Lardenois Aurélie, Becker Emmanuelle, Walther Thomas, Law Michael J, Xie Bingning, Demougin Philippe, Strich Randy, Primig Michael
Inserm U1085-IRSET, University of Rennes 1, 35042, Rennes, France.
INRA, UMR 703, ONIRIS, 44307, Nantes, France.
Mol Genet Genomics. 2015 Oct;290(5):2031-46. doi: 10.1007/s00438-015-1051-5. Epub 2015 May 10.
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.
染色质修饰酶是基因表达的重要调节因子，其中一些在从酵母到人类的进化过程中保守存在。酿酒酵母是全基因组研究的主要模式生物，这类研究旨在鉴定保守表观遗传调节因子控制下的靶基因。Ume6与上游阻遏位点1（URS1）相互作用，并通过募集保守的组蛋白脱乙酰酶Rpd3（通过共阻遏物Sin3）和染色质重塑因子Isw2来抑制转录。缺乏Ume6的细胞在生长、应激反应和减数分裂发育方面存在缺陷。RNA分析研究和体内蛋白质-DNA结合试验确定了在有丝分裂中被Ume6直接抑制的mRNA或转录本异构体。然而，对于在发酵、呼吸或孢子形成过程中构成复杂的ume6Δ突变体表型基础的转录改变，仍缺乏全面的了解。我们报告了在富含葡萄糖或乙酸盐作为碳源的培养基中培养的二倍体MAT a/α野生型和ume6/ume6突变体菌株，或孢子形成诱导培养基中的蛋白质编码转录组。我们通过将基因芯片数据与URS1基序预测以及已发表的高通量体内Ume6-DNA结合数据相结合，区分了对mRNA水平的直接和间接影响。为了深入了解连续的Ume6依赖性减数分裂基因之间的分子相互作用，我们将表达数据与蛋白质网络信息整合在一起。我们的工作鉴定了生长和发育过程中新型的Ume6抑制基因，并揭示了碳源对生长和发育停滞的ume6/ume6突变体细胞中转录本去抑制模式的强烈影响。由于酵母是研究染色质介导的基因表达效应的有用模式生物，我们的结果为进一步开展关于真核生物细胞生长和细胞分化调控的遗传和分子生物学研究提供了丰富的资源。
