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Functional interaction between the transcription factor Sfp1 and the NuA4 complex in response to nutrient availability[RNA]

ABSTRACT: In this study, we investigate gene expression profile upon carbon source shifts in yeast. RNA-sequencing was performed in Sfp1 wild-type strain and K655/657 mutants growing in different carbon sources.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE268202 | GEO | 2026/05/01

REPOSITORIES: GEO

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Functional interaction between the transcription factor Sfp1 and the NuA4 complex in response to nutrient availability [CUT&RUN]

Project description:In this study, we investigate the physical and functional interaction between the transcription factor Sfp1 and the NuA4 complex in response to nutrient changes or stress. To study the functional interaction, we rapidly deplete Sfp1 or Esa1 (the catalytic subunit of NuA4) from nucleus, and performed CUT&RUN to profile all Sfp1/NuA4-regulated genes.

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Functional interaction between the transcription factor Sfp1 and the NuA4 complex in response to nutrient availability[RNA]

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Functional interaction between the transcription factor Sfp1 and the NuA4 complex in response to nutrient availability [CUT&RUN]

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SFP1 (ChIP-seq)

Project description:We set out to determine how Sfp1 binding targets evolved over time. We sampled our species of interest to include one pre-whole genome duplicaton (WGD) species containing SFP1A (K. lactis), one post-WGD species containing both SFP1 and SFP1PL (N. castellii), two post-WGD species containing only SFP1 (S. cerevisiae and S. paradoxus) and performed ChIP for each Sfp1 homolog in each species using an antibody that recognizes a conserved subdomain of Sfp1 common to both Sfp1, Sfp1a, and Sfp1pl. Because Sfp1pl was also present in N. castellii, a second antibody was used that is more specific to Sfp1pl (denoted as IP3). We also performed ChIP in SFP1 deletion mutants in each species tested, as a control."

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Project description:In Saccharomyces cerevisiae growth, size control and cell cycle progression are strictly coordinated and regulated according to the nutritional conditions. In particular, ribosome biogenesis appears a key event in this regulatory network. SFP1 encodes a zinc-finger protein promoting the transcription of a large cluster of genes involved in ribosome biogenesis. It has been suggested that Sfp1 is a cell size modulator acting at Start. To better study the regulatory role of Sfp1 and its putative involvement in cell size and cycle control, we analysed the behaviour of an sfp1 null mutant strain and of an isogenic reference strain growing in chemostat cultures. This approach allowed us to analyze both strains at the same specific growth rate, thus eliminating the secondary effects due to the slow growing phenotype that the sfp1 null mutant shows in shake flask. We studied glucose(anaerobic)- and ethanol(aerobic)-limited cultures, as paradigms of two different metabolic states. Major alterations of the transcriptional profile were observed during growth on glucose, while no significant differences were observed when comparing ethanol growing cultures. In particular, in the former growth condition, Sfp1 appears involved in the control of ribosome biogenesis but not of ribosomal protein gene expression. Keywords: global transcriptional profile, genetic modification, ribosome biogenesis

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Project description:In this study, we investigate the physical and functional interaction between NuA4 and Sfp1. Sfp1 was rapidly depleted from yeast nuclei, and histone modification changes were detected by ChIP-sequencing.

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Sfp1 regulates yeast cell growth and division through multiple promoter binding modes

Project description:Understanding how transcriptional programs help to coordinate cell growth and division is an important unresolved problem. Here we report that the nutrient- and stress-regulated transcription factor Sfp1 is rate-limiting for expression of a large suite of genes involved in yeast cell growth, including ribosomal protein, ribosome biogenesis, and snoRNA genes. Remarkably, the spectrum of Sfp1 transcription effects is concordant with a combination of chromatin immunoprecipitation and chromatin endogenous cleavage binding analyses, which together provide evidence for two distinct modes of Sfp1 promoter binding, one requiring a co-factor and the other a specific DNA-recognition motif. In addition to growth-related genes, Sfp1 binds to and regulates the promoters of key G1/S regulon genes and that of MRS6, whose product regulates Sfp1 nuclear localization. Our findings suggest that Sfp1 acts as a master regulator of cell growth and cell size by coordinating the expression of genes implicated in mass accumulation and cell division.

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