Francesca Storici, Associate Professor
About Francesca Storici
Ph.D., Molecular Genetics, International School for Advanced Studies, Trieste, Italy
Office: Cherry Emerson 331
DNA repair, Recombination, RNA-mediated DNA repair, Gene targeting, Gene therapy
Dr. Storici Lab studies the mechanisms by which broken DNA is repaired and translates these findings into applications for gene targeting and gene therapy.
DNA-based life would no longer continue if the DNA repair mechanisms would stop working. Imperfect DNA repair leads to aging, genetic diseases, cancer. Among the most dangerous DNA lesions are double-strand breaks (DSBs). If a single DSB is left unrepaired or it is improperly repaired, it can lead to chromosome rearrangements or cell death. Indeed DSBs are regarded as one of the primary causes of cancer. On the other hand DSBs have also a positive function in inducing DNA recombination and promoting gene targeting. Gene targeting is a process to modify, by genetic engineering and homologous recombination, a mutant DNA sequence into a wild-type copy or vice versa, without removing it from its natural context in the chromosome in a living cell. In situ gene correction is the best therapy for all the monogenic diseases, currently several thousands identified, each caused by a mutation in a specific gene, and which are mostly without a cure. However, the major obstacles of gene targeting, which are delivery, efficiency and safety, must be overcome before any gene targeting approach can be turned into an effective cure for human genetic disorders. The laboratory of Dr. Storici uses the yeast Saccharomyces cerevisiae model organism and mammalian cells to characterize the molecular mechanisms involved in the repair of broken DNA and to develop more effective and safe technologies of genome modification as unique tools for structure/function studies as well as for medical and industrial applications.
DNA Transactions – Studies and Research Directions
We previously found that DNA fragments in the form of oligonucleotides provide a useful tool for probing mechanisms of repair and recombination as well as leading to novel strategies for gene targeting. Using the budding yeast as a model system we developed one of the most powerful approaches of targeted genome corrections with synthetic oligonucleotides, referred as ‘delitto perfetto’ (Storici et al., 2001; Storici and Resnick, 2006), which provides direct in vivo selection for almost any chromosomal modification. The method in its last development has exceptionally high frequency (as high as 20% of all cells) of targeted changes, achieved when a site-specific DSB is induced within the locus targeted by the designer oligonucleotides (Storici et al., 2003). In such a way the system is highly defined and provides powerful tools for dissecting complex repair and recombination processes and to characterize the function of genes relevant in pathways of damage repair and cancer.
Recent data show that oligonucleotides can be used to target and repair a DSB also in human cells. Via a direct comparison between similar yeast and human cell systems for DSB induction and repair, we aim to determine the mechanism of oligonucleotide-driven DSB repair in human cells. How much such repair in human cells is similar to the mechanism in yeast and what are the differences with the yeast system? Can we make human cell targeting as versatile and efficient as in yeast cells?
The finding that a DSB can strongly stimulate recombination also with single-strand DNA, led to the identification of a conservative mechanism for the repair of a DSB through multiple rounds of strand annealing (Storici et al., 2006). This mechanism provides a model for repair of multiple and clustered breaks, which are frequently observed after cell exposure to ionizing radiations. Using yeast and human cell models the research is directed to understand how repair via multiple rounds of strand annealing is activated and regulated in the cells. This study is relevant to understand the mechanisms how certain types of tumor cells acquire a high DNA repair potential and resist to treatment by ionizing radiation.
RNA Transactions – Studies and Research Directions
The finding of RNA-templated DNA repair in budding yeast (Storici et al., 2007) has unraveled a novel function of RNA, namely that RNA can be directly used as template in the repair of broken chromosomal DNA and directly transfer information to the DNA. The discovery of this novel RNA capacity was made possible with the use of exogenous RNA-containing oligonucleotides that were added to the cells to repair a chromosomal DSB. The molecular mechanism of RNA-templated DNA repair is unknown. Using genetics, cell biological and biochemical approaches, we investigate a series of specific questions. Can we observe DNA repair by endogenous RNA and what control such process? Which polymerase/s can copy DNA during break repair using RNA as a template in living cells? Does such repair exist in mammalian cells? The group is also interested in determining the potential of RNA for gene targeting. Can RNA molecules, which can be amplified inside the cells via transcription, be preferred donors to modify the genomic DNA? If so, the process of RNA-mediated DNA repair may open a new direction in gene therapy.
Mukherjee, K. and Storici, F. (2012). A mechanism of gene amplification driven by small DNA fragments, PLoS Genetics, 8 (12), e1003119. Link
Ruff, P., Pai and Storici. (2012). A DNA aptamer for bovine serum albumin. ISRN Mol. Biol. Article ID 939083, 9 pages doi:10.5402/2012/939083.
Shen, Y., Koh, K. D., Weiss, B. and Storici, F. (2011). Mispaired rNMPs in DNA are mutagenic and are targets of mismatch repair and RNases H.Nat. Struct. & Mol. Biol. Dec 4. doi: 10.1038/nsmb.2176. [Epub ahead of print] [Link]
Storici, F., Editor. (2011). DNA Repair - On the pathways to fixing DNA damage and errors. InTech. Open Access Publisher, Rijeka Croatia and Vienna Austria, EU. [Link]
Shen, Y., Nandi, P., Taylor, M. B., Bhadsavle, H. P., Stuckey, S., Weiss, B., and Storici, F. (2011). RNA-driven genetic changes in bacteria and in human cells. Mutat. Res., 717, 91-98.
Stuckey, S., Mukherjee, K., and Storici, F. (2011). In vivo site-specific mutagenesis and gene collage using the delitto perfettosystem in yeast Saccharomyces cerevisiae. In: "Methods in Molecular Biology", Edited by: H. Tsubouchi. Humana Press Inc., New York, NY; 745:173-191.[Link]
Shen, Y., and Storici, F. (2011). Detection of RNA-templated double-strand break repair in yeast. In: "Methods in Molecular Biology", Edited by H. Tsubouchi. Humana Press, New York, NY; 745:193-204.[Link]
Shen, Y., and Storici, F. (2010). Generation of RNA/DNA hybrids in genomic DNA by transformation using RNA-containing oligonucleotides. J. Vis. Exp. 45. [Link]
Stuckey, S., and Storici, F. (2010). Gene knockouts, in vivo site-directed mutagenesis and other modifications using the delitto perfetto system in Saccharomyces cerevisiae. In: "Methods Navigator", Edited by J. Lorsch. Elsevier Press, Oxford, UK.
Hirsch ML, Storici F, Li C, Choi VW, Samulski RJ. AAV recombineering with single strand oligonucleotides. PLoS One. 2009 Nov 2;4(11):e7705.