Single-stranded DNA ligation and XLF-stimulated incompatible DNA end ligation by the XRCC4-DNA ligase IV complex: influence of terminal DNA sequence

Abstract

The double-strand DNA break repair pathway, non-homologous DNA end joining (NHEJ), is distinctive for the flexibility of its nuclease, polymerase and ligase activities. Here we find that the joining of ends by XRCC4-ligase IV is markedly influenced by the terminal sequence, and a steric hindrance model can account for this. XLF (Cernunnos) stimulates the joining of both incompatible DNA ends and compatible DNA ends at physiologic concentrations of Mg2+, but only of incompatible DNA ends at higher concentrations of Mg2+, suggesting charge neutralization between the two DNA ends within the ligase complex. XRCC4-DNA ligase IV has the distinctive ability to ligate poly-dT single-stranded DNA and long dT overhangs in a Ku- and XLF-independent manner, but not other homopolymeric DNA. The dT preference of the ligase is interesting given the sequence bias of the NHEJ polymerase. These distinctive properties of the XRCC4-DNA ligase IV complex explain important aspects of its in vivo roles.

Structural characterization of filaments formed by human Xrcc4–Cernunnos/XLF complex involved in nonhomologous DNA end-joining

“…The crystal structure of the L4-X4-Cernunnos complex with the fulllength proteins should help to clarify the binding mode of the complete ligation complex. DSB repair studies in the presence or absence of Cernunnos have shown that Cernunnos promotes DNA end ligation by the L4-X4 complex (25,33). From our observation, we propose that the oligomerization of the X4-Cernunnos complex could be a mechanism to facilitate the recruitment of two or more L4-X4 complexes to DNA DSB repair points (Fig.…”

Unifying the DNA End-processing Roles of the Artemis Nuclease

“…The Artemis resection in 2-to 6-nt increments at blunt ends, as in Fig. 2, may liberate these short oligonucleotides, allowing them to be religated via the single-strand ligation activity of the ligase IV complex (22). This would generate the short inverted repeats observed at partially resected coding ends (27), which have previously been difficult to explain mechanistically until now.…”

Limited Repair of Critical DNA Damage in Cells Exposed to Low Dose Radiation

“…The final stage of DSBs repair by NHEJ is binding the broken DNA ends by the ligase complexes (Mahaney et al, 2009;. In the presence of Ku proteins, the full ligase complex (XRCC4/DNK-ligase IV/XLF) can couple incompatible DNA ends and, more effectively, blunt ends of breaks (Gu et al, 2007). Thus, we can assume that the main mechanism for repairing DNA DSB induced by low doses of IR is the NHEJ pathway.…”