The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends

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Abstract
Nucleolytic degradation of 5′ strands at DNA double-strand breaks in yeast is shown to be facilitated by the nucleosome remodeller Fun30, particularly within chromatin bound by the checkpoint adaptor protein known to inhibit resection, Rad9. For breakages in double-stranded DNA to be repaired, the 5′ terminal strand is resected to yield a 3′ terminal single-stranded tail. How resection occurs in the context of chromatin was unknown. The laboratories of Grzegorz Ira and Bertrand Llorente have identified the yeast Fun30 and human SMARCAD1 proteins as the chromatin re-modellers that facilitate resection. Fun30 is also required to overcome the inhibition of resection that occurs owing to binding of Rad9, a checkpoint adaptor protein, to the 5′ end of the break. Chromosomal double-strand breaks (DSBs) are resected by 5′ nucleases to form 3′ single-stranded DNA substrates for binding by homologous recombination and DNA damage checkpoint proteins. Two redundant pathways of extensive resection have been described both in cells1,2,3 and in vitro4,5,6, one relying on Exo1 exonuclease and the other on Sgs1 helicase and Dna2 nuclease. However, it remains unknown how resection proceeds within the context of chromatin, where histones and histone-bound proteins represent barriers for resection enzymes. Here we identify the yeast nucleosome-remodelling enzyme Fun30 as a factor promoting DSB end resection. Fun30 is the major nucleosome remodeller promoting extensive Exo1- and Sgs1-dependent resection of DSBs. The RSC and INO80 chromatin-remodelling complexes and Fun30 have redundant roles in resection adjacent to DSB ends. ATPase and helicase domains of Fun30, which are needed for nucleosome remodelling7, are also required for resection. Fun30 is robustly recruited to DNA breaks and spreads along the DSB coincident with resection. Fun30 becomes less important for resection in the absence of the histone-bound Rad9 checkpoint adaptor protein known to block 5′ strand processing8 and in the absence of either histone H3 K79 methylation or γ-H2A, which mediate recruitment of Rad9 (refs 9, 10). Together these data suggest that Fun30 helps to overcome the inhibitory effect of Rad9 on DNA resection.