Mec1/Tel1 Phosphorylation of the INO80 Chromatin Remodeling Complex Influences DNA Damage Checkpoint Responses

Abstract

The yeast Mec1/Tel1 kinases, ATM/ATR in mammals, coordinate the DNA damage response by phosphorylating proteins involved in DNA repair and checkpoint pathways. Recently, ATP-dependent chromatin remodeling complexes, such as the INO80 complex, have also been implicated in DNA damage responses, although regulatory mechanisms that direct their function remain unknown. Here, we show that the Ies4 subunit of the INO80 complex is phosphorylated by the Mec1/Tel1 kinases during exposure to DNA-damaging agents. Mutation of Ies4's phosphorylation sites does not significantly affect DNA repair processes, but does influence DNA damage checkpoint responses. Additionally, ies4 phosphorylation mutants are linked to the function of checkpoint regulators, such as the replication checkpoint factors Tof1 and Rad53. These findings establish a chromatin remodeling complex as a functional component in the Mec1/Tel1 DNA damage signaling pathway that modulates checkpoint responses and suggest that posttranslational modification of chromatin remodeling complexes regulates their involvement in distinct processes.

Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex

“…ATP-dependent chromatin remodeling complexes such as SWI/SNF have been shown to be involved in DNA repair and are also implicated in human cancer (Chai et al 2005;Wilson and Roberts 2011). The INO80 complex has also been shown to be involved in regulation of cell cycle checkpoints (Morrison et al 2007). Despite these emerging links, how chromatin remodeling complexes regulate the checkpoint response mechanistically remains unknown.…”

“…7). These emerging studies reveal a new network of regulations in which not only do the checkpoint kinases such as Mec1 regulate ATP-dependent chromatin remodeling complexes such as INO80 (Morrison et al 2007), but the chromatin remodeling complexes such as SWI/SNF also regulate the checkpoint kinases (Fig. 7).…”

“…Recruitment of ATP-dependent chromatin remodeling complexes to DSBs (Ray et al 2009;Lee et al 2010;Qi et al 2015) and the remodeling of the surrounding chromatin occur on a timescale similar to that of H2A phosphorylation. Moreover, it has been shown that the phosphorylation of Ies4 (a subunit of the INO80 chromatin remodeling complex) by Mec1/ Tel1 in response to DNA damage directs INO80 function toward checkpoint regulation (Morrison et al 2007). The timing and close proximity of chromatin remodeling complexes with key checkpoint kinases at damaged sites raise the possibility that ATP-dependent chromatin remodeling complexes may participate in the regulation of checkpoint kinases.…”

Chromatin dynamics coupled to DNA repair

“…This finding indicates that INO80 can modulate checkpoint responses in the Mec1/Tel1 DNA damage signaling pathway. 107 Interestingly, although the initial recruitment of INO80 to DSB is dependent on the phosphorylation of the H2AX, its chromatin remodeling and nucleosome eviction activity can occur independently of γH2AX. 97,99 It is possible that γH2AX may be initially dispensable for chromatin remodeling but it is important for maintaining the remodeled state of chromatin that enables complete repair.…”

“…105 The activity of INO80 can also be modulated by kinase action. 107 The Ies4 subunit of the INO80 complex is phosphorylated by Mec1/ Tel1 (ATR/ATM) kinases in response to DNA damage. Mutation of Ies4 phosphorylation sites does not significantly affect the DNA repair process but does influence DNA damage response.…”