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Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification

Abstract

Chromatin modification enzymes are important regulators of gene expression and some are evolutionarily conserved from yeast to human. Saccharomyces cerevisiae is a major model organism for genome-wide studies that aim at the identification of target genes under the control of conserved epigenetic regulators. Ume6 interacts with the upstream repressor site 1 (URS1) and represses transcription by recruiting both the conserved histone deacetylase Rpd3 (through the co-repressor Sin3) and the chromatin-remodeling factor Isw2. Cells lacking Ume6 are defective in growth, stress response, and meiotic development. RNA profiling studies and in vivo protein-DNA binding assays identified mRNAs or transcript isoforms that are directly repressed by Ume6 in mitosis. However, a comprehensive understanding of the transcriptional alterations, which underlie the complex ume6Δ mutant phenotype during fermentation, respiration, or sporulation, is lacking. We report the protein-coding transcriptome of a diploid MAT a/α wild-type and ume6/ume6 mutant strains cultured in rich media with glucose or acetate as a carbon source, or sporulation-inducing medium. We distinguished direct from indirect effects on mRNA levels by combining GeneChip data with URS1 motif predictions and published high-throughput in vivo Ume6-DNA binding data. To gain insight into the molecular interactions between successive waves of Ume6-dependent meiotic genes, we integrated expression data with information on protein networks. Our work identifies novel Ume6 repressed genes during growth and development and reveals a strong effect of the carbon source on the derepression pattern of transcripts in growing and developmentally arrested ume6/ume6 mutant cells. Since yeast is a useful model organism for chromatin-mediated effects on gene expression, our results provide a rich source for further genetic and molecular biological work on the regulation of cell growth and cell differentiation in eukaryotes.

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Acknowledgments

Michael Primig extends his special thanks to Rochelle Easton Esposito for her support, guidance, and mentorship during several years he spent with her as a postdoctoral researcher at the University of Chicago and as an assistant professor at the Biozentrum in Basel. We thank Olivier Collin and Olivier Sallou for GermOnline systems administration and Aaron Mitchell for the SK1 MAT aume6/ume6 mutant strain. This work was supported by a Young Investigator fellowship from the Institut National de Santé et de Recherche Médicale (Inserm) awarded to A. Lardenois and an Inserm Avenir grant (R07216NS) awarded to M. Primig.

Conflict of interest

The authors disclose no conflicts of interest.

Ethical standards

The research does not involve human participants or animals.

Author information

Correspondence to Michael Primig.

Additional information

A. Lardenois, E. Becker, T. Walther contribued equally to this work.

Communicated by A. Aguilera.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Fig S1 Progression through meiotic M-phase in SK1 MAT a/α cells A plot shows the samples from cells cultured in rich medium with acetate (YPA), sporulation medium (SPII) at the indicated time points (x-axis) versus the percentage of mono-, bi- (MI) and tetranuclear (MII) cells (y-axis). (JPEG 122 kb)

Fig S2 RNA quality control of samples from SK1 MAT a/α cells A graphical display of RNA concentrations determined for three replicates (R1-R3) in samples from growth media (YPD, YPA) and sporulation medium (SPII) is shown. (JPEG 630 kb)

Fig S3 RNA quality control of samples from SK1 MAT a/α ume6 cells Data are shown like in Online Resource Figure S2. (JPEG 615 kb)

Fig S4 GeneChip data quality control (A) Signal intensities (y-axis) are plotted against probes (x-axis) for color-coded samples as indicated. (B) The distribution of un-normalized log2-transformed signal intensity values is shown in color-coded box plots. A black line represents the median. (JPEG 885 kb)

Fig S5 The gene filtration strategy A flow diagram outlines the method used to filter genes showing differential expression signals between a wild-type strain and a ume6 mutant strain. (JPEG 161 kb)

Fig S6 SIP4 promoter analysis (A) Screen shot from GermOnline showing log2-transformed expression data for SIP4 in the strains and media as indicated. The percentile of the signal intensities is given. The standard deviation is shown. (B) The SIP4 and SPO13 upstream sequences are shown. URS1 motifs are given in bold; the core sequence is shown in red. (C) Screen shot from GermOnline showing in vivo binding data of 13 transcription factors as indicated. The log2-transformed intensity ratio is given (Harbison et al. 2004). (D) ChIP data for in vivo Ume6 binding to SIP4 and SPO13 promoters in diploid cells (MAT a/α) cultured in rich medium (YPD). The promoters (x-axis) are plotted against the fold-enrichment (y-axis). (JPEG 584 kb)

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Lardenois, A., Becker, E., Walther, T. et al. Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification. Mol Genet Genomics 290, 2031–2046 (2015). https://doi.org/10.1007/s00438-015-1051-5

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Keywords

  • Ume6
  • Rpd3
  • Sin3
  • Isw2
  • Transcriptome
  • Interactome