Fig 1: Decreased activity of the base excision repair (BER) pathway in cells with sustained p21WAF1/Cip1 expression. a Increased reactive species (RS) levels were assessed with a DCFH-DA assay in Saos2 (i) and Li-Fraumeni (ii) cells with protracted p21WAF1/Cip1 expression (*p < 0.05 (Saos2), *p = 0.05 (Li-Fraumeni), t-test; error bars indicate standard deviation; n = 5 experiments). As shown in the middle panel RS production can lead to generation of base/nucleotide oxidative lesions. b RNAseq analysis showed that essential factors of the BER pathway were statistically significantly down-regulated (p = 0.05) in 96-h induced Saos2- (i) and Li-Fraumeni- (ii) p21WAF1/Cip1 Tet-ON cells (see also Additional file 1: Figure S3 for specific real time RT-PCR validation). Note that although in Saos2- p21WAF1/Cip1 Tet-ON cells OGG1 expression was not found by RNAseq analysis, specific real-time RT-PCR and microarray analysis (see also Additional file 1: Figure S3) [9] confirmed its decreased expression. Selective immunoblots for APEX1, LIG3, TDG, and MUTY confirmed the specificity of the RNA analysis results. Note that LIG3 participates also in mismatch repair (MMR; Additional file 1: Figure S3). a-Tubulin served as loading control. c Modified alkaline Comet assay demonstrated the presence of oxidized purines like 8-oxo-dG in 96-h induced Saos2- (i) and Li-Fraumeni- (ii) p21WAF1/Cip1 Tet-ON cells, using 8-oxoguanine glycosylase (OGG1) (*p < 0.05 (Saos2), *p = 0.05 (Li-Fraumeni), t-test; error bars indicate standard deviation; n = 5 experiments). Comet data were corroborated by an 8-oxo-dG-specific assay measuring DNA incorporation of 8-oxo-dG in p21WAF1/Cip1-expressing cells [24], which indicated lower OGG1 activity (*p < 0.05 (Saos2), *p = 0.05 (Li-Fraumeni), t-test; error bars indicate standard deviation; n = 5 experiments). Consequently, as depicted in the model in the middle panel, recognition and excision of the affected nucleotide lesion is impaired in the BER process. The middle panel depicts the components and steps during BER. The BER pathway is responsible for removal of small lesions from DNA, especially oxidized, alkylated, deaminated bases and abasic sites. BER can be induced by oxidative stress and various genotoxic insults. Its specificity relies on the excision of base damage by glycosylases. In humans, the mechanism of BER involves the initial action of DNA glycosylases followed by the processing of the resulting abasic site either by the AP-lyase activity of the glycosylases or by the apurinic/apyrimidic endonucleases APE1/APE2, which incise the DNA strand. The resulting single-strand break can be processed by two BER subpathways. Either the short-patch branch is engaged, if a single nucleotide is replaced, or the long-patch branch, if 2–10 new nucleotides are synthesized. OGG1 8-oxoguanine DNA glycosylase, UNG uracil DNA glycosylase, TDG thymine DNA glycosylase, SMUG1 single-strand-selective monofunctional uracil-DNA glycosylase 1, NTH DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III), MBD4 methyl-CpG binding domain 4, DNA glycosylase, MPG N-methylpurine DNA glycosylase, MUTY adenine DNA glycosylase, NEIL1/2/3 Nei-like DNA glycosylase 1/ 2/ 3, APEX1/2 apurinic/apyrimidinic endodeoxyribonuclease 1/2, POLB/POLD, DNA polymerase beta/ delta, PCNA proliferating cell nuclear antigen, RFC replication factor C, FEN1 flap structure-specific endonuclease 1, LIG1/LIG3 DNA ligase 1/3, PARP1 poly(ADP-ribose) polymerase 1, XRCC1 X-ray repair cross complementing 1