The yeast Fun30 and human SMARCAD1 chromatin remodellers promote DNA end resection

Abstract

Several homology-dependent pathways can repair potentially lethal DNA double-strand breaks (DSBs). The first step common to all homologous recombination reactions is the 5′-3′ degradation of DSB ends that yields 3′ single-stranded DNA (ssDNA) required for loading of checkpoint and recombination proteins. The Mre11-Rad50-Xrs2/NBS1 complex and Sae2/CtIP initiate end resection while long-range resection depends on the exonuclease Exo1 or the helicase-topoisomerase complex Sgs1-Top3-Rmi1 with the endonuclease Dna21-6. DSBs occur in the context of chromatin, but how the resection machinery navigates through nucleosomal DNA is a process that is not well understood7. Here, we show that the yeast S. cerevisiae Fun30 protein and its human counterpart SMARCAD18, two poorly characterized ATP-dependent chromatin remodelers of the Snf2 ATPase family, are novel factors that are directly involved in the DSB response. Fun30 physically associates with DSB ends and directly promotes both Exo1- and Sgs1-dependent end resection through a mechanism involving its ATPase activity. The function of Fun30 in resection facilitates repair of camptothecin (CPT)-induced DNA lesions, and it becomes dispensable when Exo1 is ectopically overexpressed. Interestingly, SMARCAD1 is also recruited to DSBs and the kinetics of recruitment is similar to that of Exo1. Loss of SMARCAD1 impairs end resection, recombinational DNA repair and renders cells hypersensitive to DNA damage resulting from CPT or PARP inhibitor treatments. These findings unveil an evolutionarily conserved role for the Fun30 and SMARCAD1 chromatin remodelers in controlling end resection, homologous recombination and genome stability in the context of chromatin.

Mediator, TATA-binding Protein, and RNA Polymerase II Contribute to Low Histone Occupancy at Active Gene Promoters in Yeast

“…Little or no change was seen in steady-state-induced expression levels of CHA1 in yeast strains lacking core members of the ISW and INO80 complexes (30,31), or Fun30, which has homology to Snf2 and functions in gene silencing in heterochromatin and DNA repair (Fig. 1B) (32)(33)(34). We also tested the effect on CHA1 induction in the absence of the histone chaperone Asf1, which contributes to chromatin remodeling and transcriptional activation of the paradigmatic PHO5 gene in yeast, particularly under conditions of partial phosphate depletion (35,36), and again found no significant effect (Fig.…”

Elucidation of IgH 3′ region regulatory role during class switch recombination via germline deletion

“…4) compared with wt mice. Up-regulated miRNA in 3 0 RR-deficient mice have hundreds of ARTICLE predicted targets, including Atm, Ssb1, Ino80, Exo1, Smarcd1, Dclre1b and Atmin, which have been shown to regulate DSB resection and homologous recombination [33][34][35][36][37][38] , and histone modifying enzymes Hdac9 and Esco1. Interestingly, HDAC9 is required for DSB reparation by homologous reparation 39 , and its deletion affects antibody secretion 40 .…”

Regulation of Recombination and Genomic Maintenance

“…Histone modifications play a major role in the DNA-damage response providing binding sites for signaling and repair proteins in somatic cells, for example, g-H2AX for the Rad50-Mre11-Xrs2/NBS complex (Rogakou et al 1998;Kobayashi et al 2002). A specific role for the chromatin remodeler, Fun30, was identified in long-range end resection of DSB by Exo1 or Sgs1-Dna2 (Chen et al 2012;Costelloe et al 2012;Eapen et al 2012). Recent reviews provide excellent overviews of the effects of chromatin modifications and remodeling in response to DNA damage (Polo and Jackson 2011;Soria et al 2012;Price and D'Andrea 2013;Seeber et al 2013;Tsabar and Haber 2013).…”