Publications

Storici Lab Publications since 2007

Gombolay et al. (2021). Mapping ribonucleotides embedded in genomic DNA to single-nucleotide resolution using Ribose-Map. Nature Protocols, in press.

Marsili et al. (2021). Gene co-expression analysis of human RNASEH2A reveals functional networks associated with DNA replication, DNA damage response, and cell cycle regulation. Biology. https://doi.org/10.3390/biology10030221

El-Sayed et al. (2021). Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii. iScience. https://doi.org/10.1016/j.isci.2020.102005

Meers et al. (2020). Genetic Characterization of Three Distinct Mechanisms Supporting RNA-Driven DNA Repair and Modification Reveals Major Role of DNA Polymerase ζ. Mol Cell. https://doi.org/10.1016/j.molcel.2020.08.011

Balachander, Gombolay, Yang, and Xu et al. (2020). Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine. Nature Communications. https://doi.org/10.1038/s41467-020-16152-5

Mukherjee K, English N, Meers C, Kim H, Jonke A, Storici F, and Torres M (2020). Systematic analysis of linker histone PTM hotspots reveals phosphorylation sites that modulate homologous recombination and DSB repair. DNA Repair. https://doi.org/10.1016/j.dnarep.2019.102763

Malfatti MC, Henneke G, Balachander S, Koh KD, Newnam G, Uehara R, Crouch RJ, Storici F, Tell G (2019). Unlike the Escherichia coli counterpart, archaeal RNase HII cannot process ribose monophosphate abasic sites and oxidized ribonucleotides embedded in DNA. J Biol Chem. 30;294(35): 13061-13072. doi: 10.1074/jbc.RA119.009493

Gombolay, A. L., Vannberg, F. O., & Storici, F. (2019). Ribose-Map: a bioinformatics toolkit to map ribonucleotides embedded in genomic DNA. Nucleic Acids Researchhttps://doi.org/10.1093/nar/gky874

Michelini, F., Jalihal, A.P., Francia, S., Meers, C., Neeb, Z.T., Rossiello, F., Gioia, U., Aguado, J., Jones-Weinert, C., Luke, B., et al. (2018). From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chemical Reviews 118, 4365-4403. doi: 10.1021/acs.chemrev.7b00487

Balachander, S., Yang, T., Newnam, G., El-Sayed, W.M.M., Koh, K.D., & Storici, F. (2018). Capture of ribonucleotides in yeast genomic DNA using ribose-seq. Accepted in Methods in Molecular Biology ‘Yeast Systems Biology. Methods and Protocols’ (2nd ed), Springer. Bold – coauthors

Malfatti & Balachander et al. (2017). Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx723. Bold – coauthors

Mazina, O. M., Keskin, H., Hanamshet, K., Storici, F., & Mazin, A. V. (2017). Rad52 Inverse Strand Exchange Drives RNA-Templated DNA Double-Strand Break Repair. Molecular Cell, 67(1), 19–29.e3. http://doi.org/10.1016/j.molcel.2017.05.019

Ruff, P. and Storici, F. Genome editing by aptamer-guided gene targeting (AGT). In: “Genome Editing: The Next Step in Gene Therapy” Edited by T. Cathomen, M. Hirsch, and M. Porteus. American Society of Gene and Cell Therapy and Springer publishing. Vol 895, pp 111-124 (2016).

Evich, M., Spring-Connell, A. M., Storici, F., & Germann, M. W. (2016). Structural Impact of Single Ribonucleotide Residues in DNA. Chembiochem : A European Journal of Chemical Biology, 17(20), 1968–1977. http://doi.org/10.1002/cbic.201600385

Meers, C., Keskin, H., & Storici, F. (2016). DNA repair by RNA: Templated, or not templated, that is the question. DNA Repair, 44, 17–21. http://doi.org/10.1016/j.dnarep.2016.05.002

Keskin, H., Meers, C., & Storici, F. (2016). Transcript RNA supports precise repair of its own DNA gene. RNA Biology, 13(2), 157–165. http://doi.org/10.1080/15476286.2015.1116676

Keskin, H., & Storici, F. (2015). Defects in RNase H2 Stimulate DNA Break Repair by RNA Reverse Transcribed into cDNA. MicroRNA (Shariqah, United Arab Emirates), 4(2), 109–116.

Koh, K. D., Chiu, H.-C., Riedo, E., & Storici, F. (2015). Measuring the elasticity of ribonucleotide(s)-containing DNA molecules using AFM. Methods in Molecular Biology (Clifton, N.J.), 1297, 43–57. http://doi.org/10.1007/978-1-4939-2562-9_3

Koh, K.D., Hesselberth, J. & Storici, F. Ribose-seq: ribonucleotides in DNA to Illumina library. Protocol Exchange doi:10.1038/protex.2015.044 (19 May 2015).

Koh, K. D., Balachander, S., Hesselberth, J. R., & Storici, F. (2015). Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nature Methods, 12(3), 251–7, 3 p following 257. http://doi.org/10.1038/nmeth.3259

Storici, F., Editor. (2014) Gene Correction: Methods and Protocols – Methods in Molecular Biology; Humana Press, New York, NY; Vol. 1114.

Keskin, H., Shen, Y., Huang, F., Patel, M., Yang, T., Ashley, K., … Storici, F. (2014). Transcript-RNA-templated DNA recombination and repair. Nature, 515(7527), 436–439. http://doi.org/10.1038/nature13682

Chiu, H.-C., Koh, K. D., Evich, M., Lesiak, A. L., Germann, M. W., Bongiorno, A., … Storici, F. (2014). RNA intrusions change DNA elastic properties and structure. Nanoscale, 6(17), 10009–10017. http://doi.org/10.1039/c4nr01794c

Katz, S. S., Gimble, F. S., & Storici, F. (2014). To nick or not to nick: comparison of I-SceI single- and double-strand break-induced recombination in yeast and human cells. PloS One, 9(2), e88840. http://doi.org/10.1371/journal.pone.0088840

Stuckey, S., & Storici, F. (2014). Genetic modification stimulated by the induction of a site-specific break distant from the locus of correction in haploid and diploid yeast Saccharomyces cerevisiae. Methods in Molecular Biology (Clifton, N.J.), 1114, 309–324. http://doi.org/10.1007/978-1-62703-761-7_20

Ruff, P., Koh, K. D., Keskin, H., Pai, R. B., & Storici, F. (2014). Aptamer-guided gene targeting in yeast and human cells. Nucleic Acids Research, 42(7), e61. http://doi.org/10.1093/nar/gku101

Stuckey, S., & Storici, F. (2013). Gene knockouts, in vivo site-directed mutagenesis and other modifications using the delitto perfetto system in Saccharomyces cerevisiae. Methods in Enzymology, 533, 103–131. http://doi.org/10.1016/B978-0-12-420067-8.00008-8

Mukherjee, K., & Storici, F. (2012). A mechanism of gene amplification driven by small DNA fragments. PLoS Genetics, 8(12), e1003119. http://doi.org/10.1371/journal.pgen.1003119

Ruff, P., Pai, R. B., & Storici, F. (2012). Real-Time PCR-Coupled CE-SELEX for DNA Aptamer Selection. ISRN Molecular Biology, 2012, 939083. http://doi.org/10.5402/2012/939083

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.

Shen, Y., Koh, K. D., Weiss, B., & Storici, F. (2011). Mispaired rNMPs in DNA are mutagenic and are targets of mismatch repair and RNases H. Nature Structural & Molecular Biology, 19(1), 98–104. http://doi.org/10.1038/nsmb.2176

Shen, Y., & Storici, F. (2011). Detection of RNA-templated double-strand break repair in yeast. Methods in Molecular Biology (Clifton, N.J.), 745, 193–204. http://doi.org/10.1007/978-1-61779-129-1_12

Stuckey, S., Mukherjee, K., & Storici, F. (2011). In vivo site-specific mutagenesis and gene collage using the delitto perfetto system in yeast Saccharomyces cerevisiae. Methods in Molecular Biology (Clifton, N.J.), 745, 173–191. http://doi.org/10.1007/978-1-61779-129-1_11

Shen, Y., Nandi, P., Taylor, M. B., Stuckey, S., Bhadsavle, H. P., Weiss, B., & Storici, F. (2011). RNA-driven genetic changes in bacteria and in human cells. Mutation Research, 717(1–2), 91–98. http://doi.org/10.1016/j.mrfmmm.2011.03.016

Shen, Y., & Storici, F. (2010). Generation of RNA/DNA hybrids in genomic DNA by transformation using RNA-containing oligonucleotides. Journal of Visualized Experiments : JoVE, (45). http://doi.org/10.3791/2152

Hirsch, M. L., Storici, F., Li, C., Choi, V. W., & Samulski, R. J. (2009). AAV recombineering with single strand oligonucleotides. PloS One, 4(11), e7705. http://doi.org/10.1371/journal.pone.0007705

Yang, Y., Sterling, J., Storici, F., Resnick, M. A., & Gordenin, D. A. (2008). Hypermutability of damaged single-strand DNA formed at double-strand breaks and uncapped telomeres in yeast Saccharomyces cerevisiae. PLoS Genetics, 4(11), e1000264. http://doi.org/10.1371/journal.pgen.1000264

Storici, F. (2008). RNA-mediated DNA modifications and RNA-templated DNA repair. Current Opinion in Molecular Therapeutics, 10(3), 224–230.

Storici, F., Bebenek, K., Kunkel, T. A., Gordenin, D. A., & Resnick, M. A. (2007). RNA-templated DNA repair. Nature, 447(7142), 338–341. http://doi.org/10.1038/nature05720