High-resolution genomic assays provide insight into the division of labor between TLS and HDR in mammalian replication of damaged DNA

Resistance to DNA damage and enhanced DNA repair capacity in the hypoxia-tolerant blind mole rat, Spalax

“…Because no elevations in DNA damage in the S. carmeli control groups were observed, these cell cycle characteristics are not likely to be explained by culture conditions, such as atmospheric oxygen sensitivity, which could have slowed down the proliferation rate. Thus, these characteristics may reflect intrinsic strategies to tolerate DNA damage (Livneh et al, 2016), which may have evolved to prevent fork stalling and to expand the DNA repair checkpoint at the G2-M phase. Further investigation, such as S-phase-specific and fork progression studies, is required to answer this research question.…”

Spatiotemporal regulation of PCNA ubiquitination in damage tolerance pathways

“…Most DNA damage impedes DNA synthesis by high-fidelity replicative DNA polymerases (pols). DNA damage tolerance (DDT) mechanisms allow completion of DNA replication of lesion-containing genomic DNA (McCulloch and Kunkel 2008;Ulrich 2011;Zhang et al 2011;Sale et al 2012;Livneh et al 2016). In eukaryotes, two branches of the DDT pathway are regulated by ubiquitination of proliferating cell nuclear antigen (PCNA) at an evolutionarily conserved lysine residue, K164 (Hoege et al 2002).…”

“…Monoubiquitinated PCNA stimulates translesion DNA synthesis (TLS), and K63-linked polyubiquitination leads to homology-dependent repair (HDR) (also termed damage avoidance), which is a general term regardless of the type of biochemical reaction, e.g. template switching, complementary strand transfer, or fork regression, reviewed in Livneh et al (2016). The third branch is PCNA-ubiquitination-independent HDR, which is clearly recognized and distinguished from PCNA-polyubiquitination-dependent HDR in the budding yeast Saccharomyces cerevisiae (Papouli et al 2005;Pfander et al 2005;Zhang and Lawrence 2005;Hishida et al 2006;Gangavarapu et al 2007;Huang et al 2013).…”

“…By contrast, HDR is theoretically error-free because the DNA synthesis is thought to be predominantly performed by pol d, an accurate replicative DNA pol, using the corresponding region of the sister chromatid as its template. However, the relatively complex biochemical reactions involved, such as strand-exchange or replication fork remodeling, might pose a risk for chromosomal rearrangements, especially in higher eukaryotes with many repetitive sequences (Livneh et al 2016). Thus, the regulation of the pathway choice between TLS and HDR is critical for determining the biological outcomes of DNA damage.…”

“…Contradicting results should be considered to arrive at definitive conclusions, even when it is difficult to specify the reasons for the contradictions. For the details on the subsequent molecular mechanisms of TLS and HDR, on the significance of ubiquitination on different sites in PCNA, and on other modifications of PCNA, see the excellent recent reviews (Branzei and Psakhye 2016;Cipolla et al 2016;Garcia-Rodriguez et al 2016;Livneh et al 2016;Branzei and Szakal 2017;Kanao and Masutani 2017;Poole and Cortez 2017;Vaisman and Woodgate 2017;Leung et al 2018).…”