On April 1, 2019. Prof. Delin You’s laboratory from Zixin Deng Group published a paper titled "Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency" in PLoS Genetics. This paper reveals DNA phosphorothioate heterogeneity in the bacterial population.
Phosphorothioate (PT) modification is a novel DNA modification, previous studies showed that PT modiﬁcations in E. coli occure at GpsAAC/GpsTTC motifs, but the modification frequency at each site are not known. In this study, the authors developed the PT-IC-seq technique, based on iodine-induced selective cleavage at PT sites and high-throughput next generation sequencing, as a mean to quantitatively characterizing the genomic landscape of PT modifications. Using PT-IC-seq they found that most PT sites are partially modified at a lower PT frequency (< 5%) in E. coli B7A and Salmonella enterica serovar Cerro 87, and both show a heterogeneity pattern of PT modification similar to those of the typical methylation modification. Combining the iodine-induced cleavage and absolute quantification by droplet digital PCR, the authors developed the PT-IC-ddPCR technique to further measure the PT modification level. Consistent with the PT-IC-seq measurements, PT-IC-ddPCR analysis confirmed the lower PT frequency in E. coli B7A. These results have demonstrated the heterogeneity of PT modification in the bacterial population, and will open the door to understanding biology of this novel DNA modification.
Jinli Li, Yi Chen, Tao Zheng and Lingxin Kong are co-first authors of the paper. Prof. Delin You and Litao Yang are co-corresponding authors. The work was supported by the National Science Foundation of China, the Ministry of Science and Technology of China, Shanghai Pujiang Program from the Shanghai Municipal Council of Science and Technology.
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