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CpG islands and double-minute chromosomes
1Department of Radiation Oncology, State University of New York Health Science Center, Syracuse 13210, USA.
Abstract:
Double-minute chromosomes (DMs) amplify oncogenes in human tumors. The organization of genomic DNA in four independently isolated DMs amplifying the DHFR (dihydrofolate reductase) gene has been compared by mapping locations of CpG islands. When cleaved with methylation-sensitive rare-cutting restriction endonucleases, three hypomethylated GC-rich DNA sequences were frequently found in specific regions in these DMs. One such zone was in the CpG island containing the divergently transcribed promoter separating the DHFR and the Rep-3 genes. The other two sites were approximately 500 kb upstream and 300 kb downstream of the DHFR gene. An approximately 800-kb amplified core genomic region containing the DHFR gene using DM-specific probes has been identified in this study. All the DMs consisted of the core amplified region combined with additional DNA fragments. These additional fragments are different for each DM. Therefore, while the DNAs in each of the DMs are different, they have common hypomethylated regions in similar locations. These results suggest a role for the location of hypomethylated GC-rich sites such as the CpG islands in genesis of DMs.
Insights
Double-minute chromosomes (DMs) amplify oncogenes by carrying amplified DNA. Common hypomethylated GC-rich regions in DMs suggest their role in DM formation during cancer development.
Area of Science:
- Genetics
- Cancer Biology
- Molecular Oncology
Background:
- Double-minute chromosomes (DMs) are extrachromosomal elements frequently observed in human tumors.
- DMs are known to harbor amplified oncogenes, contributing to tumorigenesis.
- The precise genomic organization and formation mechanism of DMs remain incompletely understood.
Purpose of the Study:
- To investigate the genomic organization of DNA within double-minute chromosomes (DMs).
- To identify common structural features, specifically CpG island locations, across independently isolated DMs.
- To explore the potential role of hypomethylated GC-rich regions in DM genesis.
Main Methods:
- Comparative mapping of CpG island locations in four independently isolated DMs amplifying the DHFR gene.
- Cleavage with methylation-sensitive rare-cutting restriction endonucleases to identify hypomethylated regions.
- Use of DM-specific probes to define the amplified core genomic region.
Main Results:
- Three common hypomethylated GC-rich DNA sequences were identified in specific regions within the DMs.
- One hypomethylated zone was located in the CpG island of the promoter region between DHFR and Rep-3 genes.
- An approximately 800-kb core amplified region containing the DHFR gene was identified, with additional unique DNA fragments in each DM.
Conclusions:
- The presence of common hypomethylated GC-rich sites in similar locations across different DMs suggests their involvement in DM formation.
- CpG islands and their associated hypomethylated states may play a critical role in the genesis of double-minute chromosomes.
- These findings provide insights into the structural organization and potential origin of extrachromosomal elements in cancer.