AI Article Synopsis
- Double-strand breaks (DSBs) are harmful DNA damage events that can cause genome instability, prompting cells to use repair methods like non-homologous end joining (NHEJ), microhomology mediated end joining (MMEJ), and homology-directed recombination (HDR).
- These repair processes can introduce DNA sequence variations, such as insertions and deletions, at the break site, necessitating accurate analysis through high throughput sequencing.
- The study introduces a method for visualizing the complex patterns of sequence variations around DSBs, facilitating better comparison across different experimental conditions.
Article Abstract
Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end joining (MMEJ), and homology-directed recombination (HDR). These repair processes may lead to DNA sequence variations (e.g., nucleotide insertions, deletions, and substitutions) at the location of the break. Studying DNA DSB repair processes often involves the use of high throughput sequencing assays to precisely quantify the sequence variations near the break with software tools. Often methods of assessing and visualizing these data have not taken into account the full complexity of the sequencing data, such as the frequency, type, and position of the sequence variations in a single comprehensive representation. Here we present a method that allows visualization of the overall variation pattern as well as comparison of these patterns among experimental setups.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10793479 | PMC |
Publication Analysis
Top Keywords
Similar Publications
Concurrent transmission of Zika virus during the 2023 dengue outbreak in Dhaka, Bangladesh.
PLoS Negl Trop Dis
January 2025
Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.
Background: During the 2023-dengue outbreak in Bangladesh, a diagnostic evaluation study was conducted to investigate concurrent Zika virus (ZIKV) and dengue virus (DENV) transmission in Dhaka in 2023.
Aims: The study explored to simultaneously detect the presence of ZIKV, DENV, and/or CHIKV while considering relevant clinical and epidemiological risk factors, using a real-time multiplex RT-PCR system. Following this, it was planned to sequence the selected samples to identify genetic variations of the ZIKV infections within the population.
Russia is a country with a high incidence of tick-borne encephalitis (TBE). In northwestern regions of Russia, 110 TBE cases were registered in 2021. The largest numbers of TBE cases were registered in the Arkhangelsk region and St.
View Article and Find Full Text PDFMulti-omics sequencing of gastroesophageal junction adenocarcinoma reveals prognosis-relevant key factors and a novel immunogenomic classification.
Gastric Cancer
January 2025
Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
Background: Gastroesophageal junction adenocarcinoma (GEJAC) exhibits distinct molecular characteristics due to its unique anatomical location. We sought to investigate effective and reliable molecular classification of GEJAC to guide personalized treatment.
Methods: We analyzed the whole genomic, transcriptomic, T-cell receptor repertoires, and immunohistochemical data in 92 GEJAC patients and delineated the landscape of genetic and immune alterations.
Influence of Ty3/gypsy and Ty1/copia LTR-retrotransposons on the large genomes of Alstroemeriaceae: genome landscape of Bomarea edulis (Tussac) Herb.
Protoplasma
January 2025
Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil.
Repetitive elements are the main components of many plant genomes and play a crucial role in the variation of genome size and structure, ultimately impacting species diversification and adaptation. Alstroemeriaceae exhibits species with large genomes, not attributed to polyploidy. In this study, we analysed the repetitive fraction of the genome of Bomarea edulis through low-coverage sequencing and in silico characterization, and compared it to the repeats of Alstroemeria longistaminea, a species from a sister genus that has been previously characterized.
View Article and Find Full Text PDFG-quadruplex structures in 16S rRNA regions correlate with thermal adaptation in prokaryotes.
Nucleic Acids Res
January 2025
Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, United States.
G-quadruplex (G4) structure is a nucleic acid secondary structure formed by guanine-rich sequences, playing essential roles in various biological processes such as gene regulation and environmental stress adaptation. Although prokaryotes growing at high temperatures have higher GC contents, the pattern of G4 structure associated with GC content variation in thermal adaptation remains elusive. This study analyzed 681 bacterial genomes to explore the role of G4 structures in thermal adaptation.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!