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Modulation of enediyne-induced DNA damage by chromatin structures in transcriptionally active genes
1Division of Bioengineering and Environmental Health, Massachusetts Institute of Technology, Cambridge 02139, USA.
Abstract:
To better understand how the cellular environment of DNA affects it as a target for genotoxins, we have used ligation-mediated PCR to map DNA damage produced by two DNA-cleaving enediyne antibiotics, esperamicins A1 and C, in the transcriptionally active human p53 and phosphoglycerate kinase (pgk1) genes in vivo. Esperamicin A1, which is limited to damaging the linker region between nucleosome cores due to intercalation of an anthranilate moiety, did not detect the presence of a nucleosome proposed to reside between exons 5 and 6 of p53. This may be due to the absence of a nucleosome at this site in the p53 gene or to the altered structure of nucleosomes in transcriptionally active genes. In studies of the upstream region of the active pgk1 gene, we found that DNA damage produced by both enediynes was enhanced in sequences located between several transcription factor binding sites, while patterns of DNA damage within the binding sites were consistent with known drug binding modes and structures of the protein-DNA complexes. For both drugs, the DNA sequence appeared to be the major determinant of the location of DNA damage, with chromatin structures modulating the quantity of DNA damage.
Insights
Cellular DNA environments influence genotoxin targeting. Esperamicin antibiotics revealed DNA sequence as the primary determinant of damage, with chromatin structure modulating damage quantity in active genes.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- The cellular environment significantly impacts DNA's susceptibility to genotoxins.
- Understanding DNA damage mechanisms is crucial for drug development and cancer research.
Purpose of the Study:
- To investigate how DNA's cellular environment affects genotoxin-induced damage.
- To map DNA damage sites produced by esperamicins A1 and C in active human genes in vivo.
Main Methods:
- Ligation-mediated PCR was employed to map DNA damage.
- The study focused on transcriptionally active human p53 and phosphoglycerate kinase (pgk1) genes.
Main Results:
- Esperamicin A1 did not detect a proposed nucleosome between p53 exons 5 and 6, suggesting potential nucleosome absence or altered structure in active genes.
- DNA damage by both esperamicins was enhanced in sequences between transcription factor binding sites in the pgk1 gene.
- DNA sequence was the major determinant of damage location, while chromatin structure modulated damage quantity.
Conclusions:
- DNA sequence is the primary determinant of esperamicin-induced DNA damage.
- Chromatin structure plays a role in modulating the extent of DNA damage in active genes.
- Findings provide insights into drug-DNA interactions within the cellular context.