Extrachromosomal Circular DNA from TCGA Tumors Is Generated from Common Genomic Loci, Is Characterized by Self-Homology and DNA Motifs near Circle Breakpoints
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Data Acquisition
2.2. Generating Random Circular DNA for Control Comparisons
2.3. Pan-Cancer Genome-Wide Analysis of Circle Location
2.4. Identifying Circles with Genes and Circles without Genes
2.5. Gene Expression Analysis
2.6. Homology and Microhomology Analysis
2.7. Motif Enrichment
3. Results
3.1. Circles Are Commonly Generated at Specific Genomic Loci Independent of Cancer Type
3.2. Characteristics of Circular DNAs from TCGA Samples
3.3. Genes on Circles Are More Likely to Be Expressed and Are More Highly Expressed, than Other Genes in the Genome
3.4. Some Circles Are Self-Homologous
3.5. Most Circles Are Self-Microhomologous
3.6. Circle Ends Are Enriched in Transcription Factor DNA Binding Motifs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Tatman, P.D.; Black, J.C. Extrachromosomal Circular DNA from TCGA Tumors Is Generated from Common Genomic Loci, Is Characterized by Self-Homology and DNA Motifs near Circle Breakpoints. Cancers 2022, 14, 2310. https://doi.org/10.3390/cancers14092310
Tatman PD, Black JC. Extrachromosomal Circular DNA from TCGA Tumors Is Generated from Common Genomic Loci, Is Characterized by Self-Homology and DNA Motifs near Circle Breakpoints. Cancers. 2022; 14(9):2310. https://doi.org/10.3390/cancers14092310
Chicago/Turabian StyleTatman, Philip D., and Joshua C. Black. 2022. "Extrachromosomal Circular DNA from TCGA Tumors Is Generated from Common Genomic Loci, Is Characterized by Self-Homology and DNA Motifs near Circle Breakpoints" Cancers 14, no. 9: 2310. https://doi.org/10.3390/cancers14092310