Faculty Guide

Title

Abraham and Etta Goodman Professor of Biology and Director, Rosenstiel Basic Medical Sciences Research Center

Biology
Rosenstiel Basic Medical Sciences Research Center

Expertise

Repair of broken chromosomes. Genetics and molecular biology of yeast meiotic and mitotic recombination. DNA damage responses and checkpoints. Control of recombination donor accessibility (donor preference in mating-type switching). Chromosome dynamics.

Profile

Member of the US National Academy of Sciences, Fellow of the American Academy of Microbiology and the American Association of Arts and Sciences. Thomas Hunt Morgan Medal for Lifetime Achievement in Genetics.

Awards and Honors

2011 Genetics Society of America Thomas Hunt Morgan Medal for lifetime achievement in genetics (2010)

Member, National Academy of Sciences (2010)

Member, American Academy of Arts and Sciences (2009)

Radcliffe Institute Fellowship for 2008/9 (2008)

NIH MERIT award (2007)

elected Secretary Genetics Society of America (2006)

Elected Fellow, American Association for the Advancement of Science (2005)

Keynote Speaker, Keystone Symposium on Mechanisms of DNA Replication and Recombination (2005)

Director, Genetics Society of America (2003)

Keynote Speaker FASEB Summer Research Conference on Recombination (2003)

John Simon Guggenheim Fellowship (2001)

Giovanni Magni Lecturer, Milan, Italy (2000 - 2001)

Guggenheim Foundation Fellowship (1999)

Abraham and Etta Goodman Chair in Biology (1996)

Fellow, American Academy of Microbiology (1996)

Sloan Foundation Sabbatical Supplement (1990)

National Science Foundation Postdoctoral Fellowship (1970)

US Public Health Service Traineeship (1965 - 1969)

Woodrow Wilson Fellowship (honorary) (1965)

Courses Taught

BIOL	22a	Genetics and Molecular Biology
BIOL	122a	Molecular Genetics
BIOL	200a	Proseminar
BIOL	316a	Mechanisms of Recombination
BIOL	316b	Mechanisms of Recombination
BIOL	316d	Mechanisms of Recombination
BIOL	320a	Current Topics in Chromatin Structure
BIOL	320b	Current Topics in Chromatin Structure

Scholarship

Haber, James E. "Yeast Mating-Type Genes." Yeastbook. vol. (in press) Ed. A. Hinnebusch. Genetics, 2012 (forthcoming)

Dotiwala, F., Eapen, V.V., Harrison, J.C., Arbel-Eden, A., Ranade, V., Yoshida, S., and Haber, J.E.. "DNA damage checkpoint triggers autophagy to regulate the initiation of anaphase." Proceedings of the National Academy of Sciences of the United States of America 110. (2013): E41-49.

Eapen, V.V., and Haber, J.E.. "DNA damage signaling triggers the cytoplasm-to-vacuole pathway of autophagy to regulate cell cycle progression." Autophagy 9. (2013): 440-441.

Sugawara, N., and Haber, J.E.. "Monitoring DNA recombination initiated by HO endonuclease." Methods Mol Biol 920. (2013): 349-370.

Eapen, V.V., Sugawara, N., Tsabar, M., Wu, W.H., and Haber, J.E.. "The Saccharomyces cerevisiae chromatin remodeler Fun30 regulates DNA end resection and checkpoint deactivation." Molecular and cellular biology 32. (2012): 4727-4740.

Haber, James E. "Mating-type genes and MAT switching in Saccharomyces cerevisiae." Genetics 191. (2012): 33-64.

J Li, E Coïc, K Lee, C-S Lee, Q Wu and Haber, James E. "Regulation of Budding Yeast Mating-Type Switching Donor Preference by the FHA Domain of Fkh1." PLoS Genetics in press. (2012).

Malkova, A and Haber, James E. "Mutations Arising during Recombination." Annu Rev Genet,. vol. 46, 2012. 455-473.

Coïc, E, Marin, J, Kondev, J and Haber, JE. "Dynamics of homology searching during gene conversion in Saccharomyces cerevisiae revealed by donor competition." Genetics 189. 4 (2011): 1225-33.

Hicks, W. M., Yamaguchi, M., Haber, J. E.. "Inaugural Article: Real-time analysis of double-strand DNA break repair by homologous recombination." Proc Natl Acad Sci U S A (2011).

Kim, J. A., Hicks, W. M., Li, J., Tay, S. Y., Haber, J. E.. "Protein phosphatases pph3, ptc2, and ptc3 play redundant roles in DNA double-strand break repair by homologous recombination." Mol Cell Biol 31. 3 (2011): 507-16.

Dotiwala, F., Harrison, J.C., Jain, S., Sugawara, N., and Haber, J.E.. "Mad2 prolongs DNA damage checkpoint arrest caused by a double-strand break via a centromere-dependent mechanism.." Curr Biol. 20. (2010): 328-332.

Hicks, W. M., Kim, M., Haber, J. E.. "Increased mutagenesis and unique mutation signature associated with mitotic gene conversion." Science 329. 5987 (2010): 82-5.

Lydeard, J. R., Lipkin-Moore, Z., Jain, S., Eapen, V. V., Haber, J. E.. "Sgs1 and exo1 redundantly inhibit break-induced replication and de novo telomere addition at broken chromosome ends." PLoS Genet 6. 5 (2010): e1000973.

Lydeard, J. R., Lipkin-Moore, Z., Sheu, Y. J., Stillman, B., Burgers, P. M., Haber, J. E.. "Break-induced replication requires all essential DNA replication factors except those specific for pre-RC assembly." Genes Dev 24. 11 (2010): 1133-44.

Saponaro, M., Callahan, D., Zheng, X., Krejci, L., Haber, J.E., Klein, H.L., and Liberi, G.. "Cdk1 targets Srs2 to complete synthesis-dependent strand annealing and to promote recombinational repair.." PLoS Genet 6. 2 (2010): e1000858.

Toh, G. W., Sugawara, N., Dong, J., Toth, R., Lee, S. E., Haber, J. E., Rouse, J.. "Mec1/Tel1-dependent phosphorylation of Slx4 stimulates Rad1-Rad10-dependent cleavage of non-homologous DNA tails." DNA Repair (Amst) 9. 6 (2010): 718-26.

Jain, S., Sugawara, N., Lydeard, J., Vaze, M., Tanguy Le Gac, N., Haber, J. E.. "A recombination execution checkpoint regulates the choice of homologous recombination pathway during DNA double-strand break repair." Genes Dev 23. 3 (2009): 291-303.

Kim, J. A., Haber, J. E.. "Chromatin assembly factors Asf1 and CAF-1 have overlapping roles in deactivating the DNA damage checkpoint when DNA repair is complete." Proc Natl Acad Sci U S A 106. 4 (2009): 1151-6.

Prakash, R., Satory, D., Dray, E., Papusha, A., Scheller, J., Kramer, W., Krejci, L., Klein, H., Haber, J. E., Sung, P., Ira, G.. "Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination." Genes Dev 23. 1 (2009): 67-79.

Coic, E., Feldman, T., Landman, A. S., Haber, J. E.. "Mechanisms of Rad52-independent spontaneous and UV-induced mitotic recombination in Saccharomyces cerevisiae." Genetics 179. 1 (2008): 199-211.

Coic, E., Feldman, T., Landman, A. S., Haber, J. E.. "Mechanisms of Rad52-independent spontaneous and UV-induced mitotic recombination in Saccharomyces cerevisiae." Genetics 179. 1 (2008): 199-211.

Coic, E., Feldman, T., Landman, A. S., Haber, J. E.. "Mechanisms of Rad52-independent spontaneous and UV-induced mitotic recombination in Saccharomyces cerevisiae." Genetics 179. 1 (2008): 199-211.

Haber, J. E.. "Alternative endings." Proc Natl Acad Sci U S A 105. 2 (2008): 405-6.

Haber, J. E.. "Evolution of Models of Homologous Recombination." Genome Dynamics and Stability. vol. 3 Ed. Egel, R.. Berlin: Springer-Verlag, 2008. (in press).

Jazayeri, A., Balestrini, A., Garner, E., Haber, J. E., Costanzo, V.. "Mre11-Rad50-Nbs1-dependent processing of DNA breaks generates oligonucleotides that stimulate ATM activity." Embo J 27. 14 (2008): 1953-62.

Kim, H. S., Vijayakumar, S., Reger, M., Harrison, J. C., Haber, J. E., Weil, C., Petrini, J. H.. "Functional interactions between sae2 and the mre11 complex." Genetics 178. 2 (2008): 711-23.

Cortes-Ledesma, F., de Piccoli, G., Haber, J. E., Aragon, L., Aguilera, A.. "SMC Proteins, new players in the maintenance of genomic stability." Cell Cycle 6. 8 (2007): 914-918.

De Koning, L., Corpet, A., Haber, J. E., Almouzni, G.. "Histone chaperones: an escort network regulating histone traffic." Nat Struct Mol Biol 14. 11 (2007): 997-1007.

Dotiwala, F., Haase, J., Arbel-Eden, A., Bloom, K., Haber, J. E.. "The yeast DNA damage checkpoint proteins control a cytoplasmic response to DNA damage." Proc Natl Acad Sci U S A 104. 27 (2007): 11358-63.

Flott, S., Alabert, C., Toh, G. W., Toth, R., Sugawara, N., Campbell, D. G., Haber, J. E., Pasero, P., Rouse, J.. "Phosphorylation of Slx4 by Mec1 and Tel1 regulates the single-strand annealing mode of DNA repair in budding yeast." Mol Cell Biol 27. (2007): 6433-45.

Haber, J.E.. "Decisions, decisions: donor preference during budding yeast mating-type switching." Sex in fungi: molecular determination and evolutionary implications. Ed. Heitman, J., Kronstad, J.W., Taylor, J.W., Casselton, L.A.. ASM Press, 2007. 159-170.

Kim, J. A., Kruhlak, M., Dotiwala, F., Nussenzweig, A., Haber, J. E.. "Heterochromatin is refractory to gamma-H2AX modification in yeast and mammals." J Cell Biol 178. 2 (2007): 209-18.

Lydeard, J. R., Jain, S., Yamaguchi, M., Haber, J. E.. "Break-induced replication and telomerase-independent telomere maintenance require Pol32." Nature 448. 7155 (2007): 820-3.

Morrison, A. J., Kim, J. A., Person, M. D., Highland, J., Xiao, J., Wehr, T. S., Hensley, S., Bao, Y., Shen, J., Collins, S. R., Weissman, J. S., Delrow, J., Krogan, N. J., Haber, J. E., Shen, X.. "Mec1/Tel1 Phosphorylation of the INO80 Chromatin Remodeling Complex Influences DNA Damage Checkpoint Responses." Cell 130. 3 (2007): 499-511.

Torres-Rosell, J., De Piccoli, G., Cordon-Preciado, V., Farmer, S., Jarmuz, A., Machin, F., Pasero, P., Lisby, M., Haber, J. E., Aragon, L.. "Anaphase onset before complete DNA replication with intact checkpoint responses." Science 315. 5817 (2007): 1411-5.

Coic, E., Richard, G. F., Haber, J. E.. "Saccharomyces cerevisiae donor preference during mating-type switching is dependent on chromosome architecture and organization." Genetics 173. 3 (2006): 1197-206.

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

De Piccoli, G., Cortes-Ledesma, F., Ira, G., Torres-Rosell, J., Uhle, S., Farmer, S., Hwang, J. Y., Machin, F., Ceschia, A., McAleenan, A., Cordon-Preciado, V., Clemente-Blanco, A., Vilella-Mitjana, F., Ullal, P., Jarmuz, A., Leitao, B., Bressan, D., D. "Smc5-Smc6 mediate DNA double-strand-break repair by promoting sister-chromatid recombination." Nat Cell Biol 8. 9 (2006): 1032-4.

Haber, J. E., Debatisse, M.. "Gene amplification: yeast takes a turn." Cell 125. 7 (2006): 1237-40.

Haber, J. E.. "Chromosome breakage and repair." Genetics 173. 3 (2006): 1181-5.

Haber, J. E.. "Transpositions and translocations induced by site-specific double-strand breaks in budding yeast." DNA Repair (Amst) 5. 9-10 (2006): 998-1009.

Harrison, J. C., Haber, J. E.. "Surviving the breakup: the DNA damage checkpoint." Annu Rev Genet 40. (2006): 209-35.

Ira, G., Satory, D., Haber, J. E.. "Conservative inheritance of newly synthesized DNA in double-strand break-induced gene conversion." Mol Cell Biol 26. 24 (2006): 9424-9.

Keogh, M. C., Kim, J. A., Downey, M., Fillingham, J., Chowdhury, D., Harrison, J. C., Onishi, M., Datta, N., Galicia, S., Emili, A., Lieberman, J., Shen, X., Buratowski, S., Haber, J. E., Durocher, D., Greenblatt, J. F., Krogan, N. J.. "A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery." Nature 439. 7075 (2006): 497-501.

McEachern, M. J., Haber, J. E.. "Break-induced replication and recombinational telomere elongation in yeast." Annu Rev Biochem 75. (2006): 111-35.

Sugawara, N., Haber, J. E.. "Repair of DNA double strand breaks: in vivo biochemistry." Methods Enzymol 408. (2006): 416-29.

Valencia-Burton, M., Oki, M., Johnson, J., Seier, T. A., Kamakaka, R., Haber, J. E.. "Different mating-type-regulated genes affect the DNA repair defects of Saccharomyces RAD51, RAD52 and RAD55 mutants." Genetics 174. 1 (2006): 41-55.

Clatworthy, A. E., Valencia-Burton, M. A., Haber, J. E., Oettinger, M. A.. "The MRE11-RAD50-XRS2 complex, in addition to other non-homologous end-joining factors, is required for V(D)J joining in yeast." J Biol Chem 280. 21 (2005): 20247-52.

Corda, Y., Lee, S. E., Guillot, S., Walther, A., Sollier, J., Arbel-Eden, A., Haber, J. E., Geli, V.. "Inactivation of Ku-mediated end joining suppresses mec1Delta lethality by depleting the ribonucleotide reductase inhibitor Sml1 through a pathway controlled by Tel1 kinase and the Mre11 complex." Mol Cell Biol 25. 23 (2005): 10652-64.

Liberi, G., Maffioletti, G., Lucca, C., Chiolo, I., Baryshnikova, A., Cotta-Ramusino, C., Lopes, M., Pellicioli, A., Haber, J. E., Foiani, M.. "Rad51-dependent DNA structures accumulate at damaged replication forks in sgs1 mutants defective in the yeast ortholog of BLM RecQ helicase." Genes Dev 19. 3 (2005): 339-50.

Malkova, A., Naylor, M. L., Yamaguchi, M., Ira, G., Haber, J. E.. "RAD51-dependent break-induced replication differs in kinetics and checkpoint responses from RAD51-mediated gene conversion." Mol Cell Biol 25. 3 (2005): 933-44.

McEachern, M. J., Haber, J. E.. "Telomerase-independent chromosome maintenance in yeast." Telomeres. Ed. T. de Lange, V. Lundblad, E. Blackburn. Cold Spring Harbor, NY: Cold Spring Harbor Press, 2005

Haber,James E and Wang X. "Role of Saccharomyces Single-Stranded DNA-Binding Protein RPA in the Strand Invasion Step of Double-Strand Break Repair." PLoS Biol. 2. (2004): 104-112.

Haber,James E, Bressan DA, J. Vazquez. "Mating type-dependent constraints on the mobility of the left arm of yeast chromosome III." J. Cell Biol. 164. (2004): 361-371.

Haber,James E, Ira G, Pellicio A, Balijja A, Want X, Fiorani S. Carotenuto W, Liberi G, Bressan D, Wan L,. "DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1." (2004): 1011-7.

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

Haber,James E, Kaye, J. A., Melo, J. A., Cheung, S. K., Vaze, M. B., and Toczyski, D. P.. "DNA breaks promote genomic instability by impeding proper chromosome segregation." Curr Biol 14. (2004): 2096-2106.

Haber,James E, Kaye, J. A., Melo, J.A. Cheung, S. K., Vaze M.B, and Tocayski, D.P.. "DNA breaks promote genomic instability by impeding proper chromosome segregation." Curr. Biol (2004): 2096-2106.

Haber,James E, Lucca C, Vanoli F, Cotta-Ramusino C, Pellicioli A, Liberi G, Foiani M.. "Checkpoint-mediated control of replisome-fork association and signalling in response to replication pausing.." Oncogene Nature 23. (2004): 1206-1213.

Haber,James E, Malkova, A., Swanson, J., German, M., McCusker J.H. Housworth E. A. Stahl, F.W.. "Gene conversion and crossing over along the 405-kb left arm of Saccharomyces cerevisie chromosome VII." Genetics (2004): 49-63.

Haber,James E, Malkova, A., Swanson, J., German, M., McCusker, J. H., Housworth, E. A., Stahl, F. W.. "Gene conversion and crossing over along the 405-kb left arm of Saccharomyces cerevisiae chromosome VII." Genetics 168. (2004): 49-63.

Haber,James E, Miyazaki, T., Bressan, D. A., Shinohara, M., and Shinohara, A.. "In vivo assembly and disassembly of Rad51 and Rad52 complexes during double-strand break repair." Embo J 23. (2004): 939-949.

Haber,James E, Miyazaki, T., Bressan, D.A. Shinohara, M., and Shinohara. "In vivo assembly and disasembly of Rad52 compleses during double-strand break repair." (2004): 939-949.

Haber,James E, Morrison, A. J., Highland, J., Krogan, N. J., Arbel-Eden, A., Greenblatt, J. F., and Shen, X.. "(2004). INO80 and gamma-H2AX Interaction Links ATP-dependent chromatin remodeling to DNA damage repair." Cell 119. (2004): 767-775.

Haber,James E, Morrison, A.J. Highland, J. Krogan, N.J. Arbel-Eden, A. Greenbalt, J.F and Shen X. "IN080 and gamma-H2AX Interaction Links ATP-dependent chromatin remodeling to DNA damage repair." (2004): 767-775.

Haber,James E, Shroff, R., Arbel-Eden, A. Pilch, D., Ira, G., Bonner, W. M., Petrini, J. and Lichten, M.. "Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break." Curr Biol (2004): 1703-1711.

Haber,James E, Shroff, R., Arbel-Eden, A., Pilch, D., Ira, G., Bonner, W. M., Petrini, J. H., and Lichten, M.. "Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break." Curr Biol 14. (2004): 1703-1711.

Haber,James E, Sugawara, N., Goldfarb, T., Studamire, B., Alani, E.. "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. (2004): 9315-9320.

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

Haber,James E, Wang, X., Ira, G., Tercero, J. A., Holmes, A. M., Diffley, J. F.. "Role of DNA replication proteins in double-strand break-induced recombination in Saccharomyces cerevisiae." Mol Cell Biol 24. (2004): 6891-6899.

Haber,James E, Yu J, K. Marshall, M. Yamaguchi and C.F. Weil. "Microhomology-dependent end joining and repair of transposon-induced DNA hairpins by host factors in Saccharomyces cerevisiae." Mol. Cell Biol. 24. (2004): 1351-64.

Haber,James E. "Telomeres thrown for a loop.." (2004).

Haber,James E and Sugawara, N., X. Wang. "In vivo roles of Rad52, Rad54, and Rad55 proteins in Rad51-mediated homologous recombination." Mol. Cell. 12. (2003): 209-219.

Haber,James E, Clatworthy, A.E., M.A. Valencia, and M.A. Oettinger. "V(D)J Recombination and RAG-Mediated Transposition in Yeast." Mol. Cell 12. (2003): 489-499..

Haber,James E, G. Ira, A. Malkova and N. Sugawara. "Repairing a double-strand chromosome break by homologous recombination: revisiting Robin Hollidays model." Phil. Trans. R. Soc. Lond. 359. (2003): 79-86.

Haber,James E, Ira, G., A. Malkova, G. Liberi, M. Foiani. "Srs2 and Sgs1 ¿Top3 suppress crossovers during double-strand break repair in yeast.." Cell 115. (2003): 401-411.

Haber,James E, Lee, S.E., A. Pellicioli, M.B. Vaze, N. Sugawara, A. Malkova, M. Foiani. "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. (2003).

Haber,James E, Leroy, C. S.E. Lee, M.B. Vaze, F.Ochsenbien, R. Guerois, and M.-C. Marsolier-Kergoat. "(2003) PP2C phosphatases Ptc2 and Ptc3 are required for DNA checkpoint inactivation after a double-strand break.." Mol. Cell 11. (2003): 1-20.

Haber,James E, Ma, J.-M., E.M. Kim, and S.E. Lee. "Yeast Mre11 and Rad1 proteins define a Ku-independent mechanism to repair double strand breaks lacking overlapping end sequences." Mol. Cell. Biol. 23. (2003): 8820-8828.

Haber,James E. "Aging: the sins of the parents." Curr. Biol. 13. (2003): R843-R845.