Prof. Martin Kupiec

Education

1977-1978 B.Sc. Hebrew University, Jerusalem, Biology

 

1980-1985 PhD. Hebrew University, Jerusalem, Genetics

 

Employment

2003-present Full Professor, Department of Molecular Microbiology and Biotechnology, Tel Aviv University.

2002-2004 Chairman, Department of Molecular Microbiology and Biotechnology, Tel Aviv University.

2000-2001 Visiting Scientist, Whitehead Institute, M.I.T., Cambridge, MA, USA

1998-2003 Associate Professor, Department of Molecular Microbiology and Biotechnology, Tel Aviv University.

1994-1995 Visiting Scientist, Department of Genetics, University of Washington, Seattle, WA, USA.

1992-1998 Senior lecturer, Department of Molecular Microbiology and Biotechnology, Tel Aviv University.

1988-1992 Lecturer, Department of Molecular Microbiology and Biotechnology, Tel Aviv University.

1985-1988 Research associate, Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL., USA. Area: Homologous recombination in yeast

 

Other Appointments and Awards

1988 The Alon Fellowship Prize

1994-1995 Visiting Scientist, Department of Genetics, University of Washington, Seattle, WA, USA

1999 The Prof. Nathan Treinin Prize, by the Israel Cancer Association

1999-present Editor, Current Genetics.

2000-2001 Visiting Scientist, Whitehead Institute, M.I.T., Cambridge, MA, USA.

2003-2013 Editor, FEMS Microbiology Reviews.

2006-2009 Board of Directors, The Genetic Society of Israel.

2007 The Tel Aviv University Prize for Research Excellence.

2008-present The Pasha Gol Chair for Applied Microbiology

2010-present Editor, Genetics Research International.

2011-present Editorial Board member, Molecular and Cellular Biology.

2011-present Elected Fellow of the American Academy of Microbiology.

2011-present Director, The Joan and Haim Constantiner Center for Molecular Genetics.

2012-present Editor, Journal of Fungal Genomics and Biology.

2012-present Editorial Board Member, Open Access Genetics.

2012-present Editorial Board Member, Open Access Genetics.

2012-present Editorial Board Member, Open Access Genetics.

2013-present President, Genetic Society of Israel.

 

The Kupiec laboratory uses “the awesome power of yeast genetics” to investigate basic universal processes that are very hard to study in other organisms. Our basic methodology involves Molecular Biology techniques. As yeast is today the best understood eukaryotic organism, with more than half of its genes with a known function/activity, the new genetic and molecular tools developed in yeast have jump-started a REVOLUTION IN BIOLOGY: Systems Biology. We are able, for the first time, to ask very basic questions about the way genomes are organized, genes interact, proteins talk to each other, etc. This genome-wide approach requires novel tools, which we are helping to develop in cooperation with people from Computer Science at TAU. Most of the essential pathways, complexes and genes involved in basic cellular processes are conserved in evolution, and human orthologs are present for most of the genes we study.

Here are some of the basic biological questions that we are trying to understand, using the baker’s yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe) as a model organisms:

• DNA repair:  Our cells are constantly exposed to radiation and chemicals that cause damage to the DNA or even break the chromosomes in pieces. Even natural cellular metabolism creates oxidative stress and DNA damage. Luckily we have efficient mechanisms to repair the damage. 
• Stability of the eukaryotic genome: Normal cells have remarkably stable karyotypes. You can easily identify to what species a cell belongs, just by looking at its chromosomes. However, cancer cells lose this stability, and start accumulating translocations, deletions, amplifications, etc. Many of the endpoints of these rearrangements fall in repeated sequences (sometimes called “junk DNA”) that fill-up our genomes. What prevents a high level of chromosomal aberrations as a consequence of recombination between repeated sequences? 
• Telomeres:  Telomeres are nucleoprotein complexes at the end of the eukaryotic chromosomes. We would like to know how do all these genes work together to regulate telomere length. Are there several pathways? Complexes? What are the interactions between the various elements? To answer these questions we are using a combination of Molecular Biology, Systems Biology, Genetics and Biochemistry. Bioinformatic models are used as a basis to plan possible experiments. The results are then incorporated into the model, to generate more predictions in a continuous cycle that progressively refines the model.
• The TOR protein kinase:  The TOR protein kinases exhibit a conserved role in regulating cellular growth and proliferation. We would like to answer some of the following questions: What is the function of each of the Tor proteins? What is the nature of their interactions? How are they regulated? Why are mammalian cells and budding yeast so affected by rapamycin (an anticancer drug in clinical trials), whereas fission yeast can grow in its presence? How do the Tor proteins integrate signals from the environment to know when to grow? And how do they talk to the cell cycle machinery to coordinate growth (in volume) with cell division?

 

For a full list

 

Since 2009

Tuller T, Kupiec M. and E. Ruppin (2009) Co-evolutionary networks of genes and cellular processes across fungal species. Genome Biol. 10:R48.

 

Schonbrun, M., Laor D., Lopez-Maury-L., Bahler J., M. Kupiec and Weisman R. (2009) The TORC2 complex regulates DNA damage response, gene silencing, and telomere length maintenance. Mol. Cell. Biol., 29(16):4584-4594.

 

Yosef N., Ungar L., Zalckvar E., Kimchi A., Kupiec M., Ruppin E., Sharan R. (2009) Toward accurate reconstruction of functional protein networks. Mol Syst Biol. 5:248.

 

Mitchell A., Romano G.H., Groisman B., Yona A., Dekel E., Kupiec M., Dahan O. and Y. Pilpel (2009) Adaptive prediction of environmental changes by microorganisms. Nature 460(7252):220-224. News and views in: Nature (2009) 460(7252):181 and Cell 138:409 (2009).

 

Mazor, Y. and M. Kupiec (2009) Developmentally regulated MAPK pathways modulate heterochromatin in Saccharomyces cerevisiae. Nucl. Acid Research 37(14):4839-4849.

 

Ungar, L., Sela, Y., Yosef, N., Sharan, R. Ruppin, E. and M. Kupiec (2009) A genome-wide screen for essential yeast genes that affect telomere length maintenance. Nucl. Acid Research 37(12):3840-3849.

 

Yosef N., M. Kupiec, Ruppin E. and Sharan R. (2009) A complex-centric view of protein network evolution. Nucleic Acid Research 37(12):e88.

 

Fridman, V., Gerson-Gurwitz A., Movshovitz N., Kupiec, M. and L. Gheber (2009) Midzone organization restricts interpolar microtubule plus-end dynamics during spindle elongation. EMBO Reports, 10: 387-393.

 

Tuller, T., Rubinstein U., Bar D., Gurevitch M., Ruppin E. and M. Kupiec (2009) Higher-order genomic organization of cellular functions in yeast. J Comput Biol. 16: 303-316.

 

Parnas O, Zipin-Roitman A, Mazor Y, Liefshitz B, Ben-Aroya S, M. Kupiec (2009) The ELG1 clamp loader plays a role in sister chromatid cohesion. PLoS ONE 4: e5497.

 

Agmon, N., Pur, S., Liefshitz, B. and M. Kupiec (2009) Analysis of repair mechanism choice during homologous recombination. Nucl. Acid Res. 37: 5081-5092.

 

Tuller, T., Ruppin E. and M. Kupiec (2009) Properties of untranslated regions of the S. cerevisiae genome. BMC Genomics, 10: 391-398.

 

Tuller, T. Birin, H., Gophna, U., Kupiec, M. and E. Ruppin (2010) Reconstructing Ancestral Genomic Sequences by Co-Evolution. Genome Research 20: 122-132.

 

Ben-Aroya, S., Agmon N., Yuen, K., Kwok, T, McManus K., Kupiec M. and P. Hieter (2010) Proteasome nuclear activity affects chromosome stability by controlling the turnover of Mms22, a protein important for DNA repair. PLoS Genetics 6: e1000852.

 

Romano, G.H., Gurvich Y., Lavi O., Ulitsky I., Shamir, R. and M. Kupiec (2010) Different sets of QTLs affect fitness variation in yeast. Molec. Systems Biology 6:346-357.

 

Tuller, T., Waldman Y., Kupiec M. and E. Ruppin (2010) Translation Efficiency Is Determined By Both Codon Bias and Folding Energy. Proc. Natl. Acad. Sci. USA 107:3645-3650.

 

Gat-Viks, I., Meller, R., Kupiec, M. and R. Shamir (2010) Understanding gene sequence variation in the context of transcription regulation in yeast. PLoS Genetics 6: e1000800.

 

Tuller, T., Felder, Y. and M. Kupiec (2010). Discovering local patterns of co-evolution: computational aspects and biological examples. BMC Bioinformatics 11: 43- 62.

 

Parnas O., Zipin-Roitman, A., Pfander, B., Liefshitz, B., Mazor, Y., Ben-Aroya, S., Jentsch, S. and M. Kupiec (2010) Elg1, an alternative subunit of the RFC clamp loader, preferentially interacts with SUMOylated PCNA. EMBO J. 29: 2611 - 2622.

 

Parnas, O. and M. Kupiec (2010) Establishment of sister chromatid cohesion: The role of the clamp loaders. Cell Cycle 9: 4615. (Invited comment on: Maradeo et al., “Rfc5p regulates alternate RFC complex functions in sister chromatid pairing reactions in budding yeast”. Cell Cycle 2010; 9:4370–4378.

 

Tuller, T., Birin H., Kupiec, M., and Eytan Ruppin (2010) Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Denitions, Computational Issues, and Biological Examples. Journal of Computational Biology, 17:1327-1344.

 

Barzel A, Naor A, Privman E, Kupiec M. and U. Gophna (2011) Homing endonucleases residing within inteins: evolutionary puzzles awaiting genetic solutions. Biochem Soc Trans. 39:169-73.

 

Zhang X., Kupiec, M., Gophna, U. and T. Tuller (2011) Analysis of Co-evolving Gene Families Using Evolutionarily Reciprocal Orthologous Modules. Genome Biology and Evolution 3:413-423.

 

Barzel, A., Privman, E., Pe’eri, M., Naor, A., Sachar, E., Burstein, D., Lazary, R., Gophna, U., Pupko, T. and M. Kupiec (2011) Native homing endonucleases can target conserved target sites in humans and in animal models. Nucleic Acid Research 39: 6646-6659.

 

Tuller, T., Girshovich, Y., Sella Y., Kreimer A., Freilich S., Kupiec, M., Gophna, U. and E. Ruppin (2011) Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res. 2011 Feb 22.

 

Barzel, A., Obolski U., Gogarten, J.P., Kupiec, M. and Hadany L. (2011) Home and away, the evolutionary dynamics of homing endonucleases. BMC Evol Biology 11: 324.

 

Agmon, N., Yovel, M., Harari, Y., Liefshitz, B. and M. Kupiec (2011) The role of Holliday Junction resolvases in the repair of spontaneous and induced DNA damage. Nucleic Acid Research 39: 7009-7019.

 

Reuveni, S., I. Meilijson, M. Kupiec, E. Ruppin and T. Tuller (2011). Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model. PLoS Comput Biol. 7(9):e1002127.

 

Parnas, O., Amishay R., Liefshitz, B., Zipin-Roitman A., and M. Kupiec (2011) Elg1, the major subunit of an alternative RFC complex, interacts with SUMO-processing proteins. Cell Cycle 10: 17.

 

Liefshitz, B. and M. Kupiec (2011) The roles of RSC, Rad59 and cohesin in DSB repair. Mol Cell Biol. 2011 Oct;31(19):3921-3. Epub 2011 Aug 15. (invited commentary on Oum et al., “RSC facilitates Rad59-dependent homologous recombination between sister chromatids by promoting cohesin loading at DNA double strand breaks”. Mol Cell Biol. 2011 Oct;31(19):3924-37. Epub 2011 Aug 1)

 

Tuller, T., Veksler, I., Gazit, N., Kupiec, M., Ruppin, E., M. Ziv-Ukelson (2011) Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol. 12: R110.

 

Ungar, L., Harari, Y. Toren, A. and M. Kupiec (2011) Tor Complex 1 controls telomere length by regulating the level of Ku. Current Biology 21: 2115-2120.

 

Freilich, S., R. Zarecki, O. Eilam, E.Shtifman-Segal, C.S.Henry, M. Kupiec, U. Gophna, R. Sharan and E. Ruppin (2011) Competitive and cooperative metabolic interactions in bacterial communities. Nature Communications 2:589. doi: 10.1038/ncomms1597.

 

Harari, Y., Rubinstein L. and M. Kupiec (2011) An anti-checkpoint role for Rif1 (invited commentary on Xue et al: “A novel checkpoint and RPA inhibitory pathway regulated by Rif1”. PLoS Genet 7: e1002417) PLoS Genetics e1002421. Epub 2011 Dec 15.

 

Ben-Shitrit, T., Yosef, N., Shemesh, K., Sharan, R., Ruppin, E., and M. Kupiec (2012) Systematic identification of gene annotation errors in the widely used yeast mutation collections. Nature Methods 9: 373-378. News and Views in: Baryshnikova, A. and B. Andrews (2012) Neighboring-gene effect: a genetic uncertainty principle. Nature Methods 9: 341–343.

 

Dominissini, D., Moshitch-Moshkovitz, S.,Schwartz, S., Salmon-Divon, M., Ungar, L., Osenberg, S., Cesarkas, K., Jakob-Hirsch, J., Amariglio, N., Kupiec, M., Sorek, R., and G. Rechavi (2012) Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485: 201-206.

 

Silberberg Y, Gottlieb A, Kupiec M., Ruppin E, Sharan R. (2012) Large-scale elucidation of drug response pathways in humans. J Comput Biol. 19:163-174.

 

Kupiec, M. and R. Weisman (2012) TOR links starvation responses to telomere length maintenance. Cell Cycle 11: 1-4.

 

Gazy, I. and M. Kupiec (2012) The importance of being modified: PCNA modification and DNA damage response. Cell Cycle. 2012 Jul 15;11(14).

 

Mazón G., Lam A.F., Ho C.K., Kupiec M. and L.S. Symington (2012) The Rad1-Rad10 nuclease promotes chromosome translocations between dispersed repeats. Nat. Struct. Mol. Biol. 19: 964-971. nsmb.2359.

 

Yona,A.H., Manor,Y.S., Romano,G.H., Herbst,R.H., Mitchell,A., Kupiec,M., Dahan, O. and Y. Pilpel (2012) Chromosomal duplication is a transient evolutionary solution to stress. Proc. Nat. Acad. Sci. USA 109:21010-21015.

 

Singh, S., Shemesh, K., Liefshitz B. and M. Kupiec (2013) Genetic and physical interactions between the yeast ELG1 gene and orthologs of the Fanconi Anemia pathway. Cell cycle 12:1625-1636.

 

Agmon, N., Liefshitz, B., Zimmer, C., Fabre, E. and M. Kupiec (2013) Effect of nuclear architecture on the efficiency of double-strand break repair. Nature Cell Biology 15: 694-699.

 

Gazy, I. Liefshitz, B., Bronstein, A., Parnas, O., Atias, N., Sharan, R. and M. Kupiec (2013) A genetic screen for high-copy-number suppressors of the synthetic lethality between elg1 and srs2 in yeast. Genes, Genomes and Genetics 3: 917-926.

 

Schonbrun , M., Kolesnikov, M., Kupiec M. and R. Weisman (2013) TORC2 is required to maintain genome stability during S phase in fission yeast. Journal of Biochemical Chemistry 288:19649-19660.

 

Romano, G-H, Harari, Y., Yehuda, T., Podhorzer, A., Rubinstein, L., Shamir, R., Gottlieb, A., Silberberg, Y., Pe’er D., Ruppin, E., Sharan, R. and M. Kupiec (2013) Environmental stresses disrupt telomere length homeostasis. PLoS Genetics, 9(9):e1003721. doi:10.1371/journal.pgen.1003721.

 

Harari, Y., Romano, G.-H., Ungar, L. and M. Kupiec (2013) Nature vs nurture: Interplay between the genetic control of telomere length and environmental factors. Cell Cycle 12:3465-3470.

 

Gazy, I. and M. Kupiec (2013) Genomic instability and repair mediated by common repeated sequences. Proc. Natl. Academy Sci. USA. 110:19664-19665. Comment on Aksenova AY, et al. (2013) Genome rearrangements caused by interstitial telomeric sequences in yeast. Proceedings of the National Academy of Sciences USA 110:19866-19871.

 

Laor, D., Cohen, A., Pasmanik-Chor, M., Oron-Karni, V., Kupiec, M. and R. Weisman (2013) Isp7 is a novel regulator of amino acid uptake in the TOR signaling pathway. Mol. Cell. Biol., in press.

 

Kupiec, M. (2014) Biology of telomeres: lessons from budding yeast. FEMS Microbiology Reviews, in press.

 

Harari, Y. and M. Kupiec (2014) Genome-wide studies in budding yeast dissect the mechanisms that maintain telomere length. Fungal Genomics, in press.