Transcription-coupled repair pathway in UVC-induced SupF gene mutation in Tet-on 293 cell line

Objective： To explore the role of transcription-coupled repair （TCR） pathway in the UVC-induced SupF gene mutation in Tet-on 293 cell line, we designed and constructed a Tet-responsive plasmid DNA pTCR-C1, and utilized this pTCR-C 1 plasmid to obtain the mutation frequency of SupF reporter gene induced by UVC in Tet-on 293 cell line. Methods： SupF gene was cloned into a Tet-responsive plamid pBI-L, which include a bidirectional Tet-responsive promoter, and was named pTCR-C1. The pTCR-C1 plasmid was transfected into Tet-on 293 cell line, and the mutation frequency of SupF reporter gene was detected in the presence and absence of DOX. Results： The pTCR-C1 plasmid was identified with the methods of restriction digestion and DNA sequencing. The mutation frequency of SupF reporter gene in the presence of DOX was higher than in the absence of DOX. Conclusion： The TCR pathway takes part in the UVC-induced SupF gene mutation in Tet-on 293 cell line.

NEIGHBORING-NUCLEOTIDE EFFECTS ON THE MUTATION PATTERNS OF THE RICE GENOME

DNA composition dynamics across genomes of diverse taxonomy is a major subject of genome analyses. DNA composition changes are characteristics of both replication and repair machineries. We investigated 3,611,007 single nucleotide polymorphisms （SNPs） generated by comparing two sequenced rice genomes from distant inbred lines （subspecies）, including those from 242,811 introns and 45,462 protein-coding sequences （CDSs）. Neighboring-nucleotide effects （NNEs） of these SNPs are diverse, depending on structural content-based classifications （genomewide, intronic, and CDS） and sequence context-based categories （A/C, A/G, A/T, C/G, C/T, and G/T substitutions） of the analyzed SNPs. Strong and evident NNEs and nucleotide proportion biases surrounding the analyzed SNPs were observed in 1-3 bp sequences on both sides of an SNP. Strong biases were observed around neighboring nucleotides of protein-coding SNPs, which exhibit a periodicity of three in nucleotide content, constrained by a combined effect of codon-related rules and DNA repair mechanisms. Unlike a previous finding in the human genome, we found negative correlation between GC contents of chromosomes and the magnitude of corresponding bias of nucleotide C at -1 site and G at ＋1 site. These results will further our understanding of the mutation mechanism in rice as well as its evolutionary implications.