DNA Ligase IV Guides End-Processing Choice during Nonhomologous End Joining

Nonhomologous end joining (NHEJ) must adapt to diverse end structures during repair of chromosome breaks. Here, we investigate the mechanistic basis for this flexibility. DNA ends are aligned in a paired-end complex (PEC) by Ku, XLF, XRCC4, and DNA ligase IV (LIG4); we show by single-molecule analysis how terminal mispairs lead to mobilization of ends within PECs and consequent sampling of more end-alignment configurations. This remodeling is essential for direct ligation of damaged and mispaired ends during cellular NHEJ, since remodeling and ligation of such ends both require a LIG4-specific structural motif, insert1. Insert1 is also required for PEC remodeling that enables nucleolytic processing when end structures block direct ligation. Accordingly, cells expressing LIG4 lacking insert1 are sensitive to ionizing radiation. Cellular NHEJ of diverse ends thus identifies the steps necessary for repair through LIG4-mediated sensing of differences in end structure and consequent dynamic remodeling of aligned ends. [Display omitted] •Mobility of DNA ends aligned by NHEJ factors increases when ends are mispaired•Increased end mobility requires insert1, a motif unique to the NHEJ ligase (LIG4)•End mobilization is also essential for cellular repair of damaged and mispaired ends•This mechanism explains the remarkable flexibility of NHEJ in the repair of diverse ends Conlin et al. show that, when DNA double-strand breaks have terminal mispairs or damage, an unstructured loop unique to DNA ligase IV allows for dynamic remodeling of the alignment and end repair; the loop is also required for cellular resistance to ionizing radiation.