The Fission Yeast Homeodomain Protein Yox1p Binds to MBF and Confines MBF-Dependent Cell-Cycle Transcription to G1-S via Negative Feedback

Abstract

The regulation of the G1- to S-phase transition is critical for cell-cycle progression. This transition is driven by a transient transcriptional wave regulated by transcription factor complexes termed MBF/SBF in yeast and E2F-DP in mammals. Here we apply genomic, genetic, and biochemical approaches to show that the Yox1p homeodomain protein of fission yeast plays a critical role in confining MBF-dependent transcription to the G1/S transition of the cell cycle. The yox1 gene is an MBF target, and Yox1p accumulates and preferentially binds to MBF-regulated promoters, via the MBF components Res2p and Nrm1p, when they are transcriptionally repressed during the cell cycle. Deletion of yox1 results in constitutively high transcription of MBF target genes and loss of their cell cycle–regulated expression, similar to deletion of nrm1. Genome-wide location analyses of Yox1p and the MBF component Cdc10p reveal dozens of genes whose promoters are bound by both factors, including their own genes and histone genes. In addition, Cdc10p shows promiscuous binding to other sites, most notably close to replication origins. This study establishes Yox1p as a new regulatory MBF component in fission yeast, which is transcriptionally induced by MBF and in turn inhibits MBF-dependent transcription. Yox1p may function together with Nrm1p to confine MBF-dependent transcription to the G1/S transition of the cell cycle via negative feedback. Compared to the orthologous budding yeast Yox1p, which indirectly functions in a negative feedback loop for cell-cycle transcription, similarities but also notable differences in the wiring of the regulatory circuits are evident.

A homeodomain transcription factor regulates the DNA replication checkpoint in yeast

“…These results were not predicted by the observations that Nrm1 is unable to bind the Cdc10-C4 mutant protein and that Yox1 binding to MBFregulated promoters is Nrm1-dependent. 12,23 Hence, in addition to confirming the key role of Yox1 in the regulation of MBFdependent gene expression, our data suggests that Yox1 can function independently of Nrm1 to inhibit MBF activity.…”

“…Previous work established that Yox1 and Nrm1 act as repressors of MBFdependent gene expression in S. pombe 12,13 and, moreover, several lines of evidence suggested that Yox1 and Nrm1 may act in the same pathway. 12 It has also been shown that MBF-dependent gene expression is specifically derepressed at the permissive temperature (25°C) in cells containing the temperature sensitive cdc10-C4 allele, which encodes a C-terminal truncation of the MBF component Cdc10, and moreover that MBF-dependent gene expression decreases when these mutant cells are placed at the non-permissive temperature (>32°C). 9,24 Interestingly, Nrm1 is unable to bind the mutant Cdc10 protein, suggesting that the derepression of MBF-regulated genes at the permissive temperature is due to the inability of mutant Cdc10 to bind Nrm1.…”

“…Previous work suggested that Yox1 and Nrm1 act in the same pathway to repress MBF-dependent gene expression. 12 Furthermore, it has been demonstrated that Nrm1 is unable to bind to the Cdc10 protein encoded by the cdc10-C4 allele and that Yox1 binding to MBF-regulated promoters is Nrm1-dependent. 12,23 However, the observation that loss of Yox1 function can suppress the cdc10-C4 mutation at the non-permissive temperature suggests that Yox1 may also act independently of Nrm1.…”

“…12 Furthermore, it has been demonstrated that Nrm1 is unable to bind to the Cdc10 protein encoded by the cdc10-C4 allele and that Yox1 binding to MBF-regulated promoters is Nrm1-dependent. 12,23 However, the observation that loss of Yox1 function can suppress the cdc10-C4 mutation at the non-permissive temperature suggests that Yox1 may also act independently of Nrm1. Indeed, this conclusion is consistent with our findings that loss of either Nrm1 or Yox1, but not both together, increases the resistance of rad3 + cells to HU.…”

“…[7][8][9][10][11] Recently, two repressor proteins were identified that regulate MBF; Nrm1 and the homeodomain protein Yox1. 12,13 Thus, both the regulated activation and repression of transcription is utilized to determine the precise timing of specific gene expression during the cell division cycle. Interestingly, although there are some differences in their utilization, similar transcription factors, including MBF, the Yox1-related proteins Yox1 and Yhp1, and Nrm1, regulate the expression of genes at equivalent times in the cell division cycle in the distantly related S. cerevisiae.…”