Browsing by Author "Aguilera, Andrés"
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Item Open Access Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways.(Microbial cell (Graz, Austria), 2019-01-07) Klein, Hannah L; Bačinskaja, Giedrė; Che, Jun; Cheblal, Anais; Elango, Rajula; Epshtein, Anastasiya; Fitzgerald, Devon M; Gómez-González, Belén; Khan, Sharik R; Kumar, Sandeep; Leland, Bryan A; Marie, Léa; Mei, Qian; Miné-Hattab, Judith; Piotrowska, Alicja; Polleys, Erica J; Putnam, Christopher D; Radchenko, Elina A; Saada, Anissia Ait; Sakofsky, Cynthia J; Shim, Eun Yong; Stracy, Mathew; Xia, Jun; Yan, Zhenxin; Yin, Yi; Aguilera, Andrés; Argueso, Juan Lucas; Freudenreich, Catherine H; Gasser, Susan M; Gordenin, Dmitry A; Haber, James E; Ira, Grzegorz; Jinks-Robertson, Sue; King, Megan C; Kolodner, Richard D; Kuzminov, Andrei; Lambert, Sarah Ae; Lee, Sang Eun; Miller, Kyle M; Mirkin, Sergei M; Petes, Thomas D; Rosenberg, Susan M; Rothstein, Rodney; Symington, Lorraine S; Zawadzki, Pawel; Kim, Nayun; Lisby, Michael; Malkova, AnnaUnderstanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.Item Open Access Spontaneous deamination of cytosine to uracil is biased to the non-transcribed DNA strand in yeast.(DNA repair, 2023-06) Williams, Jonathan D; Zhu, Demi; García-Rubio, María; Shaltz, Samantha; Aguilera, Andrés; Jinks-Robertson, SueTranscription in Saccharomyces cerevisiae is associated with elevated mutation and this partially reflects enhanced damage of the corresponding DNA. Spontaneous deamination of cytosine to uracil leads to CG>TA mutations that provide a strand-specific read-out of damage in strains that lack the ability to remove uracil from DNA. Using the CAN1 forward mutation reporter, we found that C>T and G>A mutations, which reflect deamination of the non-transcribed and transcribed DNA strands, respectively, occurred at similar rates under low-transcription conditions. By contrast, the rate of C>T mutations was 3-fold higher than G>A mutations under high-transcription conditions, demonstrating biased deamination of the non-transcribed strand (NTS). The NTS is transiently single-stranded within the ∼15 bp transcription bubble, or a more extensive region of the NTS can be exposed as part of an R-loop that can form behind RNA polymerase. Neither the deletion of genes whose products restrain R-loop formation nor the over-expression of RNase H1, which degrades R-loops, reduced the biased deamination of the NTS, and no transcription-associated R-loop formation at CAN1 was detected. These results suggest that the NTS within the transcription bubble is a target for spontaneous deamination and likely other types of DNA damage.