Dynamic alternative DNA structures in biology and disease

G Wang, KM Vasquez - Nature Reviews Genetics, 2023 - nature.com
Repetitive elements in the human genome, once considered 'junk DNA', are now known to
adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed …

Endogenous DNA damage as a source of genomic instability in cancer

A Tubbs, A Nussenzweig - Cell, 2017 - cell.com
Genome instability, defined as higher than normal rates of mutation, is a double-edged
sword. As a source of genetic diversity and natural selection, mutations are beneficial for …

[HTML][HTML] Transcription-replication conflict orientation modulates R-loop levels and activates distinct DNA damage responses

S Hamperl, MJ Bocek, JC Saldivar, T Swigut… - Cell, 2017 - cell.com
Conflicts between transcription and replication are a potent source of DNA damage. Co-
transcriptional R-loops could aggravate such conflicts by creating an additional barrier to …

Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance

T Wein, NF Hülter, I Mizrahi, T Dagan - Nature communications, 2019 - nature.com
Plasmid acquisition is an important mechanism of rapid adaptation and niche expansion in
prokaryotes. Positive selection for plasmid-coded functions is a major driver of plasmid …

Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis

E Letouzé, J Shinde, V Renault, G Couchy… - Nature …, 2017 - nature.com
Genomic alterations driving tumorigenesis result from the interaction of environmental
exposures and endogenous cellular processes. With a diversity of risk factors, liver cancer is …

Conflict resolution in the genome: how transcription and replication make it work

S Hamperl, KA Cimprich - Cell, 2016 - cell.com
The complex machineries involved in replication and transcription translocate along the
same DNA template, often in opposing directions and at different rates. These processes …

Mitotic DNA synthesis is caused by transcription-replication conflicts in BRCA2-deficient cells

FJ Groelly, RA Dagg, M Petropoulos, GG Rossetti… - Molecular Cell, 2022 - cell.com
Aberrant replication causes cells lacking BRCA2 to enter mitosis with under-replicated DNA,
which activates a repair mechanism known as mitotic DNA synthesis (MiDAS). Here, we …

DNA damage response and immune defense

C Nastasi, L Mannarino, M D'Incalci - International journal of molecular …, 2020 - mdpi.com
DNA damage is the cause of numerous human pathologies including cancer, premature
aging, and chronic inflammatory conditions. The DNA damage response (DDR), in turn …

Replication stress, DNA damage, inflammatory cytokines and innate immune response

S Ragu, G Matos-Rodrigues, BS Lopez - Genes, 2020 - mdpi.com
Complete and accurate DNA replication is essential to genome stability maintenance during
cellular division. However, cells are routinely challenged by endogenous as well as …

Starfish infers signatures of complex genomic rearrangements across human cancers

L Bao, X Zhong, Y Yang, L Yang - Nature cancer, 2022 - nature.com
Complex genomic rearrangements (CGRs) are common in cancer and are known to form via
two aberrant cellular structures—micronuclei and chromatin bridges. However, which of …