CRISPR-based genome editing through the lens of DNA repair

TS Nambiar, L Baudrier, P Billon, A Ciccia - Molecular cell, 2022 - cell.com
Genome editing technologies operate by inducing site-specific DNA perturbations that are
resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks …

DNA–protein crosslinks and their resolution

P Weickert, J Stingele - Annual Review of Biochemistry, 2022 - annualreviews.org
Covalent DNA–protein crosslinks (DPCs) are pervasive DNA lesions that interfere with
essential chromatin processes such as transcription or replication. This review strives to …

The EcoCyc database in 2021

IM Keseler, S Gama-Castro, A Mackie… - Frontiers in …, 2021 - frontiersin.org
The EcoCyc model-organism database collects and summarizes experimental data for
Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual …

A genetic map of the response to DNA damage in human cells

M Olivieri, T Cho, A Álvarez-Quilón, K Li… - Cell, 2020 - cell.com
The response to DNA damage is critical for cellular homeostasis, tumor suppression,
immunity, and gametogenesis. In order to provide an unbiased and global view of the DNA …

REV1-Polζ maintains the viability of homologous recombination-deficient cancer cells through mutagenic repair of PRIMPOL-dependent ssDNA gaps

A Taglialatela, G Leuzzi, V Sannino, R Cuella-Martin… - Molecular cell, 2021 - cell.com
BRCA1/2 mutant tumor cells display an elevated mutation burden, the etiology of which
remains unclear. Here, we report that these cells accumulate ssDNA gaps and spontaneous …

Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing

Y He, X Zhou, C Chang, G Chen, W Liu, G Li, X Fan… - Molecular Cell, 2024 - cell.com
Current base editors (BEs) use DNA deaminases, including cytidine deaminase in cytidine
BE (CBE) or adenine deaminase in adenine BE (ABE), to facilitate transition nucleotide …

Replication-coupled DNA repair

D Cortez - Molecular cell, 2019 - cell.com
The replisome quickly and accurately copies billions of DNA bases each cell division cycle.
However, it can make errors, especially when the template DNA is damaged. In these cases …

C-to-G editing generates double-strand breaks causing deletion, transversion and translocation

ME Huang, Y Qin, Y Shang, Q Hao, C Zhan, C Lian… - Nature Cell …, 2024 - nature.com
Base editors (BEs) introduce base substitutions without double-strand DNA cleavage.
Besides precise substitutions, BEs generate low-frequency 'stochastic'byproducts through …

AID in antibody diversification: there and back again

Y Feng, N Seija, JM Di Noia, A Martin - Trends in immunology, 2020 - cell.com
Activation-Induced cytidine Deaminase (AID) initiates affinity maturation and isotype
switching by deaminating deoxycytidines within immunoglobulin genes, leading to somatic …

New insights into abasic site repair and tolerance

PS Thompson, D Cortez - DNA repair, 2020 - Elsevier
Thousands of apurinic/apyrimidinic (AP or abasic) sites form in each cell, each day. This
simple DNA lesion can have profound consequences to cellular function, genome stability …