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

Abstract

ATP-dependent chromatin remodeling complexes alter chromatin structure through interactions with chromatin substrates such as DNA, histones, and nucleosomes. However, whether chromatin remodeling complexes have the ability to regulate nonchromatin substrates remains unclear. Saccharomyces cerevisiae checkpoint kinase Mec1 (ATR in mammals) is an essential master regulator of genomic integrity. Here we found that the SWI/SNF chromatin remodeling complex is capable of regulating Mec1 kinase activity. In vivo, Mec1 activity is reduced by the deletion of Snf2, the core ATPase subunit of the SWI/SNF complex. SWI/SNF interacts with Mec1, and cross-linking studies revealed that the Snf2 ATPase is the main interaction partner for Mec1. In vitro, SWI/SNF can activate Mec1 kinase activity in the absence of chromatin or known activators such as Dpb11. The subunit requirement of SWI/SNFmediated Mec1 regulation differs from that of SWI/SNF-mediated chromatin remodeling. Functionally, SWI/SNFmediated Mec1 regulation specifically occurs in S phase of the cell cycle. Together, these findings identify a novel regulator of Mec1 kinase activity and suggest that ATP-dependent chromatin remodeling complexes can regulate nonchromatin substrates such as a checkpoint kinase.

3.9 Å structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP

“…The Mec1 N terminus is highly flexible, with more than 200 amino acids (residues 1 to 235) invisible in the structure. Consistently, no cross-linking signals were detected within this region (14). Similarly, the N terminus of the mTOR is also invisible in the 4.4 Å cryo-EM reconstruction (10).…”

Loss of Snf5 Induces Formation of an Aberrant SWI/SNF Complex

“…SWI/SNF was purified using a Snf2 FLAG-tagged strain as described previously (Kapoor et al, 2015). The complex was further purified over an SP Sepharose column to remove FLAG peptide before crosslinking with BS3 (Thermo Scientific).…”

Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress

“…INO80C recruitment may be influenced in part by promoter-specific factors. We note that Mec1 also forms a transient complex with the SWI/SNF complex, which is another chromatin remodeler implicated in both DSB repair and transcriptional control (Kapoor et al 2015). Transient interactions such as these may be mediated by post-translational modifications, allowing rapid translation of signal cascades into chromatin configurations.…”