Nonhomologous end joining (NHEJ) can effectively resolve chromosome breaks despite diverse end structures; however, it is unclear how the steps employed for resolution are determined. We sought to address this question by analysing cellular NHEJ of ends with systematically mispaired and damaged termini. We show NHEJ is uniquely proficient at bypassing subtle terminal mispairs and radiomimetic damage by direct ligation. Nevertheless, bypass ability varies widely, with increases in mispair severity gradually reducing bypass products from 85 to 6%. End-processing by nucleases and polymerases is increased to compensate, although paths with the fewest number of steps to generate a substrate suitable for ligation are favoured. Thus, both the frequency and nature of end processing are tailored to meet the needs of the ligation step. We propose a model where the ligase organizes all steps during NHEJ within the stable paired-end complex to limit end processing and associated errors.
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We would like to thank the Ramsden laboratory, Lynn Harrison, Scott Houck, Steve Roberts, Tristan de Buysscher, Hemant Kelkar, Maria Sambade, Janiel Shields, Dennis Simpson and William Kauffman for help with reagents and rationale. The Ramsden Laboratory was supported by R01 CA84442, J.M.P. by the LCCC T32 training grant, the Hendrickson Laboratory by R01s GM088351 and CA154461, and D.T.M. and B.F.Q. by the BIOS core grant.