ERCC6L2 safeguards genome editing outcomes – published in Nature Communications

DNA double-strand breaks (DSBs) are among the most dangerous forms of DNA damage, threatening genome stability but also serving as essential intermediates for many genome-editing technologies. A key question in the field is how cells repair different types of DSBs and what factors ensure that repair outcomes remain accurate.

In our new study, we uncover an important role for the DNA repair factor ERCC6L2 in safeguarding the repair of staggered DNA breaks, a type of DSB produced by several genome-editing tools. This exciting new work way led by our postdocs Eric Aird and Sebastian Siegner together with Almudena Serrano-Benítez from the Jackson lab (UCAM), together with the Cejka (USI) and Cathomen groups and colleagues from the University of Freiburg and IBSAL.

Using genome-wide CRISPR interference (CRISPRi) screening, we identified ERCC6L2 as a critical factor required for accurate repair of staggered DSBs generated by Cas12, TALENs, or dual Cas9 nicks. Interestingly, ERCC6L2 was not required for repairing the blunt DSBs typically produced by Cas9, revealing that different break structures rely on distinct repair mechanisms.

We found that ERCC6L2 protects staggered DNA ends and prevents harmful repair outcomes such as large deletions and chromosomal translocations. Mechanistically, ERCC6L2 counteracts the activity of the MRN complex (MRE11–RAD50–NBS1), limiting excessive DNA end resection and promoting accurate end joining.

Loss of ERCC6L2 sensitized cells to damage caused by multiple staggered breaks and increased genome instability following genome editing. These findings highlight ERCC6L2 as an important guardian of genome integrity and provide new insight into how cells respond to structurally diverse DNA breaks.

Beyond fundamental DNA repair biology, this work also has practical implications for genome engineering. Because many editing systems create staggered DNA ends, understanding how ERCC6L2 shapes repair outcomes may help improve editing accuracy and guide the safe use of these tools, particularly in therapeutic contexts. Our data reveal a protective role of ERCC6L2 in staggered-end DSB repair, shedding light on the molecular basis of pathology of ERCC6L2 mutations, which in humans most commonly present as inherited bone marrow failure and leukemia. The findings also suggest caution when considering therapeutic genome-editing strategies that rely on nucleases generating DNA overhangs for their treatment.

For more info, check out our new paper in Nature Communications!