Mechanisms of mutagenesis and chromosomes rearrangements in Saccharomyces cerevisiae
Alterations to the genome, from simple mutations to chromosome rearrangements, are prerequisite to evolution as well as a pervasive feature of various somatic diseases. In many cancers, the disturbance of normal cellular activities associated with oncogenic transformation initiates with changes in the genome. Identifying key factors affecting genome stability is, therefore, central to understanding how cancer develops.
Transcription, although it is generally considered distinctly separate, shares the genomic DNA as template with replication and repair processes. The observation that certain highly transcribed genes are hotspots of spontaneous recombination and mutagenesis demonstrates the importance of the interplay among transcription, replication, and repair in genome maintenance. Our research objective is to better understand the molecular basis of transcription-associated recombination (TAR) and mutagenesis (TAM) through genetic approaches in the model organism, Saccharomyces cerevisiae.
In highly transcribed areas of the yeast genome, a higher rate of mutagenesis as well as a unique spectrum of mutations have been observed. Recent discoveries point to the accumulation of endogenous DNA damages as the main cause of such transcription-associated genome instability. In particular, an elevated incorporation of atypical nucleotides such as uracil and ribonucleotides in highly transcribed regions of the yeast genome results in accumulation of unique types of mutations such as A:T to C:G base changes and short deletions at tandem repeats. We are currently studying how the imbalance in the nucleotide composition is achieved in highly transcribed regions and how this imbalance affects genomic stability.
Another research interest in the lab involves the formation of non-canonical/non-B form DNA structures during activated transcription. Such structures can hinder the efficient movement of DNA replication and potentially lead to elevated genomic instability. An example of such “At-Risk-Motifs” (ARMS) is the highly G/C rich and repetitive sequence that assemble into a G-quadruplex or G4 DNA structure with runs of guanines forming stable G quartets. By integrating G4 DNA-forming sequence motifs into the yeast genome, we are studying how such sequences become hotspots of genome instability and contribute to gross chromosomal rearrangements.
DNA sequences rich in guanines can form four-stranded secondary DNA structures called G-quadruplexes (G4). G4 structures arise when four guanine DNA bases undergo Hoogsteen hydrogen bonds with each other, forming guanine tetrads that can stack on top of one another. Due the stability of these structures, G4 DNA formation can compromise essential cellular processes such as replication and transcription. Increasing evidence supports an association with G4 forming DNA sequences and genome instability in many organisms, including yeast and humans. My research is centered around understanding the role G4 structures play within yeast cells and genomic instability.
Williams, J. D., Fleetwood, S., Berroyer, A., Kim, N., and Larson, E. D. (2015). Sites of instability in the human TCF3 (E2A) gene adopt G-quadruplex DNA structures in vitro. Frontiers in Genetics. 6 (177): 1-11.
Reading, swimming, and playing with my dog.
Chris Lopez, Ph.D.
Dr. Lopez is interested in mechanisms that protect the integrity of the genome by preventing deletions, insertions, mutations, and chromosomal rearrangements. His research focus on how cells solve the problems caused by non-canonical DNA structures, specifically G-quadruplex DNA. These structures are hotspots for genetic changes that alter the genome of an organism. He is specifically investigating how loss of topoisomerase I activity leads to genomic instability at G-quadruplex forming sequences in the model organism Saccharomyces cerevisiae.
- Hang,L.E., Lopez, C.R., Liu, X., Williams, J., Chung, I., Lei, W., Bertuch, A.A.,and Zhao, X. (2014) Regulation of Ku-DNA Association by YKU70 C-terminal tail and SUMO modification. J Biol Chem, 289(15): 10308-10317.
- Lopez C.R., Ribes-Zamora A, Indiviglio SM, Williams CL, Haricharan S, et al. (2011) Ku Must Load Directly onto the Chromosome End in Order to Mediate Its Telomeric Functions. PLoS Genet 7(8): e1002233.
- Yang, S., Lopez, C.R., and Zechiedrich, E.L. (2006) Quorum sensing and multidrug transporters in Escherichia coli. Proc Natl Acad Sci USA, 103: 2386-2391.
- Lopez, C.R., Yang, S., Deibler, R.W., Ray, S.A., Pennington, J., DiGate, R.J., Hastings, P.J., Rosenberg, S.M., and Zechiedrich, E.L. (2005) A role for topoisomerase III in a recombination pathway alternative to RuvABC. Mol Microbiol, 58: 80-101.
Dr. Lopez’s hobbies include reading mystery novels, listening to music, and watching Sci-Fi movies.
Shivani Singh, Ph.D.
My current research focuses on understanding the mechanism of how G4 sequences are transformed into hotspot of genome instability, in the model organism Saccharomyces cerevisiae. Using genetic and molecular approaches, I aim to define the role of topoisomerase 1 in the G4 DNA-associated genome instability. I also plan to test whether and how DNA damage elevates the instability of G4 forming sequences.
- Singh S, Shemesh K, Liefshitz B, Kupiec M. Genetic and physical interactions between the yeast ELG1 gene and orthologs of the Fanconi anemia pathway. Cell Cycle. 2013 May 15;12(10):1625-36. doi: 10.4161/cc.24756. Epub 2013 Apr 25.
- Ranjan R, Chugh M, Kumar S, Singh S, Kanodia S, Hossain MJ, Korde R, Grover A, Dhawan S, Chauhan VS, Reddy VS, Mohmmed A, Malhotra P. Proteome analysis reveals a large merozoite surface protein-1 associated complex on the Plasmodium falciparum merozoite surface. J Proteome Res. 2011 Feb 4;10(2):680-91. doi: 10.1021/pr100875y. Epub 2010 Dec 22.
- Manzar J. Hossain, Reshma Korde, Shivani Singh, Asif Mohmmed, P.V.N. Dasaradhi,V.S. Chauhan, Pawan Malhotra. Tudor domain proteins in protozoan parasites and characterization of Plasmodium falciparum tudor staphylococcal nuclease, International Journal for Parasitology 38 (2008) 513–526.
- M.V. Rajam, R. Kumria, S. Singh. Molecular biology and genetic engineering of polyamines in plants. In: Plant Biotechnology and Molecular Markers (Eds. P.S. Srivastava, A. Narula and S. Srivastava), Anamaya Publishers, New Delhi, pp. 60-77.
I love to spend time with my kids. And if time permits, reading books (I have already read the complete Harry Potter series thrice), and exploring the city.