Set2 Methyltransferase Facilitates DNA Replication and Promotes Genotoxic Stress Responses through MBF-Dependent Transcription

Abstract

SummaryChromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting MluI cell-cycle box (MCB) binding factor (MBF)-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR) expression, reduced deoxyribonucleoside triphosphate (dNTP) synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay. Accordingly, prolonged S phase in the absence of Set2 is suppressed by increasing dNTP synthesis. Furthermore, H3K36 is di- and tri-methylated at these MBF gene promoters, and Set2 loss leads to reduced MBF binding and transcription in response to genotoxic stress. Together, these findings provide new insights into how H3K36 methylation facilitates DNA replication and promotes genotoxic stress responses in fission yeast.

Nutritional cell cycle reprogramming reveals that inhibition of Cdk1 is required for proper MBF-dependent transcription

“…Our findings are in agreement with recent results reporting that loss of the Set2 histone H3 lysine 36 (H3K36) methyl transferase generates reduced MBF-dependent ribonucleotide reductase (cdc22 + ) expression, causing a drop in the dNTP pools, abnormal replication origin firing, S phase delay and genotoxic stress (Pai et al, 2017). As in the rum1Δ ste9Δ mutant, the delay in S phase and the replication stress can be supressed in set2Δ cells by increasing the dNTP levels by deleting the MBF repressor nrm1 + (our work) or yox1 + (Pai et al, 2017) or the RNR inhibitor spd1 + (Liu et al, 2003;Håkansson et al, 2006).…”

“…The correct supply of deoxyribonucleoside triphosphates (dNTPs) during S phase is crucial in maintaining genome integrity (Chabes and Stillman, 2007;Fleck et al, 2013). Recently, it has been shown that reduced MBF-dependent ribonucleotide reductase (RNR) expression generates DNA replication stress and checkpoint activation, phenotypes that can be reversed by increasing the dNTP pools (Pai et al, 2017). Low levels of RNR provide sufficient dNTPs for mitochondrial DNA synthesis and for DNA repair in quiescent cells and during the G1 phase of the cell cycle, but RNR levels and activity have to increase to high levels as cells enter S phase (Stillman, 2013).…”

“…Most MBF target genes encode proteins involved in the initiation of DNA replication, nucleotide biogenesis and the regulation of S phase (Bähler, 2005). Deregulation of MBF promotes genotoxic stress in S phase (Pai et al, 2017;Caetano et al, 2014;Pfister et al, 2015).…”

Set2 methyltransferase facilitates cell cycle progression by maintaining transcriptional fidelity

“…Further support for this was also recently provided by Pai et al. , who showed that Set2 in S. pombe is required for efficient DNA replication by regulating the MBF transcriptional program ( 44 ). However, the mechanistic basis by which Set2 controls S-phase progression and proper checkpoint activation remains unknown.…”

The role of dNTP metabolites in control of the embryonic cell cycle

“…This contradiction may be explained by the recent finding that the high speed of a progressing fork can induce DNA replication stress and slowdown the cell cycle [93]. On the other hand, the dNTP concentrations in yeast are controlled by multiple genes, and some of them are associated with mitotic entry or replication stress response [94,95], raising the complexity of interpretation compared with cultured cells. Moreover, it can be speculated that the embryonic cell cycle of metazoans controlled by dNTP may be underlying by further yet unknown mechanisms.…”