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Research Paper

Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae

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Pages 772-782 | Received 08 Apr 2016, Accepted 13 May 2016, Published online: 05 Aug 2016

References

  • Li H, Stillman B. The origin recognition complex: a biochemical and structural view. Sub-cell Biochem 2012; 62:37-58; PMID:22918579; http://dx.doi.org/10.1007/978-94-007-4572-8_3
  • Bell SP, Mitchell J, Leber J, Kobayashi R, Stillman B. The multidomain structure of Orc1p reveals similarity to regulators of DNA replication and transcriptional silencing. Cell 1995; 83:563-8; PMID:7585959; http://dx.doi.org/10.1016/0092-8674(95)90096-9
  • Klemm RD, Austin RJ, Bell SP. Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complex. Cell 1997; 88:493-502; PMID:9038340; http://dx.doi.org/10.1016/S0092-8674(00)81889-9
  • Vader G, Blitzblau HG, Tame MA, Falk JE, Curtin L, Hochwagen A. Protection of repetitive DNA borders from self-induced meiotic instability. Nature 2011; 477:115-9; PMID:21822291; http://dx.doi.org/10.1038/nature10331
  • Wery M, Descrimes M, Vogt N, Dallongeville AS, Gautheret D, Morillon A. Nonsense-Mediated Decay Restricts LncRNA Levels in Yeast Unless Blocked by Double-Stranded RNA Structure. Mol Cell 2016; 61(3):379-92; PMID:26805575
  • Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. The transcriptional program of sporulation in budding yeast. Science 1998; 282:699-705; PMID:9784122; http://dx.doi.org/10.1126/science.282.5389.699
  • Primig M, Williams RM, Winzeler EA, Tevzadze GG, Conway AR, Hwang SY, Davis RW, Esposito RE. The core meiotic transcriptome in budding yeasts. Nat Genet 2000; 26:415-23; PMID:11101837; http://dx.doi.org/10.1038/82539
  • Rabitsch KP, Toth A, Galova M, Schleiffer A, Schaffner G, Aigner E, Rupp C, Penkner AM, Moreno-Borchart AC, Primig M, et al. A screen for genes required for meiosis and spore formation based on whole-genome expression. Curr Biol 2001; 11:1001-9; PMID:11470404; http://dx.doi.org/10.1016/S0960-9822(01)00274-3
  • Lardenois A, Liu Y, Walther T, Chalmel F, Evrard B, Granovskaia M, Chu A, Davis RW, Steinmetz LM, Primig M, et al. 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 U S A 2011; 108:1058-63; PMID:21149693; http://dx.doi.org/10.1073/pnas.1016459108
  • Maier P, Rathfelder N, Maeder CI, Colombelli J, Stelzer EH, Knop M. The SpoMBe pathway drives membrane bending necessary for cytokinesis and spore formation in yeast meiosis. EMBO J 2008; 27:2363-74; PMID:18756268; http://dx.doi.org/10.1038/emboj.2008.168
  • Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz LM, Jacquier A. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 2009; 457:1038-42; PMID:19169244; http://dx.doi.org/10.1038/nature07747
  • Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM. Bidirectional promoters generate pervasive transcription in yeast. Nature 2009; 457:1033-7; PMID:19169243; http://dx.doi.org/10.1038/nature07728
  • Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science 2012; 335:552-7; PMID:22194413; http://dx.doi.org/10.1126/science.1215110
  • Xu L, Ajimura M, Padmore R, Klein C, Kleckner N. NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae. Mol Cell Biol 1995; 15:6572-81; PMID:8524222; http://dx.doi.org/10.1128/MCB.15.12.6572
  • Corbi D, Sunder S, Weinreich M, Skokotas A, Johnson ES, Winter E. Multisite phosphorylation of the Sum1 transcriptional repressor by S-phase kinases controls exit from meiotic prophase in yeast. Mol Cell Biol 2014; 34:2249-63; PMID:24710277; http://dx.doi.org/10.1128/MCB.01413-13
  • Xie J, Pierce M, Gailus-Durner V, Wagner M, Winter E, Vershon AK. Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae. Embo J 1999; 18:6448-54; PMID:10562556; http://dx.doi.org/; http://dx.doi.org/10.1093/emboj/18.22.6448
  • Pierce M, Benjamin KR, Montano SP, Georgiadis MM, Winter E, Vershon AK. Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression. Mol Cell Biol 2003; 23:4814-25; PMID:12832469; http://dx.doi.org/10.1128/MCB.23.14.4814-4825.2003
  • Tsuchiya D, Yang Y, Lacefield S. Positive feedback of NDT80 expression ensures irreversible meiotic commitment in budding yeast. PLoS Genet 2014; 10:e1004398; PMID:24901499; http://dx.doi.org/10.1371/journal.pgen.1004398
  • Winter E. The Sum1/Ndt80 transcriptional switch and commitment to meiosis in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 2012; 76:1-15; PMID:22390969; http://dx.doi.org/10.1128/MMBR.05010-11
  • Klutstein M, Siegfried Z, Gispan A, Farkash-Amar S, Zinman G, Bar-Joseph Z, Simchen G, Simon I. Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes. BMC Genomics 2010; 11:478; PMID:20716365; http://dx.doi.org/10.1186/1471-2164-11-478
  • Spivak AT, Stormo GD. ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res 2012; 40:D162-8; PMID:22140105; http://dx.doi.org/10.1093/nar/gkr1180
  • Van Loo P, Marynen P. Computational methods for the detection of cis-regulatory modules. Brief Bioinform 2009; 10:509-24; PMID:19498042; http://dx.doi.org/10.1093/bib/bbp025
  • Lardenois A, Stuparevic I, Liu Y, Law MJ, Becker E, Smagulova F, Waern K, Guilleux MH, Horecka J, Chu A, et al. The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Nucleic Acids Res 2015; 43:115-28; PMID:25477386; http://dx.doi.org/10.1093/nar/gku1185
  • Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM. High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biol 2010; 11:R24; PMID:20193063; http://dx.doi.org/10.1186/gb-2010-11-3-r24
  • Darde TA, Sallou O, Becker E, Evrard B, Monjeaud C, Le Bras Y, Jégou B, Collin O, Rolland AD, Chalmel F. The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. Nucleic Acids Res 2015; 43:W109-16; PMID:25883147; http://dx.doi.org/10.1093/nar/gkv345
  • Lardenois A, Gattiker A, Collin O, Chalmel F, Primig M. GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. Database 2010; 2010:baq030; PMID:21149299; http://dx.doi.org/10.1093/database/baq030
  • Chang DT, Huang CY, Wu CY, Wu WS. YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. Nucleic Acids Res 2011; 39:D647-52; PMID:21045055; http://dx.doi.org/10.1093/nar/gkq1086
  • Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, et al. Population genomics of domestic and wild yeasts. Nature 2009; 458:337-41; PMID:19212322; http://dx.doi.org/10.1038/nature07743
  • Kim Guisbert KS, Zhang Y, Flatow J, Hurtado S, Staley JP, Lin S, Sontheimer EJ. Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. RNA 2012; 18:1142-53; PMID:22539527; http://dx.doi.org/10.1261/rna.030510.111
  • Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008; 453:1239-43; PMID:18488015; http://dx.doi.org/10.1038/nature07002
  • Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Régnault B, Devaux F, Namane A, Séraphin B, et al. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 2005; 121:725-37; PMID:15935759; http://dx.doi.org/10.1016/j.cell.2005.04.030
  • Hongay CF, Grisafi PL, Galitski T, Fink GR. Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 2006; 127:735-45; PMID:17110333; http://dx.doi.org/10.1016/j.cell.2006.09.038
  • van Werven FJ, Neuert G, Hendrick N, Lardenois A, Buratowski S, van Oudenaarden A, Primig M, Amon A. Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell 2012; 150:1170-81; PMID:22959267; http://dx.doi.org/10.1016/j.cell.2012.06.049
  • Pelechano V, Steinmetz LM. Gene regulation by antisense transcription. Nat Rev Genet 2013; 14:880-93; PMID:24217315; http://dx.doi.org/10.1038/nrg3594
  • Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN. Structure of the sporulation-specific transcription factor Ndt80 bound to DNA. EMBO J 2002; 21:5721-32; PMID:12411490; http://dx.doi.org/10.1093/emboj/cdf572
  • Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 1998; 2:65-73; PMID:9702192; http://dx.doi.org/10.1016/S1097-2765(00)80114-8
  • Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998; 9:3273-97; PMID:9843569; http://dx.doi.org/10.1091/mbc.9.12.3273
  • Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 2006; 34:D108-10; PMID:16381825; http://dx.doi.org/10.1093/nar/gkj143
  • 3-900051-07-0 RDCTI. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2012.
  • Bembom O. seqLogo: Sequence logos for DNA sequence alignments.R package
  • Lardenois A, Stuparevic I, Liu Y, Law MJ, Becker E, Smagulova F, Waern K, Guilleux MH, Horecka J, Chu A, et al. The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Nucleic Acids Res 2015; 43:115-28; PMID:25477386; http://dx.doi.org/10.1093/nar/gku1185
  • Horecka J, Davis RW. The 50:50 method for PCR-based seamless genome editing in yeast. Yeast 2014; 31:103-12; PMID:24639370; http://dx.doi.org/10.1002/yea.2992

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