Molecular Biology Faculty
Virginia A. Zakian
Professor of Molecular Biology
 (609) 258-6770 |
 Lewis Thomas Lab, 103 |
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Lab (609) 258-2723 |
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Faculty Assistant
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Carolynne Lewis-Arévalo
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This email address is being protected from spambots. You need JavaScript enabled to view it.
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(609) 258-2933 |
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
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. May 15. [Epub ahead of print]
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: 581-593. 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: 20362-20369. 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: 678-691. 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: 1955-1959. 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: 1438-1445. 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: 3760-3772. PubMed
Boulé JB, Zakian VA. (2010) Characterization of the helicase activity and anti-telomerase properties of yeast Pif1p in vitro. Methods Mol Biol. 587: 359-376. PubMed
Bochman ML, Sabouri N, Zakian VA. (2010) Unwinding the functions of the Pif1 family helicases. DNA Repair (Amst) 9: 237-249. 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: 14-6. 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: 722-734. 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: 6594–6608. PubMed
Sabourin M, Zakian VA. (2008) ATM-like kinases and regulation of telomerase: lessons from yeast and mammals. Trends Cell Biol. 18: 337-346. 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: 2019-2029. PubMed
Mondoux MA, Zakian VA. (2007) Subtelomeric elements influence but do not determine silencing levels at Saccharomyces cerevisiae telomeres. Genetics 177: 2541-2546. PubMed
Boulé JB, Zakian VA. (2007) The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates. Nucleic Acids Res 35: 5809-5818. PubMed
Sabourin M, Tuzon CT, Zakian VA. (2007) Telomerase and Tel1p preferentially associate with short telomeres in S. cerevisiae. Mol Cell. 27: 550-561. PubMed
Vega LR, Phillips J, Thornton BR, Benanti JA, Onigbanjo MT, Toczyski DP, 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, Hopkins B, Lee J-H, Zhang X, Gautier J, Zakian VA, Paull TT. (2007) Rad50 Adenylate kinase activity regulates DNA tethering activities of Mre11/Rad50 complexes. Mol Cell 25: 647-661. PubMed
Sabourin M, Tuzon CT, Fisher TS, and 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, Wakeham A, Iorio C, Zakian V, Squire J, Harrington L. (2007) Murine Pif1 interacts with telomerase and is dispensable for telomere function in vivo. Mol Cell Biol 27: 1017-1026. PubMed
Sabourin M, Tuzon CT, Fisher TS, and 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 and Zakian VA. (2006) Human PIF helicase is cell cycle regulated and associates with telomerase. Cell Cycle 5: 2796-2804. PubMed
Goudsouzian LK, Tuzon CT and Zakian VA. (2006) S. cerevisiae Tel1p and Mre11p are required for normal levels of Est1p and Est2p telomere association. Mol Cell 24: 603-610. PubMed
Boule JB and Zakian VA. (2006) Roles of Pif1-like helicases in the maintenance of genomic stability. Nucl Acids Res 34: 4147-4153. PubMed
Boule JB, Vega LR and Zakian VA (2005). The yeast Pif1p helicase removes telomerase from telomeric DNA. Nature 438: 57-61. PubMed
Fisher TS and Zakian VA (2005). Ku: a multifunctional protein involved in telomere maintenance. DNA Repair (Amst) 4: 1215-1226. PubMed
Fisher TS, Taggart AKP, and Zakian VA (2004). Cell cycle-dependent regulation of yeast telomerase by Ku. Nat Struct Mol Biol 11: 1198-1205. 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: 1205-1218. PubMed
Torres JZ, Schnakenberg SL and 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: 3198-3212. PubMed
Torres JZ, Bessler JB and 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, Goudsouzian LK, Schnakenberg SL, et al. (2003). The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes. Mol Cell 12: 1525-1536. PubMed
Vega LR, Mateyak MK and Zakian VA (2003). Getting to the end: telomerase access in yeast and humans. Nat Rev Mol Cell Biol 4: 948-959. PubMed
Callahan JL, Andrews KJ, Zakian VA and Freudenreich CH (2003). Mutations in yeast replication proteins that increase CAG/CTG expansions also increase repeat fragility. Mol Cell Biol 23: 7849-7860. PubMed
Taggart AK and Zakian VA (2003). Telomerase: what are the Est proteins doing? Curr Opin Cell Biol 15: 275-280. PubMed
Alexander MK and Zakian VA (2003). Rap1p telomere association is not required for mitotic stability of a C(3)TA(2) telomere in yeast. Embo J 22: 1688-1696. PubMed
Ivessa AS and Zakian VA (2002). To fire or not to fire: origin activation in Saccharomyces cerevisiae ribosomal DNA. Genes Dev 16: 2459-2464. PubMed
Taggart AK, Teng SC and Zakian VA (2002). Est1p as a cell cycle-regulated activator of telomere-bound telomerase. Science 297: 1023-1026. PubMed
Tham WH and Zakian VA (2002). Transcriptional silencing at Saccharomyces telomeres: implications for other organisms. Oncogene 21: 512-521. PubMed
Zhou J-Q, Qi H, Schulz VP, Mateyak MK, Monson EK, and 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: 2180-2191. PubMed
Ivessa AS, Zhou JQ, Schulz VP, Monson EK and Zakian VA (2002). Saccharomyces Rrm3p, a 5' to 3' DNA helicase that promotes replication fork progression through telomeric and subtelomeric DNA. Genes Dev 16: 1383-1396. PubMed
Mangahas JL, Alexander MK, Sandell LL, and Zakian VA (2001). Repair of chromosome ends after telomere loss in Saccharomyces. Mol Biol Cell 12: 4078-4089. PubMed
Tsukamoto Y, Taggart AKP, and Zakian VA (2001). The role of the Mre11-Rad50-Xrs2 complex in telomerase mediated lengthening of Saccharomyces telomeres. Curr Biol 11: 1328-1335. PubMed
Tham W-H, Wyithe JSB, Ko Ferrigno P, Silver PA, and Zakian VA (2001). Localization of yeast telomeres to the nuclear periphery is separable from transcriptional repression and telomere stability functions. Mol Cell 8: 189-199. PubMed
Bessler JB, Torres JZ, and 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, and Zakian VA (2000) Telomerase-independent lengthening of yeast telomeres occurs by an abrupt Rad50p-dependent, Rif-inhibited recombinational process. Mol Cell 6: 947-952. PubMed
de Bruin D, Kantrow SM, Liberatore RA, and 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 and Zakian VA (2000). Telomeric tethers. Nature 403: 34-35. PubMed
Balakumaran BS, Freudenreich CH, and 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, and Zakian VA (2000). Pif1p helicase, a catalytic inhibitor of telomerase in yeast. Science 289: 771-774. PubMed
Qi H and 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: 1777-1788. PubMed
Ivessa AS, Zhou J-Q, and 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: 479-489. PubMed
Teng SC and Zakian VA (1999). Telomere-telomere recombination is an efficient bypass pathway for telomere maintenance in Saccharomyces cerevisiae. Mol Cell Biol 19: 8083-8093. PubMed
Stavenhagen JB and Zakian VA (1998). Yeast telomeres exert a position effect on recombination between internal tracts of yeast telomeric DNA. Genes Dev 12: 3044-3058. PubMed
Bourns BB, Alexander MK, Smith AM, and Zakian VA (1998) Sir proteins, Rif proteins, and Cdc13p bind Saccharomyces telomeres in vivo. Mol Cell Biol 18: 5600-5608. PubMed
Freudenreich CH, Kantrow SM, and Zakian VA (1998) Expansion and length-dependent fragility of CTG repeats in yeast. Science 279: 853-856. PubMed
Monson EK, DeBriun D, and Zakian VA (1997). The yeast Cac1 protein is required for the stable inheritance of transcriptionally repressed chromatin at telomeres. PNAS 94: 13081-13086. PubMed
Zakian VA (1997) Life and cancer without telomerase. Cell 91: 1-3. PubMed
Freudenreich CH, Stavenhagen JB, and Zakian VA (1997) Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome. Mol Cell Biol 17: 2090-2098. PubMed
Lin JJ and 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. PNAS 93: 13760-13765. PubMed
Zakian VA (1996) Structure, function and replication of Saccharomyces cerevisiae telomeres. Annu Rev Genet 30: 141-172. PubMed
Schulz VP, Zakian VA, Ogburn CE, McKay J, Jarzebowicz AA, Edland SD, Martin GM (1996) Accelerated loss of telomeric repeats may not explain accelerated replicative decline of Werner syndrome cells. Hum Genet 97: 750-754. PubMed
Runge KW and Zakian VA (1996) TEL2, an essential gene required for telomere length regulation and telomere position effect in Saccharomyces cerevisiae. Mol Cell Biol 16: 3094-3105. PubMed
Wellinger RJ, Etier K, Labreque P, and Zakian VA (1996) Evidence for a new step in telomere maintenance. Cell 85: 423-433. PubMed
Zakian VA (1995) ATM-related genes: what do they tell us about functions of the human gene? Cell 82: 685-687. PubMed
Lin JJ and Zakian VA (1995) An in vitro assay for Saccharomyces telomerase requires EST1. Cell 81: 1127-1135. PubMed
Zakian VA (1995) Telomeres: beginning to understand the end. Science 270: 1601-1607. PubMed
Wright JH and Zakian VA (1995) Protein-DNA interactions in soluble telosomes from Saccharomyces cerevisiae. Nucl Acids Res 23: 1454-1460. PubMed
Wiley E and 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 and 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: 4906-4913. PubMed
Sandell LL, Gottschling DE, and Zakian VA (1994) Transcription through a yeast telomere reduces telomere position effect without affecting chromosome stability. PNAS 91: 12061-12065. PubMed
Stavenhagen J and Zakian VA (1994) Internal tracts of telomeric DNA act as silencers in Saccharomyces cerevisiae. Genes Dev 8: 1411-1422. PubMed
Schulz VP and Zakian VA (1994) The Saccharomyces PlFl DNA helicase inhibits telomere elongation and de novo telomere formation Cell 76: 145-155. PubMed
Sandell LL and Zakian VA (1993) Loss of a yeast telomere: arrest, recovery and chromosome loss. Cell 75: 729-739. PubMed
Wellinger RJ, Wolf AJ, and 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: 4057-4065. PubMed
Wellinger RJ, Wolf A, and 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, and Zakian VA (1992) Saccharomyces telomeres assume a non-nucleosomal chromatin structure. Genes Dev 6: 197-210. PubMed
Conrad MN, Wright J, Wolf A, and Zakian VA (1990) RAP1 protein interacts with yeast telomeres in vivo: Overproduction alters telomere structure and decreases chromosome stability. Cell 63: 739-750. PubMed
Gottschling DE, Aparicio DM, Billington BL, and Zakian VA (1990) Position effect at Saccharomyces cerevisiae telomeres: reversible repression of polII transcription. Cell 63: 751-762. PubMed
Wang S-S and Zakian VA (1990) Sequence analysis of Saccharomyces telomeres cloned using T4 DNA polymerase reveals two domains. Mol Cell Biol 10: 4415-4419. PubMed
Wang S-S and Zakian VA (1990) Telomere-telomere recombination provides an express pathway for telomere acquisition. Nature 345: 456-458. PubMed
Zakian VA (1989) Structure and function of telomeres. Ann Rev Genet 23: 579-604. PubMed
Pluta AF and Zakian VA (1989) Recombination occurs during telomere formation in Saccharomyces cerevisiae. Nature 337: 429-433. PubMed
Gottschling DE and 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, and Zakian VA (1984) Elaboration of telomeres in yeast: Recognition and modification of termini from Oxytricha macronuclear DNA. PNAS 81: 1475-1479. PubMed
Dani GM and Zakian VA (1983) Mitotic and meiotic stability of linear plasmids in yeast. PNAS 80: 3406-3410. PubMed
