Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements

Abstract

The ability to determine the global location of transcription factor binding sites in vivo is important for a comprehensive understanding of gene regulation in human cells. We have developed a technology, called serial analysis of binding elements (SABE), involving subtractive hybridization of chromatin immunoprecipitation-enriched DNA fragments followed by the generation and analysis of concatamerized sequence tags. We applied the SABE technology to search for p53 target genes in the human genome, and have identified several previously described p53 targets in addition to numerous potentially novel targets, including the DNA mismatch repair genes MLH1 and PMS2. Both of these genes were determined to be responsive to DNA damage and p53 activation in normal human fibroblasts, and have p53-response elements within their first intron. These two genes may serve as a sensor in DNA repair mechanisms and a critical determinant for the decision between cell-cycle arrest and apoptosis. These results also demonstrate the potential for use of SABE as a broadly applicable means to globally identify regulatory elements for human transcription factors in vivo.chromatin immunoprecipitation ͉ DNA binding ͉ transcription factor

Distinct p53 genomic binding patterns in normal and cancer-derived human cells

“…The overlapping sites tended to be the strongest binding sites in both studies (28% of PET3 clusters and 52% of PET5 clusters overlapped with high-confidence ChIP-seq peaks, Table S7A). Similarly, ChIP-seq peaks with height of 31-50 were more likely to overlap with PET3 + clusters than peaks with height of [16][17][18][19][20] (Table S7B). Greater overlap between the higher ranked sites is expected in genome-wide studies.…”

“…3,17 Recent advances in sequencing technologies combined with chromatin immunoprecipitation (ChIP) have lead to the identification of thousands of p53 binding sites, providing unmatched opportunities for analysis and comparison of the global genomic p53 binding pattern under different experimental conditions. Notably, all de novo p53 binding studies published to date [18][19][20][21][22][23][24][25] have used cancer-derived cell lines. Binding of transcription factors (TF) to DNA is known to be context-dependent, governed in vivo by chromatin architecture and epigenetic modifications, 26 and these are subjected to major changes during tumor development.…”

Mapping genetic alterations causing chemoresistance in cancer: identifying the roads by tracking the drivers

“…Although the type of DNA lesion preferentially targeted by each mechanism is known, 183 notably, there is evidence for direct interaction between components of the different repair systems as well as between DNA repair and the p53 pathway. [186][187][188][189][190][191][192][193][194] Although loss of apoptotic/senescent function in theory should be expected to cause therapy resistance, the opposite may be the case in DNA repair. Drugs like alkylating agents generate 8-oxoguanine and single-strand breaks subject to repair by BER, whereas platinum-containing compounds generate interstrand crosslinks and double-strand breaks.…”

The dark side of a tumor suppressor: anti-apoptotic p53

“…In addition to these transcriptionindependent mechanisms, p53 transcriptionally upregulates at least in some cell types expression of the MLH1, PMS2 and MSH2 genes 11,12 whose products critically control the MMR pathway. Although overexpression of many MMRrelated proteins including those described above is sufficient to induce apoptosis, other studies report an increased sensitization following downregulation of MLH1 and MSH2.…”