Characterizing Age-Related Extrachromosomal Circular DNA in Mouse Liver: Potential Biomarker for Liver Aging [ChIP-Seq]
Background: Extrachromosomal circular deoxyribonucleic acid (eccDNA) is progressively being recognized as a useful biomarker, however, its presence in the liver remains relatively understudied.  Methods: Through the application of Circle-Seq, this research reports on the identification and subsequent analysis of eccDNAs in both young and aging livers of the house mouse species. As a complement, RNA-Seq tests were conducted, and results subjected to a combined analysis with the initial Circle-Seq findings.  Results: In total, Hundreds of thousands of unique eccDNAs were identified and methodically characterized. The eccDNAs detected were predominantly GC-rich. The majority of eccDNAs were under the size of 10000 base pairs, accumulating predominantly in two distinct peaks. The genomic distribution analysis of the eccDNAs revealed their presence across all chromosomes, concentrating on the 5'UTR and CpG islands. Analysis of the junction sequences infer that microhomology and palindromic repeats may contribute to eccDNA formation. The frequency of eccDNAs in aged mice exceeded that of their youthful counterparts. In addition, there was a noticeable positive correlation between the substantial production of eccDNA and the transcription of its corresponding mRNA, all of which were reported as senescence-related genes.  Conclusions: This research offers the inaugural comprehensive characterisation of aging-related eccDNAs in the liver. It underscores the potential of eccDNA as a valuable biomarker for liver aging. Overall design: The C57 murine models employed for this investigation were sourced from SPF Biotechnology (Beijing) and were accommodated within SPF-grade animal housing until they attained an age of 24 months. A parallel younger control group was integrated into this research, comprised of a set of 3-month-old C57 mice, which maintained a consistent genetic lineage with the more mature collective. All mice used were male, with 6 mice per group.The mice were euthanized using carbon dioxide anesthesia followed by cervical dislocation, hepatic tissues from mice were collected and subsequently homogenized utilizing a tissue homogenizer. For the sequencing of eccDNA, we pooled the livers from three mice within the same group for the isolation of eccDNA.