Publications

Storici Lab Publications since 2007

Xu et al. (2023). Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome. Nucleic Acids Research.

Kundnani and Storici (2021). FeatureCorr: An R package to study feature correlations aided with data transformation for sequencing and microarray data. Software Impacts.

Xu and Storici (2021). Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases. Nucleic Acids Research.

Xu and Storici (2021). RESCOT: Restriction enzyme set and combination optimization tools for rNMP capture techniques. Theoretical Computer Science.

Gombolay and Storici (2021). Ribose-Map: A bioinformatics toolkit for ribonucleotide sequencing experiments. Software Impacts.

Gombolay and Storici. (2021). Mapping ribonucleotides embedded in genomic DNA to single-nucleotide resolution using Ribose-Map. Nature Protocols.

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

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 Research. https://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