) Structure, function and replication of Saccharomyces cerevisiae telomeres. Annu Rev Genet. 30: 141-72. PubMed

Schulz VP, Zakian VA, Ogburn CE, et al. (1996) Accelerated loss of telomeric repeats may not explain accelerated replicative decline of Werner syndrome cells. Hum Genet. 97: 750-54. PubMed

Runge KW, Zakian VA. (1996) TEL2, an essential gene required for telomere length regulation and telomere position effect in Saccharomyces cerevisiae. Mol Cell Biol. 16: 3094-105. PubMed

Wellinger RJ, Etier K, Labreque P, Zakian VA. (1996) Evidence for a new step in telomere maintenance. Cell. 85: 423-33. PubMed

Zakian VA. (1995) ATM-related genes: what do they tell us about functions of the human gene? Cell. 82: 685-87. PubMed

Lin JJ, Zakian VA (1995) An in vitro assay for Saccharomyces telomerase requires EST1. Cell. 81: 1127-35. PubMed

Zakian VA. (1995) Telomeres: beginning to understand the end. Science. 270: 1601-07. PubMed

Wright JH, Zakian VA. (1995) Protein-DNA interactions in soluble telosomes from Saccharomyces cerevisiae. Nucl Acids Res. 23: 1454-60. PubMed

Wiley E, Zakian VA. (1995) Extra telomeres, but not internal tracts of telomeric DNA, reduce transcriptional repression at Saccharomyces telomeres. Genetics. 139: 67-79. PubMed

Lin J-J, Zakian VA. (1994) Isolation and characterization of two Saccharomyces genes that encode proteins that bind to TG1-3 single-strand telomeric DNA in vitro. Nucl Acids Res. 22: 4906-13. PubMed

Sandell LL, Gottschling DE, Zakian VA. (1994) Transcription through a yeast telomere reduces telomere position effect without affecting chromosome stability. Proc Natl Acad Sci. 91: 12061-65. PubMed

Stavenhagen J, Zakian VA. (1994) Internal tracts of telomeric DNA act as silencers in Saccharomyces cerevisiae. Genes Dev. 8: 1411-22. PubMed

Schulz VP, Zakian VA. (1994) The Saccharomyces PlFl DNA helicase inhibits telomere elongation and de novo telomere formation Cell. 76: 145-55. PubMed

Sandell LL, Zakian VA. (1993) Loss of a yeast telomere: arrest, recovery and chromosome loss. Cell. 75: 729-39. PubMed

Wellinger RJ, Wolf AJ, Zakian VA. (1993) Origin activation and formation of single-strand TG1-3 tails occur sequentially in late S phase on a linear plasmid. Mol Cell Biol. 13: 4057-65. PubMed

Wellinger RJ, Wolf A, Zakian VA. (1993) Single strand TG1-3 tails acquired by Saccharomyces telomeres late in S phase mediate telomere-telomere interactions. Cell. 72: 51-60. PubMed

Wright JH, Gottschling DE, Zakian VA. (1992) Saccharomyces telomeres assume a non-nucleosomal chromatin structure. Genes Dev. 6: 197-210. PubMed

Conrad MN, Wright J, Wolf A, Zakian VA. (1990) RAP1 protein interacts with yeast telomeres in vivo: Overproduction alters telomere structure and decreases chromosome stability. Cell. 63: 739-50. PubMed

Gottschling DE, Aparicio DM, Billington BL, Zakian VA. (1990) Position effect at Saccharomyces cerevisiae telomeres: reversible repression of polII transcription. Cell. 63: 751-62. PubMed

Wang S-S, Zakian VA. (1990) Sequence analysis of Saccharomyces telomeres cloned using T4 DNA polymerase reveals two domains. Mol Cell Biol. 10: 4415-19. PubMed

Wang S-S, Zakian VA. (1990) Telomere-telomere recombination provides an express pathway for telomere acquisition. Nature. 345: 456-58. PubMed

Zakian VA. (1989) Structure and function of telomeres. Annu Rev Genet. 23: 579-604. PubMed

Pluta AF, Zakian VA. (1989) Recombination occurs during telomere formation in Saccharomyces cerevisiae. Nature. 337: 429-33. PubMed

Gottschling DE, Zakian VA. (1986) Telomere Proteins: Specific recognition and protection of natural termini of Oxytricha macronuclear DNA. Cell. 47: 195-205. PubMed

Pluta AF, Dani GM, Spear BB, Zakian VA. (1984) Elaboration of telomeres in yeast: Recognition and modification of termini from Oxytricha macronuclear DNA. Proc Natl Acad Sci. 81: 1475-79. PubMed

Dani GM, Zakian VA. (1983) Mitotic and meiotic stability of linear plasmids in yeast. Proc Natl Acad Sci. 80: 3406-10. PubMed


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