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James E. Haber, Ph.D.
Professor of Biology
Director, Rosenstiel Basic Medical Sciences Research Center

Yeast Genetics and Molecular Biology

Ph.D., University of California, Berkeley

contact information
(781) 736-2462

Haber Lab Web Site

Broken chromosomes must be repaired if a cell is to survive; consequently cells have evolved a variety of mechanisms to repair double-strand breaks (DSBs). Both homologous recombination, in which the ends of the broken DNA seek out intact templates with the same sequence, and nonhomologous end-joining pathways are found in Saccharomyces as they are in humans. In addition cells have evolved a damage-sensing checkpoint system whereby the cells do delay entry into mitosis until the break has been repaired.

Recombination between homologous sequences is a fundamentally important process both in meiosis and in mitotic cells. We are interested in understanding at the molecular level how recombination occurs and what roles are played by the many proteins involved in DNA recombination, repair and replication. Using synchronized cells undergoing recombination that is initiated at a specific site on a chromosome by an inducible endonuclease, we use physical monitoring techniques (Southern blots, PCR analysis) to follow the sequence of molecular events that occur in real time. We are interested in determining what are the specific biochemical roles played by the many proteins implicated in DNA recombination, repair and replication. This "in vivo biochemistry" approach has enabled us to demonstrate that there are in fact several independent, competing pathways of homologous recombination, each with its own genetic requirements.

Analysis of homologous recombination.

We have identified the proteins necessary to carry out the initial steps in strand invasion and the beginning of new DNA synthesis. We have been surprised to learn that DNA repair uses virtually all of the DNA replication components necessary for normal chromosome replication. Moreover, the invasion of DNA strands into a donor template region often requires the action of gene products that can apparently rearrange chromatin to allow access to "closed" regions of DNA. We are especially interested in gene targeting methods and in figuring out why these types of gene replacement and modification are quite inefficient, even in yeast. Finally we want to compare how recombination occurs in mitosis and in meiosis. To this end we have expressed the site-specific HO endonuclease in meiotic cells so that we can compare recombination events at the same loci where we have used HO to stimulate recombination in mitotic cells.

Donor preference.

We are especially fascinated by the process of yeast mating-type gene switching, in which cells replace about 700 bp of Ya or Y-alpha-specific DNA sequences at the MAT locus by recombining with one of two donor loci, called HML-alpha and HMRa. The two donor loci are maintained in a chromatin configuration that prevents them from being transcribed or being cleaved by the HO endonuclease that cuts the same sequence at MAT to initiate switching. In addition to determining how this process occurs and how various mutations affect it, we are especially interested in the phenomenon of donor preference, whereby MATa cells choose the donor on the left while MAT-alpha elects to recombine with the donor on the right, even if we replace HML by HMR or vice versa. Recently we have shown that this regulation involves changes in chromosome or chromatin structure that extend over surprisingly long distances. MATa cells activate the entire left arm of the chromosome, so that a donor placed anywhere in that region is selected over a donor placed at any other location. In contrast MAT-alpha cells inactivate this entire region, so that the donor on the right is the only efficient donor. Amazingly, this control resides in a small cis-acting DNA sequence located on the left arm of the chromosome. Understanding how this element influences more than 100 kb of DNA is our current challenge. We have narrowed this region down to 244 bp and have identified several important cis-acting sequences and trans-acting factors.

Nonhomologous End-Joining and Repair.

In addition to repair of a double-strand chromosomal break by homologous recombination mechanisms, we have also demonstrated that yeast--like mammalian cells--also invoke several nonhomologous repair pathways. These include the formation of new telomere sequences to stabilize the end of a chromosome and the formation of deletions and small insertions of DNA to rejoin the ends of broken DNA molecules. Recently we discovered that there are two distinct nonhomologous end-joining pathways that have different genetic requirements. Even more surprising, the insertion-forming pathway appears to operate only in cells in the S and G2 phases of the cell cycle, so that only deletions are recovered when a broken chromosome is created in G1 cells. Again, we have developed physical monitoring assays to ask when and how each of these types of events occurs. So far 9 different proteins have been implicated in putting even perfectly complementary 4 bp ends back together.

Most recently, we discovered that broken chromosome ends can also be repaired by "capturing" a segment of DNA derived from the long terminal repeat of a retrotransposon, Ty1. This type of insertion of a cDNA-derived segment of DNA may explain how, in mammalian chromosomes, repeated elements such as Alu and pseudogenes could have been integrated at many different chromosomal sites.

Cell cycle regulation in response to DNA damage.

Recently we have also turned our attention to the ways that a cell "knows" that there is DNA damage and how it then arrests cell growth until that damage is repaired. The control of the DNA damage "check point" is not well understood. What is the actual signal that tells the cell it has a broken or damaged chromosome? How is that signal transmitted to arrest mitosis? How do cells know when to resume growth? We are analyzing mutants of yeast that fail to respond normally to these check point signals. We have shown, for example, that the cell actually cannot prevent mitosis when there is only one region of a chromosome that is still undergoing replication.

Most recently we have been studying the phenomenon of adaptation, where cells that have an unrepaired (and unrepairable) DSB will eventually escape from the G2/M DNA damage arrest checkpoint and resume growth, despite the continued presence of the broken chromosome. We have discovered that the ability of cells to adapt depends on the extent of the DNA damage the cell is experiencing. We have discovered that the Ku70 DNA end-binding protein and the Mre11/RAd50/Xrs2 exonuclease play antagonistic roles in this process. A deletion of Ku70 speeds up DNA degradation by a bout a factor of two, and prevents cells from escaping G2/M arrest. The absence of Mre11 or RAd50 proteins slows down DNA degradation and suppresses the effect of deleting Ku70p. Surprisingly, this system is so delicately balanced that a wild type cell will also be prevented from G2/M adaptation if it experiences two DSBs. Thus one break x twice the normal degradation = two breaks x normal degradation! The single-stranded DNA that is produced by degradation is apparently monitored by a third DNA binding protein family, RPA. A mutation in RPA suppresses permanent G2/M arrest both in the one-DSB Ku70-deleted cell and in the two-DSB wild type cell.

Selected Publications:

Ira G, Satory D, Haber JE. (2006) Conservative inheritance of newly synthesized DNA in double-strand break-induced gene conversion.Mol Cell Biol. 2006 Dec;26(24):9424-9. [abstract]

De Piccoli G, Cortes-Ledesma F, Ira G, Torres-Rosell J, Uhle S, Farmer S, Hwang JY, Machin F, Ceschia A, McAleenan A, Cordon-Preciado V, Clemente-Blanco A, Vilella-Mitjana F, Ullal P, Jarmuz A, Leitao B, Bressan D, Dotiwala F, Papusha A, Zhao X, Myung K, Haber JE, Aguilera A, Aragon L. (2006) Smc5-Smc6 mediate DNA double-strand-break repair by promoting sister-chromatid recombination. Nat Cell Biol. 2006 Sep;8(9):1032-4. [abstract]

Haber JE. Chromosome breakage and repair. (2006) Genetics. 2006 Jul;173(3):1181-5. No abstract available.

Haber JE, Debatisse M. Gene amplification: yeast takes a turn. (2006) Cell. 2006 Jun 30;125(7):1237-40. Review. [abstract]

Coic E, Sun K, Wu C, Haber JE. (2006) Cell cycle-dependent regulation of Saccharomyces cerevisiae donor preference during mating-type switching by SBF (Swi4/Swi6) and Fkh1.Mol Cell Biol. 2006 Jul;26(14):5470-80. [abstract]

Haber JE. (2006) Transpositions and translocations induced by site-specific double-strand breaks in budding yeast.DNA Repair (Amst). 2006 Sep 8;5(9-10):998-1009. Epub 2006 Jun 27. Review. [abstract]

Harrison JC, Haber JE. (2006) Surviving the breakup: the DNA damage checkpoint. Annu Rev Genet. 2006;40:209-35. [abstract]

Sugawara N, Haber JE. (2006) Repair of DNA double strand breaks: in vivo biochemistry.Methods Enzymol. 2006;408:416-29. [abstract]

Valencia-Burton M, Oki M, Johnson J, Seier TA, Kamakaka R, Haber JE. (2006) Different mating-type-regulated genes affect the DNA repair defects of Saccharomyces RAD51, RAD52 and RAD55 mutants. Genetics. 2006 Sep;174(1):41-55. [abstract]

McEachern MJ, Haber JE. (2006) Break-induced replication and recombinational telomere elongation in yeast.Annu Rev Biochem. 2006;75:111-35. [abstract]

Coic E, Richard GF, Haber JE. (2006) Saccharomyces cerevisiae donor preference during mating-type switching is dependent on chromosome architecture and organization.Genetics. 2006 Jul;173(3):1197-206. [abstract]

Keogh MC, Kim JA, Downey M, Fillingham J, Chowdhury D, Harrison JC, Onishi M, Datta N, Galicia S, Emili A, Lieberman J, Shen X, Buratowski S, Haber JE, Durocher D, Greenblatt JF, Krogan NJ. (2006) A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery. Nature. 2006 Jan 26;439(7075):497-501. [abstract]

Clatworthy AE, Valencia-Burton MA, Haber JE, Oettinger MA. (2005) The MRE11/RAD50/XRS2 complex, in addition to other NHEJ factors, is required for V(D)J joining in yeast. J Biol Chem. 2005 Mar 9. [abstract]

Malkova A, Naylor ML, Yamaguchi M, Ira G, Haber JE. (2005) RAD51-dependent break-induced replication differs in kinetics and checkpoint responses from RAD51-mediated gene conversion. Mol Cell Biol. 25:933-44. [abstract]

Unal E, Arbel-Eden A, Sattler U, Shroff R, Lichten M, Haber JE, Koshland D. (2004) DNA damage response pathway uses histone modification to assemble a double-strand break-specific cohesin domain. Mol Cell. 16:991-1002. [abstract]

Morrison AJ, Highland J, Krogan NJ, Arbel-Eden A, Greenblatt JF, Haber JE, Shen X. (2004) INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Cell. 119:767-75. [abstract]

Kaye JA, Melo JA, Cheung SK, Vaze MB, Haber JE, Toczyski DP. (2004) DNA breaks promote genomic instability by impeding proper chromosome segregation. Curr Biol. 14: 2096-106. [abstract]

Ira G, Pellicioli A, Balijja A, Wang X, Fiorani S, Carotenuto W, Liberi G, Bressan D, Wan L, Hollingsworth NM, Haber JE, Foiani M. (2004) DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature. 431:1011-7. [abstract]

Shroff R, Arbel-Eden A, Pilch D, Ira G, Bonner WM, Petrini JH, Haber JE, Lichten M. (2004) Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break. Curr Biol. 14:1703-11. [abstract]

Malkova A, Swanson J, German M, McCusker JH, Housworth EA, Stahl FW, Haber JE. (2004) Gene conversion and crossing over along the 405-kb left arm of Saccharomyces cerevisiae chromosome VII. Genetics. 168:49-63. [abstract]

Wang X, Ira G, Tercero JA, Holmes AM, Diffley JF, Haber JE. (2004) Role of DNA replication proteins in double-strand break-induced recombination in Saccharomyces cerevisiae. Mol Cell Biol. 24(16):6891-9. [abstract]

Sugawara N, Goldfarb T, Studamire B, Alani E, Haber JE. (2004) Heteroduplex rejection during single-strand annealing requires Sgs1 helicase and mismatch repair proteins Msh2 and Msh6 but not Pms1. Proc Natl Acad Sci U S A. 101(25):9315-20. [abstract]

Haber JE, Ira G, Malkova A, Sugawara N. (2004) Repairing a double-strand chromosome break by homologous recombination: revisiting Robin Holliday's model. Philos Trans R Soc Lond B Biol Sci. 359(1441):79-86. [abstract]

Bressan DA, Vazquez J, Haber JE. (2004) Mating type-dependent constraints on the mobility of the left arm of yeast chromosome III. J Cell Biol. 164(3):361-71. [abstract]

Wang X, Haber JE. (2004) Role of Saccharomyces Single-Stranded DNA-Binding Protein RPA in the Strand Invasion Step of Double-Strand Break Repair. PLoS Biol. 2(1):E21. [abstract]

Ira G, Malkova A, Liberi G, Foiani M, Haber JE. (2003) Srs2 and Sgs1-Top3 suppress crossovers during double-strand break repair in yeast. Cell. 115(4):401-11. [abstract]

Lee SE, Pellicioli A, Vaze MB, Sugawara N, Malkova A, Foiani M, Haber JE. (2003) Yeast Rad52 and Rad51 recombination proteins define a second pathway of DNA damage assessment in response to a single double-strand break. Mol Cell Biol. 23(23):8913-23. [abstract]

Haber JE. (2003) Aging: the sins of the parents. Curr Biol. 13(21):R843-5.

Sugawara N, Wang X, Haber JE. (2003) In vivo roles of Rad52, Rad54, and Rad55 proteins in Rad51-mediated recombination. Mol Cell. 12(1):209-19. [abstract]

Ira, G and J.E. Haber. (2002) Characterization of RAD51-independent break-induced replication that acts preferentially with short homologous sequences. Mol. Cell. Biol.22: 6384-6392. [abstract]

Vaze, M., A. Pellicioli, S.E. Lee, G. Ira, G. Liberi, A. Arbel-Eden, M. Foiani and J.E. Haber. (2002) Recovery from checkpoint-mediated arrest after repair of a double-strand break requires Srs2 helicase. Mol. Cell. 10: 373-385. [abstract]

Sun, K., E. Coïc, Z. Zhou. P. Durrens and J.E. Haber (2002) Saccharomyces forkhead protein Fkh1 regulates donor preference through the recombination enhancer during mating-type switching. Genes Dev. 16: 2085-2096. [abstract]

Lee, S.E., D.A. Bressan, J.H.J. Petrini, and J.E. Haber. (2002) Complementation between N-terminal Saccharomyces cerevisiae mre11 alleles in DNA repair and telomere length maintenance. DNA Repair 1: 27-40. [abstract]

Valencia M, Bentele M, Vaze MB, Herrmann G, Kraus E, Lee SE, Schar P, Haber JE. (2001) NEJ1 controls non-homologous end joining in Saccharomyces cerevisiae. Nature. 414:666-9. PMID: 11740566 [abstract]

Haber JE, Heyer WD. (2001) The fuss about Mus81. Cell. 5:551-4. Review. PMID: 11733053 [abstract]

Haber JE. (2001) Hypermutation: give us a break. Nat Immunol. 10:902-3. No abstract available. PMID: 11577343.

Lee, SE., A. Pellicioli, J. Demeter, M. Vaze, AP. Gasch, A. Malkova, P. Brown, T. Stearns, M. Foiani and J.E. Haber. (2001) Arrest, adaptation and recovery following a chromosome double-strand break in Saccharomyces cerevisiae. Cold Spring Harbor Symp. Quant. Biol. 65: 303-314.

Pellicioli, A., S.E. Lee, C. Lucca, M. Foiani and J.E. Haber (2001) Regulation of Saccharomyces Rad53 checkpoint kinase during adaptation from G2/M arrest. Mol. Cell 7: 293-300. [abstract]

Signon, L., A. Malkova, M. Naylor, and J.E. Haber (2001) Genetic requirements for RAD51- and RAD54-independent break-induced replication repair of a chromosomal double-strand break. Mol. Cell. Biol. 21: 2048-2056. [abstract]

Pâques, F., G.-F. Richard and J.E. Haber (2001) Expansions and contractions in 36-bp minisatellite by gene conversion in yeast Genetics 158:155-66. [abstract]

Malkova, A., L. Singnon, C.B. Schaefer, M.L. Naylor, J.F. Theis, C.S. Newlon and J.E. Haber (2001) RAD51-independent break-induced replication to repair a broken chromosome depends on a distant enhancer site. Genes Dev. 15:1055-1160. [abstract]

Lee, S.E., A. Pellicioli, A. Malkova, M. Foiani and J.E. Haber (2001b) The Saccharomyces recombination protein Tid1p is required for adaptation from G2/M arrest induced by a single double-strand break. Curr. Biol. 11:1053-1057 [abstract]

Kraus E., W.-Y. Leung and J.E. Haber (2001) Break-induced replication: A review and an example in budding yeast.Proc Natl Acad Sci U S A. 98:8255-8262. [abstract]

Malkova A, Klein F, Leung WY, Haber JE (2000) HO endonuclease-induced recombination in yeast meiosis resembles Spo11-induced events. Proc Natl Acad Sci USA. 97:14500-5. [abstract]

Demeter J, Lee SE, Haber JE, Stearns T. (2000) The DNA damage checkpoint signal in budding yeast is nuclear limited. Mol Cell. 6:487-92. [abstract]

Haber JE. (2000) Lucky breaks: analysis of recombination in Saccharomyces. Mutat Res. 451:53-69.

Evans E, Sugawara N, Haber JE, Alani E. (2000) The Saccharomyces cerevisiae Msh2 mismatch repair protein localizes to recombination intermediates in vivo. Mol Cell. 5:789-99. [abstract]

Sugawara N, Ira G, Haber JE. (2000) DNA length dependence of the single-strand annealing pathway and the role of Saccharomyces cerevisiae RAD59 in double-strand break repair. Mol Cell Biol. 20:5300-9. [abstract]

Richard GF, Goellner GM, McMurray CT, Haber JE. (2000) Recombination-induced CAG trinucleotide repeat expansions in yeast involve the MRE11-RAD50-XRS2 complex. EMBO J. 19:2381-90. [abstract]

Studamire B, Price G, Sugawara N, Haber JE, Alani E. (1999) Separation-of-function mutations in Saccharomyces cerevisiae MSH2 that confer mismatch repair defects but do not affect nonhomologous-tail removal during recombination. Mol Cell Biol. 19:7558-67. [abstract]

Richard, G.-F., B. Dujon and J.E. Haber (1999) Double-strand break repair can lead to high frequencies of deletions within short CAG/CTG trinucleotide repeats. Mol. Gen. Genet. 261: 871-82. [abstract]

Paques, F., and J.E. Haber (1999) Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63: 349-404. [abstract]

Holmes, A.M., and J.E. Haber (1999) Double-strand break repair in yeast requires both leading and lagging strand DNA polymerases. Cell 96: 415-24. [abstract]

Lee, S.E., J.K. Moore, A. Holmes, K. Umezu, R.D. Kolodner and J.E. Haber (1998) Saccharomyces Ku70, Mre11/Rad50, and RPA proteins regulate adaptation to G2/M arrest after DNA damage. Cell 94: 399-409. [abstract]

Wu, C., K. Weiss, C. Yang, M. Harris, B.-K. Tye, C.S. Newlon, R.T. Simpson and J.E. Haber (1998) Mcm1 regulates donor preference controlled by the recombination enhancer in Saccharomyces cerevisiae mating-type switching. Genes Dev. 12: 1726-1737. [abstract] [full text]

Pâques, F. and J.E. Haber (1998) Expansions and contractions in a tandem repeat induced by double-strand break repair. Mol. Cell. Biol. 18: 2045-2054. [abstract] [full text]

Bosco, G. and J.E. Haber (1998) Chromosome break-induced DNA replication leads to nonreciprocal translocations and telomere capture. Genetics 150: 1037-47. [abstract]

Nugent, C. I., G. Bosco, L. O. Ross, S. K. Evans, A. P. Salinger, J.K. Moore, J.E. Haber and V. Lundblad (1998) Telomere maintenance is dependent on activities required for end repair of double-strand breaks. Current Biol. 8: 657-660. [abstract]

View Complete Publication List on PubMed: James Haber


Last review: June 4, 2007. E-mail comments or questions to the webmaster.

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