Rodney J. Rothstein, PhD

Profile Headshot

Overview

I began my career interested in mechanisms of genetic recombination and chose to use yeast as a model system since I could combine genetic and molecular biological tools that were rapidly being developed in the ‘70s and ‘80s. Early on we showed that plasmids containing double-strand DNA breaks were repaired using homologous genomic sequences, which lead directly to genetic engineering, gene disruption and later to the double-strand break repair model. Using the tools that we developed, I next turned my attention to both study and search for genes involved in genome stability. We examined many of the central genes involved in genetic recombination (RAD52, RAD51, RAD1, RAD10 etc.) and also discovered new key players in this process, including TOP3, SGS1, the Shu complex and IRC genes. Since DNA repair is essential for preserving genome integrity in all organisms, it is not surprising that most of these genes are evolutionarily conserved. Several years ago, using fluorescently tagged proteins, we developed yeast strains that allow us to follow events from the initiation of the damage to its repair. These strains allow us to study the movement of chromosomes and to determine their spatiotemporal relationships during the DNA damage response, uncovering the inherent choreography of this process. The lab is also interested in using the power of yeast genetic screens to identify new connections between cellular pathways. By overexpressing a protein from one pathway, we look for genetic interactions with mutations in another pathway that cause a “synthetic” effect using colony growth as a metric. As an example, we have found new connections in the secretory pathway in a collaboration with Elizabeth Miller and Randy Schekman. We are also using yeast as a model to study cancer and cancer predisposition. We are especially interested in gene overexpression, an underexploited area of cancer biology. We find that almost all of the pathways identified in our yeast screens are conserved in mammalian cells. We have on-going collaborations with many members of my department as well as the Cancer Center, including Alberto Ciccia, Chao Lu, Zhiguo Zhang, Dawn Hershman and Gary Schwartz to exploit our yeast findings in mammalian cells. During this COVID-19 pandemic, we have turned our attention to using our yeast expertise to explore the way SARS-CoV-2 viral proteins affect host pathways. We have at our disposal humanized yeast strains containing human proteins with which viral proteins interact. We have outstanding colleagues, including Vincent Racaniello and Amy Rosenfeld, with whom I am collaborating on this project. Finally, I am committed to the training and mentoring of students and post-docs. For the past 35 years at Columbia University Medical Center, I have trained 22 PhD students including 3 URMs (with 2 more PhD students in progress, one of whom is a URM) and 22 post-docs, many of whom are professors at various stages in their careers. Some are involved in the biotechnology industry, patent law or science filmmaking. More than 30 undergraduates have passed through my lab on their way to graduate or medical school.

Academic Appointments

  • Professor of Genetics & Development

Administrative Titles

  • Vice Chair, Genetics & Development Department
  • Member of Vagelos Physicians & Surgeons Office for Research Advisory Committee

Credentials & Experience

Education & Training

  • BS, 1969 Biology, Chemistry, University of Illinois at Chicago
  • PhD, 1975 Genetics, University of Chicago
  • Fellowship: 1977 University of Rochester School of Medicine & Dentistry
  • Fellowship: 1979 Cornell University - Ithaca

Honors & Awards

1969 Graduation with honors - University of Illinois, Chicago.

1976 - 1978 PHS Individual National Research Service Award

1984 - 1988 Member of the National Science Foundation Advisory Panel for Eukaryotic Genetic Biology.

1985 - 1997 Member of Editorial Board of CURRENT GENETICS.

1986 - 1990 Irma T. Hirschl Career Scientist

1986 - 1991 American Heart Association Established Investigator

1988 - 1991 Member of the Genetics Society of America Meeting Program Committee

1988 - 1993 Member of Editorial Board of Molecular and Cellular Biology

1988 - 1993 Member of the Damon Runyon - Walter Winchell Cancer Fund Scientific Advisory Committee

1989 - 1990 Member of 3 Special Study Sections for the Genome Project at NIH

1991 - 1993 Co-chairman (1991) and Chairman (1993) FASEB Summer Research Conference on Genomic Rearrangements and Genetic Recombination

1991 - 1992 Member of the Editorial Board of Genetica

1992 - 1994 Genetics Society of America Yeast Program Committee Member-at-large

1993 - 1995 Member of the National Science Foundation Advisory Panel for the MCB/NSF Young Investigator Awards

1993 - 1997 Member of the National Advisory Council for Human Genome Research of NIH

1995 - 1999 Member of Editorial Board of Genome Research

1997 Distinguished Alumnus, University of Illinois - Chicago, Department of Biology

1999 - 2000 Chair of Division X, Molecular, Cellular & General Biology of Eukaryotes, of the American Society of Microbiology

2001 Erasmus Lecture, Erasmus University Rotterdam, Netherlands

2002 Co-chair Keystone Symposium on Molecular Mechanisms in DNA Replication & Recombination

2002 - pres. Member of Editorial Board of Genes & Genetic Systems

2003 - pres. Associate Editor of DNA Repair

2004 - 2007 Member of the Israel Cancer Research Fund Scientific Review Panel

2004 - 2010 Genetics Society of America Yeast Program Committee

2005 - 2015 NIH MERIT Award (GM50237)

2005 Herbert Stern Lecture, UC San Diego, CA

2005 - 2009 Member of the Scientific Advisory Board of the European Commission Integrated Project on DNA Repair

2006 Gregor Mendel Lecture, Mendel’s Abbey, Brno, Czech Republic

2007 - pres. Fellow of the American Academy of Microbiology

2008 Co-chair FASEB Summer Research Conference on Yeast Chromosome Structure, Replication and Segregation

2008 John M. Lewis Memorial Lecture - Columbia University Medical Center, New York

2008 - pres. Fellow of the American Association for the Advancement of Science

2009 Edward Novitski Prize of the Genetics Society of America

2010 Member of MGC Study Section at NIH

2010 Giovanni Magni lecture sponsored by Fondazione Buzzati-Traverso, Milan, Italy

2011 - pres. Fellow of the American Academy of Arts & Sciences

2012 Doctor Honoris Causa in Medicine from Umeå University, Sweden

2014, 2019 Reviewer for Howard Hughes Medical Institute

2014, 2016 Co-organizer of Japanese 3R (Replication, Recombination & Repair) meeting

2015 - pres. Member of the National Academy of Sciences

2015, ’16, ‘18Ad hoc member of Pre- and Postdoc and MIRA Study Sections at NIH

2016 Genetics Society of America-sponsored Yeast Meeting: Winge-Lindegren lecture

2016 Inventor of the Year - New Jersey Inventors Hall of Fame

2017-2020 Member, Advisory Council for Institute of Quantitative Biosciences, The University of Tokyo

2019 – pres. NIH Pioneer Award Stage 1 reviewer

2019 Reviewer for Okinawa Institute of Science & Technology, Japan

2019 Keynote address at the IFOM, CRUK & MSKCC Retreat, Sardinia, Italy

2019 – pres. Member of NAS Award in Molecular Biology selection committee

Research

Harnessing the power of yeast genetics to explore biological problems

Studies on the cell biology of recombination are still in their infancy, and much remains to be uncovered in terms of the physical behavior of chromosomes, repair foci, and the factors that comprise them. The advent of cell biological techniques like protein tagging and observable chromosomal loci have permitted programs of experimentation that can address these fundamental questions of biology. By using these tools, we hope to unify physical phenomenology with genetic and biochemical models of recombination, permitting a complete understanding of this crucial process. In so doing, we hope to gain insight that may be consequential to studies of human disease and develop new and useful technologies for the manipulation of cells.

We use budding yeast as an experimental organism to study essential biological processes and we are pursuing 3 main areas of research: (1) visualization of homologous recombination processes in real time in living cells with an emphasis on the behavior of the broken ends of a double-strand break, (2) identification of new interrelationships between players in the DNA repair pathways (especially for crosslinks), (3) examining the consequences of gene dysregulation in cancer cells, or during viral infection, to discover novel genetic interaction pathways to lead to therapeutic target discovery.

1) We are currently studying the physical behavior of chromosomes in living cells and how they respond to DNA damage. We have found that increased mobility of chromosomes after DNA damage facilitates homology search. We are studying precisely how the DNA ends are processed after a double-strand break (DSB) by creating site-specific DSBs using meganucleases, TALEN®s and CRISPR-Cas9. Each DNA end flanking the DSB is fluorescently tagged along with the repair template on the homolog. After induction of a DSB, we can visualize repair proteins recruited to the ends before the homology search begins. We observe tight a temporal covariance among increased chromosome mobility, the physical pairing of homologous loci and the resultant gene conversion events. A key question is what happens to the second end of the break during HDR. We have designed a system with chromosomal tags on both ends of the break to allow us to independently visualize each end and track its behavior before, during, and after HR. By determining the precise choreography of DNA end movement during repair, we will better understand many of the open questions surrounding the resolution of DSBs. How often does synthesis-dependent strand annealing occur? How are crossovers and non-crossovers physically mediated? How are broken ends guided to repair substrates and foci? The effects on these processes of mutations in DNA repair pathway proteins are being examined to reveal the driving principles underlying how chromosomes physically respond to damage.

2) Analysis of pairwise combinations of double mutants provides a powerful method for determining relationships with a genetic pathway (e.g., epistasis or suppression). Such a genetic analysis becomes increasingly robust when combined with sensitizing conditions, such as treatment with a DNA damaging agent. We have developed an approach that focuses our attention on sub-networks of the DNA damage response by first identifying sets of strains that are sensitive to a particular DNA damaging agent. Next, under the same damaging conditions, pairwise crosses are performed of this subset of strains, which includes known DNA damage repair mutants. By applying this approach to a DNA crosslinking reagent, cisplatin, which is an important chemotherapeutic compound, we have identified over 150 genes involved in cisplatin sensitivity, some of which were not previously recognized as part of the DNA repair response network. Examination of systematic pairwise combinations of these mutations will reveal the global organization of this repair network.

3) We have developed methods to rapidly screen the entire yeast gene disruption library to reveal genetic interactions between overexpression of a protein and deletion/mutation of more than 5,500 chromosomal genes. These interactions reveal the pathways that are affected when particular proteins are mis-expressed. Although many cancer genomics and genome-wide expression studies have highlighted the important relationship between gene dosage and phenotype, little attention has been given to studying the effect of gene overexpression. To understand the biological consequences of mis-expression, we overexpress the yeast homolog of the cancer protein of interest and identify genetic interactions. These interactions are often preserved in human cells and reveal interactions that are useful in guiding personalized chemotherapy in cancer patients. During the COVID-19 pandemic, we are using our expression system to explore the pathways that are affected when SAR2-CoV-2 proteins are expressed after infection. We are focusing on viral proteins that target the endoplasmic reticulum to assemble the viral replicon.

Research Interests

  • Genomic approaches to understand the control of genome stability in normal & cancer cells
  • Genomic approaches to understand the control of genome stability in yeast
  • Investigating SARS-CoV-2 viral-host protein interactions during viral replication
  • Understanding the mechanisms of genetic recombination
  • Yeast genetic and cell biological approaches to understand the cellular response to DNA damage

Grants

MECHANISMSOF RECOMBINATION STIMULATED BY 3 -OVERHANGS, 5 -OVERHANGS OR BLUNT ENDS (Private)

Nov 14 2019 - Nov 13 2021

MOLECULAR MECHANISMS UNDERLYING DNA DOUBLE-STRAND BREAK AND CROSSLINK REPAIR (Federal Gov)

Jul 1 2016 - Aug 31 2021

CENTERS FOR CANCER SYSTEMS THERAPEUTICS (CAST) (Federal Gov)

Aug 8 2016 - Jul 31 2021

MECHANISM OF SPONTANEOUS AND DSB-INDUCED REPAIR (Federal Gov)

Sep 1 2015 - Aug 31 2019

YEAST CHROMATIN STRUCTURE AND FUNCTION (Federal Gov)

Jan 1 2015 - Dec 31 2018

YEAST CHROMATIN STRUCTURE AND FUNCTION (Federal Gov)

Jan 1 2015 - Dec 31 2018

GENETICS OF THE FORMATION OF REPAIR & RECOMBINATION FOCI (Federal Gov)

Jan 1 2003 - Feb 29 2016

DEVELOPING A NEW PARADIGM TO DISCOVER NOVEL BREAST CANCER DRUG TARGETS (NY State Gov)

Sep 1 2013 - Aug 31 2015

IN VIVO CHOREOGRAPHY OF DNA MOLECULES AND REPAIR PROTEINS DU RING SEARCH FOR HOMOLOGY (Private)

Jan 1 2010 - Dec 31 2011

MECHANISTIC INSIGHTS INTO THE SHU COMPLEX AND SGS1 IN DNA RE PAIR AND REPLICATION (Federal Gov)

Aug 1 2009 - Jun 30 2011

Selected Publications

Rothstein, R.J. Deletions of a tyrosine tRNA in Saccharomyces cerevisiae. Cell 17: 185-190, 1979.

Orr-Weaver, T., Szostak, J.W. and Rothstein, R.J. Yeast transformation: A model system for the study of recombination. Proc. Natl. Acad. Sci. USA 78: 6354-6358, 1981.

Szostak, J.W., Orr-Weaver, T.L., Rothstein, R.J. and Stahl, F.W. The double-strand-break model for genetic recombination. Cell 33: 25-35, 1983.

Rothstein, R.J. One-step gene disruption in yeast. In: Methods in Enzymology, Vol. 101, R. Wu, L. Grossman and K. Moldave, Eds., Academic Press, New York, pp. 202-211, 1983.

Thomas, B. and Rothstein, R. Elevated recombination rates in transcriptionally active DNA. Cell 56: 619-630, 1989.

Wallis, J.W., Chrebet, G., Brodsky, G., Rolfe, M. and Rothstein, R. A hyper-recombination mutation in Saccharomyces cerevisiae identifies a novel eukaryotic topoisomerase. Cell 58: 409-419, 1989.

Thomas, B. and Rothstein, R. The genetic control of direct repeat recombination in Saccharomyces: The effect of rad52 and rad1 on recombination at GAL10, a transcriptionally regulated gene. Genetics 123: 725-738, 1989.

Gangloff, S., McDonald, J. P., Bendixen, C., Arthur, L. and Rothstein, R. The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase. Molec. Cell. Biol. 14: 8391-8398, 1994.

Mortensen, U.H., Bendixen, C., Sunjevaric, I. and Rothstein, R. DNA strand annealing is promoted by the yeast Rad52 protein. Proc. Natl. Acad. Sci. 93: 10729-10734, 1996.

Zou, H. and Rothstein, R. Holliday junctions accumulate in replication mutants via a RecA homolog-independent mechanism. Cell 90: 87-96, 1997

Erdeniz, N., Mortensen, U.H. and Rothstein, R. Cloning-free PCR-based Allele Replacement Methods. Genome Res. 7: 1174-1183, 1997.

Zhao, X., Muller, E.G.D. and Rothstein, R. A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools. Molecular Cell 2: 329-340, 1998.

Lisby, M., Rothstein, R. and Mortensen, U.H. Rad52 forms DNA repair and recombination centers during S phase. Proc. Natl. Acad. Sci. USA 98: 8276-8282, 2001.

Lisby, M., Barlow, J.H., Burgess, R.C. and Rothstein, R. Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell 118: 699-713, 2004.

Shor, E., Weinstein, J. and Rothstein, R. A genetic screen for top3 suppressors in Saccharomyces cerevisiae identifies SHU1, SHU2, PSY3 and CSM2: Four genes involved in error-free DNA repair. Genetics 169: 1275-1289, 2005.

Lisby, M. and Rothstein, R. The cell biology of mitotic recombination in Saccharomyces cerevisiae. In: Topics in Current Genetics - Molecular Genetics of Recombination (A. Aguilera and R. Rothstein, eds.), Springer-Verlag, Berlin, pp. 317-333, 2007.

Alvaro, D.A., Lisby, M. and Rothstein, R. Genome-wide analysis of Rad52 foci reveals diverse mechanisms impacting recombination. PLoS Genetics 3: 2439-2449, 2007 (doi:10.1371/journal.pgen.0030228).

Barlow, J.H., Lisby, M. and Rothstein, R. Differential regulation of the cellular response to DNA double-strand breaks in G1. Molecular Cell 30: 73-85, 2008.

Dittmar, J.C., Reid, R.J.D. and Rothstein, R. ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data. BMC Bioinformatics 11: 353, 2010.

Reid, R.J.D., González-Barrera, S., Sunjevaric, I., Alvaro, D., Ciccone, S., Wagner, M. and Rothstein, R. Selective ploidy ablation, a high-throughput plasmid transfer protocol, identifies new genes affecting topoisomerase I-induced DNA damage. Genome Research 21: 477-486, 2011.

Miné-Hattab, J. and Rothstein, R. Increased chromosome mobility facilitates homology search during recombination. Nature Cell Biol., 14: 510-517, 2012.

Dittmar, J.C., Pierce, S., Rothstein, R. and Reid, R.J.D. Physical and genetic interaction density reveals functional organization and informs significance cutoffs in genome-wide screens. Proc Natl Acad Sci USA, 110: 7389-7394, 2013.

Jasin, M. and Rothstein, R. Repair of Strand Breaks by Homologous Recombination. Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a012740, 2014.

Symington, L.S., Rothstein, R. and Lisby, M. Mechanisms and regulation of mitotic recombination in Saccharomyces cerevisiae. Genetics, 198: 795-835, 2014.

Lisby, M. and Rothstein, R. Cell biology of mitotic recombination. Cold Spring Harb Perspect Biol 7:a016535, 2015.

Reid, R.J.D., Du, X., Sunjevaric, I., Rayannavar, V., Dittmar, J., Bryant, E., Maurer, M. and Rothstein, R. A synthetic dosage lethal genetic interaction between CKS1B and PLK1 is conserved in yeast and human cancer cells. Genetics 204: 807-819, 2016.

Smith, M.J. and Rothstein, R. Poetry in motion: Increased chromosomal mobility after DNA damage. DNA Repair 56: 102-108, 2017.

Miné-Hattab, J., Recamier, V., Izeddin, I., Rothstein, R., Darzacq, X. Multi-scale tracking reveals scale-dependent chromatin dynamics after DNA damage. Mol Biol Cell. E17-05-0317. doi: 10.1091, 2017.

Billon, P., Bryant, E.E., Joseph, S.A., Nambiar, T.S., Hayward, S.B., Rothstein R. and Ciccia, A. CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons. Molec. Cell 67: 1068-1079, 2017.

Smith, M.J., Bryant, E.E. and Rothstein, R. Increased chromosomal mobility after DNA damage is controlled by interactions between the recombination machinery and the checkpoint. Genes & Dev. 32: 1242-1251. doi: 10.1101/gad.317966.118, 2018.

Oh, J., Lee, S.J., Rothstein, R. and Symington, L.S. Xrs2 and Tel1 independently contribute to MR-mediated DNA tethering and replisome stability. Cell Reports 13: 1681-1692, 2018.

Šuštić, T., van Wageningen, S., Bosdriesz, E., Reid, R.J.D., Dittmar, J., Lieftink, C., Beijersbergen, R.L., Wessels, L.F.A. , Rothstein, R. and Bernards, R. A role for the Unfolded Protein Response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers. Genomic Medicine 27: 90, 2018.

Bryant, E.E., Šunjevarić, I., Berchowitz, L., Rothstein, R. and Reid, R.J.D. Rad5 dysregulation drives hyperactive recombination at replication forks resulting in cisplatin sensitivity and genome instability. Nucleic Acids Res. 47: 9144-9159, 2019.

Smith, M.J., Bryant, E.E., Joseph, F.J. and Rothstein, R. DNA damage triggers increased mobility of chromosomes in G1 phase cells. Molec. Biol. Cell 30: 2620-2625, 2019.

Books:

Aguilera, A. and Rothstein, R., editors. Topics in Current Genetics - Molecular Genetics of Recombination, Springer-Verlag, Berlin, 2007.

Rothstein, R., Forward for Weitzman, J. and Weitzman, M. 30-Second Genetics: The 50 Most Revolutionary Discoveries in Genetics, Each Explained in Half a Minute, Ivy Press, Brighton, UK, 2017