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DNA Damage and Repair: Current Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 January 2026 | Viewed by 572

Special Issue Editors


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Guest Editor
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, México
Interests: carcinogenesis; molecular oncology; transformation biomarkers; cancer stem cells
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Laboratorio de Genotoxicología, Instituto de Investigaciones Biomédicas, U.N.A.M., Mexico City 04510, Mexico
Interests: DNA damage and repair; gene expression; epigenetic effects; cell transformation; environmental exposure; human exposed populations

Special Issue Information

Dear Colleagues,

We are constantly exposed to a wide range of endogenous and exogenous compounds—originating from metabolism, diet, the environment, clothing, cosmetics, pharmaceuticals, and more—about which relatively little is known regarding their potential to disrupt the homeostasis between DNA damage and its repair via various cellular mechanisms. Furthermore, the body of evidence highlighting the crucial role of DNA repair pathways in numerous diseases, as well as their potential therapeutic applications, continues to grow rapidly.

With this in mind, this Special Volume, "DNA Damage and Repair: Current Research," welcomes the submission of original studies in this field. Our aim is to present a diverse collection of papers that reflect the breadth and depth of ongoing research on DNA damage and repair.

Dr. Mahara A. Valverde Ramírez
Dr. Emilio Rojas
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • DNA damage
  • DNA repair
  • endogenous compounds
  • exogenous compounds
  • therapy

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Published Papers (1 paper)

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Research

14 pages, 3279 KB  
Article
Identification and Characterization of eccDNA in HepG2 Cells Under DOX-Induced DNA Damage
by Jinyuan Zhang, Yuguo Li, Weijie Chen, Xingyi Du, Junnuo Zheng, Junji Chen, Xudong Huang, Chaoyang Pang and Zhiyun Guo
Int. J. Mol. Sci. 2025, 26(22), 10978; https://doi.org/10.3390/ijms262210978 - 13 Nov 2025
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Abstract
Extrachromosomal circular DNA (eccDNA) has been recognized as a key player in tumorigenesis and progression. However, eccDNA transcriptional regulatory mechanisms under DNA damage in cancer remain poorly characterized. Here, we used doxorubicin to induce DNA damage in the hepatocellular carcinoma cell line HepG2 [...] Read more.
Extrachromosomal circular DNA (eccDNA) has been recognized as a key player in tumorigenesis and progression. However, eccDNA transcriptional regulatory mechanisms under DNA damage in cancer remain poorly characterized. Here, we used doxorubicin to induce DNA damage in the hepatocellular carcinoma cell line HepG2 and performed Circle-seq to profile eccDNAs before and after the damage. We observed a significant increase in the number, length, and chromosomal distribution density of eccDNAs following DNA damage. RNA-seq revealed that the expression of genes carried on eccDNA was positively correlated with eccDNA copy number under DNA damage. Further ATAC-seq profiling identified distinct chromatin characteristics at eccDNA breakpoint regions compared to other regions of eccDNA and linear genomic regions. Additionally, eccDNAs generated under DNA damage preferentially originated from linear genomic regions characterized by low GC content and hypomethylation. Finally, by integrating Hi-C and H3K27ac ChIP-seq, we uncovered that eccDNAs with mobile enhancer activity (ME-eccDNAs) display significantly enhanced chromatin interactions and H3K27ac enrichment after DNA damage. Overall, our findings systematically elucidate the DNA damage-driven mechanisms underlying eccDNA biogenesis, chromatin characteristics and transcriptional regulation in HCC HepG2 cells. Full article
(This article belongs to the Special Issue DNA Damage and Repair: Current Research)
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