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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References
Anderson SF, Steber CM et al (1995) UME6, a negative regulator of meiosis in Saccharomyces cerevisiae, contains a C-terminal Zn2Cys6 binuclear cluster that binds the URS1 DNA sequence in a zinc-dependent manner. Protein Sci 4(9):1832–1843. doi:10.1002/pro.5560040918
Banerjee M, Uppuluri P et al (2013) Expression of UME6, a key regulator of Candida albicans hyphal development, enhances biofilm formation via Hgc1- and Sun41-dependent mechanisms. Eukaryot Cell 12(2):224–232. doi:10.1128/EC.00163-12
Bartholomew CR, Suzuki T et al (2012) Ume6 transcription factor is part of a signaling cascade that regulates autophagy. Proc Natl Acad Sci USA 109(28):11206–11210. doi:10.1073/pnas.1200313109
Baryshnikova A, Costanzo M et al (2010) Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Methods Enzymol 470:145–179. doi:10.1016/S0076-6879(10)70007-0
Carlisle PL, Kadosh D (2010) Candida albicans Ume6, a filament-specific transcriptional regulator, directs hyphal growth via a pathway involving Hgc1 cyclin-related protein. Eukaryot Cell 9(9):1320–1328. doi:10.1128/EC.00046-10
Carlisle PL, Banerjee M et al (2009) Expression levels of a filament-specific transcriptional regulator are sufficient to determine Candida albicans morphology and virulence. Proc Natl Acad Sci USA 106(2):599–604. doi:10.1073/pnas.0804061106
Carroll CW, Morgan DO (2002) The Doc1 subunit is a processivity factor for the anaphase-promoting complex. Nat Cell Biol 4(11):880–887. doi:10.1038/ncb871
Chalmel F, Rolland AD et al (2007) The conserved transcriptome in human and rodent male gametogenesis. Proc Natl Acad Sci USA 104(20):8346–8351
Childers DS, Mundodi V et al (2014) A 5′ UTR-mediated translational efficiency mechanism inhibits the Candida albicans morphological transition. Mol Microbiol 92(3):570–585. doi:10.1111/mmi.12576
Cho RJ, Campbell MJ et al (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2(1):65–73
Chu S, DeRisi J et al (1998) The transcriptional program of sporulation in budding yeast. Science 282(5389):699–705
Cliften P, Sudarsanam P et al (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301(5629):71–76
Costanzo MC, Engel SR et al (2014) Saccharomyces genome database provides new regulation data. Nucleic Acids Res 42(Database issue):D717–D725. doi:10.1093/nar/gkt1158
da Huang W, Sherman BT et al (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57. doi:10.1038/nprot.2008.211
Davey HM, Cross EJ et al (2012) Genome-wide analysis of longevity in nutrient-deprived Saccharomyces cerevisiae reveals importance of recycling in maintaining cell viability. Environ Microbiol 14(5):1249–1260. doi:10.1111/j.1462-2920.2012.02705.x
de Lichtenberg U, Jensen LJ et al (2005) Dynamic complex formation during the yeast cell cycle. Science 307(5710):724–727. doi:10.1126/science.1105103
Fazzio TG, Kooperberg C et al (2001) Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol Cell Biol 21(19):6450–6460
Gene Ontology C (2015) Gene ontology consortium: going forward. Nucleic Acids Res 43(Database issue):D1049–D1056. doi:10.1093/nar/gku1179
Goffeau A, Barrell BG et al (1996) Life with 6000 genes. Science 274(5287):546, 563–567
Goldmark JP, Fazzio TG et al (2000) The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell 103(3):423–433
Harbison CT, Gordon DB et al (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431(7004):99–104
Hillenmeyer ME, Fung E et al (2008) The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320(5874):362–365
Huntley RP, Sawford T et al (2014) The GOA database: gene ontology annotation updates for 2015. Nucleic Acids Res. doi:10.1093/nar/gku1113
Isserlin R, El-Badrawi RA et al (2011) The biomolecular interaction network database in PSI-MI 2.5. Database (Oxford) 2011: baq037. doi:10.1093/database/baq037
Kadosh D, Struhl K (1997) Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89(3):365–371
Kahana-Edwin S, Stark M et al (2013) Multiple MAPK cascades regulate the transcription of IME1, the master transcriptional activator of meiosis in Saccharomyces cerevisiae. PLoS One 8(11):e78920. doi:10.1371/journal.pone.0078920
Kassir Y, Adir N et al (2003) Transcriptional regulation of meiosis in budding yeast. Int Rev Cytol 224:111–171
Kellis M, Patterson N et al (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241–254
Kim Guisbert KS, Zhang Y et al (2012) Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. RNA 18(6):1142–1153. doi:10.1261/rna.030510.111
Kratzer S, Schuller HJ (1997) Transcriptional control of the yeast acetyl-CoA synthetase gene, ACS1, by the positive regulators CAT8 and ADR1 and the pleiotropic repressor UME6. Mol Microbiol 26(4):631–641
Kurdistani SK, Robyr D et al (2002) Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet 31(3):248–254
Lardenois A, Gattiker A et al (2010) GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. Database: the journal of biological databases and curation 2010: baq030. doi:10.1093/database/baq030
Lardenois A, Liu Y et al (2011) Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6. Proc Natl Acad Sci USA 108(3):1058–1063. doi:10.1073/pnas.1016459108
Lardenois A, Stuparevic I et al (2015) The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Nucleic Acids Res 43(1):115–128. doi:10.1093/nar/gku1185
Law MJ, Mallory MJ et al (2014) Acetylation of the transcriptional repressor Ume6p allows efficient promoter release and timely induction of the meiotic transient transcription program in yeast. Mol Cell Biol 34(4):631–642. doi:10.1128/MCB.00256-13
Liu Y, Stuparevic I et al (2015) The conserved histone deacetylase Rpd3 and the DNA binding regulator Ume6 repress BOI1′s meiotic transcript isoform during vegetative growth in Saccharomyces cerevisiae. Mol Microbiol. doi:10.1111/mmi.12976
Mallory MJ, Cooper KF et al (2007) Meiosis-specific destruction of the Ume6p repressor by the Cdc20-directed APC/C. Mol Cell 27(6):951–961
Mallory MJ, Law MJ et al (2012) Gcn5p-dependent acetylation induces degradation of the meiotic transcriptional repressor Ume6p. Mol Biol Cell 23(9):1609–1617. doi:10.1091/mbc.E11-06-0536
McCarroll RM, Esposito RE (1994) SPO13 negatively regulates the progression of mitotic and meiotic nuclear division in Saccharomyces cerevisiae. Genetics 138(1):47–60
Messenguy F, Vierendeels F et al (2000) In Saccharomyces cerevisiae, expression of arginine catabolic genes CAR1 and CAR2 in response to exogenous nitrogen availability is mediated by the Ume6 (CargRI)-Sin3 (CargRII)-Rpd3 (CargRIII) complex. J Bacteriol 182(11):3158–3164
Michaillat L, Mayer A (2013) Identification of genes affecting vacuole membrane fragmentation in Saccharomyces cerevisiae. PLoS One 8(2):e54160. doi:10.1371/journal.pone.0054160
Mitchell AP (1994) Control of meiotic gene expression in Saccharomyces cerevisiae. Microbiol Rev 58(1):56–70
Nagalakshmi U, Wang Z et al (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320(5881):1344–1349
Ngounou Wetie AG, Sokolowska I et al (2014) Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cellular and molecular life sciences : CMLS 71(2):205–228. doi:10.1007/s00018-013-1333-1
Nookaew I, Papini M et al (2012) A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res 40(20):10084–10097. doi:10.1093/nar/gks804
O’Connor L, Caplice N et al (2010) Differential filamentation of Candida albicans and Candida dubliniensis Is governed by nutrient regulation of UME6 expression. Eukaryot Cell 9(9):1383–1397. doi:10.1128/EC.00042-10
Ofir Y, Sagee S et al (2004) The role and regulation of the preRC component Cdc6 in the initiation of premeiotic DNA replication. Mol Biol Cell 15(5):2230–2242. doi:10.1091/mbc.E03-08-0617
Orchard S, Ammari M et al (2014) The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42(Database issue):D358–D363. doi:10.1093/nar/gkt1115
Orenstein Y, Linhart C et al (2012) Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data. PLoS One 7(9):e46145. doi:10.1371/journal.pone.0046145
Orlando DA, Lin CY et al (2008) Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature 453(7197):944–947
Pak J, Segall J (2002) Regulation of the premiddle and middle phases of expression of the NDT80 gene during sporulation of Saccharomyces cerevisiae. Mol Cell Biol 22(18):6417–6429
Park HD, Luche RM et al (1992) The yeast UME6 gene product is required for transcriptional repression mediated by the CAR1 URS1 repressor binding site. Nucleic Acids Res 20(8):1909–1915
Passmore LA, McCormack EA et al (2003) Doc1 mediates the activity of the anaphase-promoting complex by contributing to substrate recognition. EMBO J 22(4):786–796. doi:10.1093/emboj/cdg084
Primig M, Williams RM et al (2000) The core meiotic transcriptome in budding yeasts. Nat Genet 26(4):415–423
Prinz S, Avila-Campillo I et al (2004) Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Res 14(3):380–390. doi:10.1101/gr.2020604
Rundlett SE, Carmen AA et al (1998) Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392(6678):831–835. doi:10.1038/33952
Rustici G, Kolesnikov N et al (2013) ArrayExpress update–trends in database growth and links to data analysis tools. Nucleic Acids Res 41(Database issue):D987–D990. doi:10.1093/nar/gks1174
Saito R, Smoot ME et al (2012) A travel guide to Cytoscape plugins. Nat Methods 9(11):1069–1076. doi:10.1038/nmeth.2212
Shi L, Tu BP (2013) Acetyl-CoA induces transcription of the key G1 cyclin CLN3 to promote entry into the cell division cycle in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 110(18):7318–7323. doi:10.1073/pnas.1302490110
Shively CA, Eckwahl MJ et al (2013) Genetic networks inducing invasive growth in Saccharomyces cerevisiae identified through systematic genome-wide overexpression. Genetics 193(4):1297–1310. doi:10.1534/genetics.112.147876
Sopko R, Huang D et al (2006) Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell 21(3):319–330. doi:10.1016/j.molcel.2005.12.011
Spivak AT, Stormo GD (2012) ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res 40(Database issue):D162–D168. doi:10.1093/nar/gkr1180
Strich R, Slater MR et al (1989) Identification of negative regulatory genes that govern the expression of early meiotic genes in yeast. Proc Natl Acad Sci USA 86(24):10018–10022
Strich R, Surosky RT et al (1994) UME6 is a key regulator of nitrogen repression and meiotic development. Genes Dev 8(7):796–810
Strich R, Khakhina S et al (2011) Ume6p is required for germination and early colony development of yeast ascospores. FEMS Yeast Res 11(1):104–113. doi:10.1111/j.1567-1364.2010.00696.x
Stuparevic I, Becker E et al (2015) The histone deacetylase Rpd3/Sin3/Ume6 complex represses an acetate-inducible isoform of VTH2 in fermenting budding yeast cells. FEBS Lett. doi:10.1016/j.febslet.2015.02.022
Suzuki C, Hori Y et al (2003) Screening and characterization of transposon-insertion mutants in a pseudohyphal strain of Saccharomyces cerevisiae. Yeast 20(5):407–415
Sweet DH, Jang YK et al (1997) Role of UME6 in transcriptional regulation of a DNA repair gene in Saccharomyces cerevisiae. Mol Cell Biol 17(11):6223–6235
Tsukada M, Ohsumi Y (1993) Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett 333(1–2):169–174
Varela E, Schlecht U et al (2010) Mitotic expression of Spo13 alters M-phase progression and nucleolar localization of Cdc14 in budding yeast. Genetics 185(3):841–854. doi:10.1534/genetics.109.113746
Waern K, Snyder M (2013) Extensive transcript diversity and novel upstream open reading frame regulation in yeast. G3 (Bethesda) 3(2):343–352. doi:10.1534/g3.112.003640
Williams RM, Primig M et al (2002) The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast. Proc Natl Acad Sci USA 99(21):13431–13436
Wingender E (2008) The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform 9(4):326–332. doi:10.1093/bib/bbn016
Wyers F, Rougemaille M et al (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121(5):725–737. doi:10.1016/j.cell.2005.04.030
Xu Z, Wei W et al (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457(7232):1033–1037. doi:10.1038/nature07728
Yadon AN, Van de Mark D et al (2010) Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription. Mol Cell Biol 30(21):5110–5122. doi:10.1128/MCB.00602-10
Yoshikawa K, Tanaka T et al (2011) Comprehensive phenotypic analysis of single-gene deletion and overexpression strains of Saccharomyces cerevisiae. Yeast 28(5):349–361. doi:10.1002/yea.1843
Zeidler U, Lettner T et al (2009) UME6 is a crucial downstream target of other transcriptional regulators of true hyphal development in Candida albicans. FEMS Yeast Res 9(1):126–142. doi:10.1111/j.1567-1364.2008.00459.x
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 a/α ume6/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.
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Communicated by A. Aguilera.
A. Lardenois, E. Becker, T. Walther contribued equally to this work.
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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)
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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)
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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)
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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)
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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)
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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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DOI: https://doi.org/10.1007/s00438-015-1051-5