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Article

Cdc7-Dbf4 Is a Gene-Specific Regulator of Meiotic Transcription in Yeast

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Pages 541-557 | Received 11 Aug 2011, Accepted 10 Nov 2011, Published online: 20 Mar 2023

REFERENCES

  • Abe H, Shimoda C. 2000. Autoregulated expression of Schizosaccharomyces pombe meiosis-specific transcription factor Mei4 and a genome-wide search for its target genes. Genetics 154:1497–1508.
  • Ahmed NT, Bungard D, Shin ME, Moore M, Winter E. 2009. The Ime2 protein kinase enhances the disassociation of the Sum1 repressor from middle meiotic promoters. Mol. Cell. Biol. 29:4352–4362.
  • Allers T, Lichten M. 2001. Differential timing and control of noncrossover and crossover recombination during meiosis. Cell 106:47–57.
  • Bailis JM, Bernard P, Antonelli R, Allshire RC, Forsburg SL. 2003. Hsk1-Dfp1 is required for heterochromatin-mediated cohesion at centromeres. Nat. Cell Biol. 5:1111–1116.
  • Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP. 2006. A probability-based approach for high throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24:1285–1292.
  • Benjamin KR, Zhang C, Shokat KM, Herskowitz I. 2003. Control of landmark events in meiosis by the CDK Cdc28 and the meiosis-specific kinase Ime2. Genes Dev. 17:1524–1539.
  • Borde V, Goldman AS, Lichten M. 2000. Direct coupling between meiotic DNA replication and recombination initiation. Science 290:806–809.
  • Brachmann CB, et al. 1995. The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability. Genes Dev. 9:2888–2902.
  • Buckingham LE, et al. 1990. Nucleotide sequence and promoter analysis of SPO13, a meiosis-specific gene of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 87:9406–9410.
  • Buonomo SB, et al. 2000. Disjunction of homologous chromosomes in meiosis I depends on proteolytic cleavage of the meiotic cohesin Rec8 by separin. Cell 103:387–398.
  • Carlile TM, Amon A. 2008. Meiosis I is established through division-specific translational control of a cyclin. Cell 133:280–291.
  • Chi MH, Shore D. 1996. SUM1-1, a dominant suppressor of SIR mutations in Saccharomyces cerevisiae, increases transcriptional silencing at telomeres and HM mating-type loci and decreases chromosome stability. Mol. Cell. Biol. 16:4281–4294.
  • Cho WH, Lee YJ, Kong SI, Hurwitz J, Lee JK. 2006. CDC7 kinase phosphorylates serine residues adjacent to acidic amino acids in the minichromosome maintenance 2 protein. Proc. Natl. Acad. Sci. U. S. A. 103:11521–11526.
  • Chu S, et al. 1998. The transcriptional program of sporulation in budding yeast. Science 282:699–705. ( Erratum, 282:1421.)
  • Chu S, Herskowitz I. 1998. Gametogenesis in yeast is regulated by a transcriptional cascade dependent on Ndt80. Mol. Cell 1:685–696.
  • de los Santos T, Hollingsworth NM. 1999. Red1p: a MEK1-dependent phosphoprotein that physically interacts with Hop1p during meiosis in yeast. J. Biol. Chem. 274:1783–1790.
  • Elias JE, Gygi SP. 2007. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4:207–214.
  • Eng JK, McCormack AL, Yates JRIII. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5:976–989.
  • Fingerman I, Sutphen K, Montano SP, Georgiadis MM, Vershon AK. 2004. Characterization of critical interactions between Ndt80 and MSE DNA defining a novel family of Ig-fold transcription factors. Nucleic Acids Res. 32:2947–2956.
  • Goldmark JP, Fazzio TG, Estep PW, Church GM, Tsukiyama T. 2000. The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell 103:423–433.
  • Hardy CF, Dryga O, Seematter S, Pahl PM, Sclafani RA. 1997. mcm5/cdc46-bob1 bypasses the requirement for the S phase activator Cdc7p. Proc. Natl. Acad. Sci. U. S. A. 94:3151–3155.
  • Heller RC, et al. 2011. Eukaryotic origin-dependent DNA replication in vitro reveals sequential action of DDK and S-CDK kinases. Cell 146:80–91.
  • Henderson KA, Kee K, Maleki S, Santini P, Keeney S. 2006. Cyclin-dependent kinase directly regulates initiation of meiotic recombination. Cell 125:1321–1332.
  • Hepworth SR, Ebisuzaki LK, Segall J. 1995. A 15-base-pair element activates the SPS4 gene midway through sporulation in Saccharomyces cerevisiae. Mol. Cell. Biol. 15:3934–3944.
  • Hepworth SR, Friesen H, Segall J. 1998. NDT80 and the meiotic recombination checkpoint regulate expression of middle sporulation-specific genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 18:5750–5761.
  • Hollingsworth NM. 2008. Deconstructing meiosis one kinase at a time: polo pushes past pachytene. Genes Dev. 22:2596–2600.
  • Hollingsworth NM, Ponte L, Halsey C. 1995. MSH5, a novel MutS homolog, facilitates meiotic reciprocal recombination between homologs in Saccharomyces cerevisiae but not mismatch repair. Genes Dev. 9:1728–1739.
  • Holt LJ, et al. 2009. Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science 325:1682–1686.
  • Huttlin EL, et al. 2010. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143:1174–1189.
  • Irlbacher H, Franke J, Manke T, Vingron M, Ehrenhofer-Murray AE. 2005. Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression. Genes Dev. 19:1811–1822.
  • Jolly ER, Chin CS, Herskowitz I, Li H. 2005. Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis. BMC Bioinformatics 6:275.
  • Kadosh D, Struhl K. 1998. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol. Cell. Biol. 18:5121–5127.
  • Katis VL, et al. 2010. Rec8 phosphorylation by casein kinase 1 and Cdc7-Dbf4 kinase regulates cohesin cleavage by separase during meiosis. Dev. Cell 18:397–409.
  • Keeney S. 2001. Mechanism and control of meiotic recombination initiation. Curr. Top. Dev. Biol. 52:1–53.
  • Kim JM, Takemoto N, Arai K, Masai H. 2003. Hypomorphic mutation in an essential cell-cycle kinase causes growth retardation and impaired spermatogenesis. EMBO J. 22:5260–5272.
  • Klein F, et al. 1999. A central role for cohesins in sister chromatid cohesion, formation of axial elements and recombination during meiosis. Cell 98:91–103.
  • Krisak L, et al. 1994. SMK1, a developmentally regulated MAP kinase, is required for spore wall assembly in Saccharomyces cerevisiae. Genes Dev. 8:2151–2161.
  • Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN. 2002. Structure of the sporulation-specific transcription factor Ndt80 bound to DNA. EMBO J. 21:5721–5732.
  • Law DT, Segall J. 1988. The SPS100 gene of Saccharomyces cerevisiae is activated late in the sporulation process and contributes to spore wall maturation. Mol. Cell. Biol. 8:912–922.
  • Lindgren A, et al. 2000. The pachytene checkpoint in Saccharomyces cerevisiae requires the Sum1-transcriptional repressor. EMBO J. 19:6489–6497.
  • Lo H-C, Wan L, Rosebrock A, Futcher B, Hollingsworth NM. 2008. Cdc7-Dbf4 regulates NDT80 transcription as well as reductional segregation during budding yeast meiosis. Mol. Biol. Cell 19:4956–4967.
  • Longtine MS, et al. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14:953–961.
  • Mallory MJ, Cooper KF, Strich R. 2007. Meoisis-specific destruction of the Ume6p repressor by the Cdc20-directed APC/C. Mol. Cell 27:951–961.
  • Marston AL, Amon A. 2004. Meiosis: cell-cycle controls shuffle and deal. Nat. Rev. 5:983–997.
  • Masai H, et al. 2006. Phosphorylation of MCM4 by Cdc7 kinase facilitates its interaction with Cdc45 on the chromatin. J. Biol. Chem. 281:39249–39261.
  • Matos J, et al. 2008. Dbf4-dependent CDC7 kinase links DNA replication to the segregation of homologous chromosomes in meiosis I. Cell 135:662–678.
  • Mavrich TN, et al. 2008. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 18:1073–1083.
  • McCord R, et al. 2003. Rfm1, a novel tethering factor required to recruit the Hst1 histone deacetylase for repression of middle sporulation genes. Mol. Cell. Biol. 23:2009–2016.
  • Mok J, et al. 2010. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci. Signal. 3:ra12.
  • Montagnoli A, et al. 2006. Identification of Mcm2 phosphorylation sites by S-phase-regulating kinases. J. Biol. Chem. 281:10281–10290.
  • Montano SP, et al. 2002. Crystal structure of the DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast. Proc. Natl. Acad. Sci. U. S. A. 99:14041–14046.
  • Moore M, et al. 2007. Ar-Pro-X-Ser/Thr is a consensus phosphoacceptor sequence for the meiosis-specific Ime2 protein kinase in Saccharomyces cerevisiae. Biochemistry 46:271–278.
  • Murakami H, Keeney S. 2008. Regulating the formation of DNA double-strand breaks in meiosis. Genes Dev. 22:286–292.
  • Murakami H, Nurse P. 2001. Regulation of premeiotic S phase and recombination-related double-strand DNA breaks during meiosis in fission yeast. Nat. Genet. 28:290–293.
  • Niu H, et al. 2009. Regulation of meiotic recombination via Mek1-mediated Rad54 phosphorylation. Mol. Cell 36:393–404.
  • Ogino K, et al. 2006. Hsk1 kinase is required for induction of meiotic dsDNA breaks without involving checkpoint kinases in fission yeast. Proc. Natl. Acad. Sci. U. S. A. 103:8131–8136.
  • 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. 22:6417–6429.
  • Pak J, Segall J. 2002. Role of Ndt80, Sum1, and Swe1 as targets of the meiotic recombination checkpoint that control exit from pachytene and spore formation in Saccharomyces cerevisiae. Mol. Cell. Biol. 22:6430–6440.
  • Percival-Smith A, Segall J. 1986. Characterization and mutational analysis of a cluster of three genes expressed preferentially during sporulation of Saccharomyces cerevisiae. Mol. Cell. Biol. 6:2443–2451.
  • Petronczki M, Siomos MF, Nasmyth K. 2003. Un menage a quatre: the molecular biology of chromosome segregation in meiosis. Cell 112:423–440.
  • Pierce M, et al. 2003. Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression. Mol. Cell. Biol. 23:4814–4825.
  • Primig M, et al. 2000. The core meiotic transcriptome in budding yeasts. Nat. Genet. 26:415–423.
  • Rabitsch KP, et al. 2003. Kinetochore recruitment of two nucleolar proteins is required for homolog segregation in meiosis I. Dev. Cell 4:535–548.
  • Randell JC, et al. 2010. Mec1 is one of multiple kinases that prime the Mcm2-7 helicase for phosphorylation by Cdc7. Mol. Cell 40:353–363.
  • Rubin-Bejerano I, Mandel S, Robzyk K, Kassir Y. 1996. Induction of meiosis in Saccharomyces cerevisiae depends on conversion of the transcriptional repressor Ume6 to a positive regulator by its regulated association with the transcriptional activator Ime1. Mol. Cell. Biol. 16:2518–2526.
  • Rundlett SE, Carmen AA, Suka N, Turner BM, Grunstein M. 1998. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392:831–835.
  • Rusche LN, Rine J. 2001. Conversion of a gene-specific repressor to a regional silencer. Genes Dev. 15:955–967.
  • Sasanuma H, et al. 2008. Cdc7-dependent phosphorylation of Mer2 facilitates initiation of yeast meiotic recombination. Genes Dev. 22:398–410.
  • Schild D, Byers B. 1978. Meiotic effects of DNA-defective cell division cycle mutations of Saccharomyces cerevisiae. Chromosoma 70:109–130.
  • Sclafani RA. 2000. Cdc7p-Dbf4p becomes famous in the cell cycle. J. Cell Sci. 113:2111–2117.
  • Sheu YJ, Stillman B. 2006. Cdc7-Dbf4 phosphorylates MCM proteins via a docking site-mediated mechanism to promote S phase progression. Mol. Cell 24:101–113.
  • Shin ME, Skokotas A, Winter E. 2010. The Cdk1 and Ime2 protein kinases trigger exit from meiotic prophase in Saccharomyces cerevisiae by inhibiting the Sum1 transcriptional repressor. Mol. Cell. Biol. 30:2996–3003.
  • Smith AV, Roeder GS. 1997. The yeast Red1 protein localizes to the cores of meiotic chromosomes. J. Cell Biol. 136:957–967.
  • Sopko R, Raithatha S, Stuart D. 2002. Phosphorylation and maximal activity of Saccharomyces cerevisiae meiosis-specific transcription factor Ndt80 is dependent on Ime2. Mol. Cell. Biol. 22:7024–7040.
  • Sourirajan A, Lichten M. 2008. Polo-like kinase Cdc5 drives exit from pachytene during budding yeast meiosis. Genes Dev. 22:2627–2632.
  • Strich R, et al. 1994. UME6 is a key regulator of nitrogen repression and meiotic development. Genes Dev. 8:796–810.
  • Sutton A, et al. 2001. A novel form of transcriptional silencing by Sum1-1 requires Hst1 and the origin recognition complex. Mol. Cell. Biol. 21:3514–3522.
  • Sym M, Engebrecht J, Roeder GS. 1993. ZIP1 is a synaptonemal complex protein required for meiotic chromosome synapsis. Cell 72:365–378.
  • Tanny JC, Dowd GJ, Huang J, Hilz H, Moazed D. 1999. An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing. Cell 99:735–745.
  • Tanny JC, Moazed D. 2001. Coupling of histone deacetylation to NAD breakdown by the yeast silencing protein Sir2: evidence for acetyl transfer from substrate to an NAD breakdown product. Proc. Natl. Acad. Sci. U. S. A. 98:415–420.
  • Tong A, Boone C. 2005. Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae. Methods Mol. Biol. 313:171–192.
  • Toth A, et al. 2000. Functional genomics identifies monopolin: a kinetochore protein required for segregation of homologs during meiosis i. Cell 103:1155–1168.
  • Tung KS, Hong EJ, Roeder GS. 2000. The pachytene checkpoint prevents accumulation and phosphorylation of the meiosis-specific transcription factor Ndt80. Proc. Natl. Acad. Sci. U. S. A. 97:12187–12192.
  • Valentin G, Schwob E, Della Seta F. 2006. Dual role of the CDC7-regulatory protein DBF4 during yeast meiosis. J. Biol. Chem. 281:2828–2834.
  • Venters BJ, Pugh BF. 2009. How eukaryotic genes are transcribed. Crit. Rev. Biochem. Mol. Biol. 44:117–141.
  • Vershon AK, Hollingsworth NM, Johnson AD. 1992. Meiotic induction of the yeast HOP1 gene is controlled by positive and negative regulatory elements. Mol. Cell. Biol. 12:3706–3714.
  • Vershon AK, Pierce M. 2000. Transcriptional regulation of meiosis in yeast. Curr. Opin. Cell Biol. 12:334–339.
  • Wan L, et al. 2008. Cdc28-Clb5 (CDK-S) and Cdc7-Dbf4 (DDK) collaborate to initiate meiotic recombination in yeast. Genes Dev. 22:386–397.
  • Wan L, Zhang C, Shokat KM, Hollingsworth NM. 2006. Chemical inactivation of Cdc7 kinase in budding yeast results in a reversible arrest that allows efficient cell synchronization prior to meiotic recombination. Genetics 174:1767–1774.
  • Wang Y, Chang CY, Wu JF, Tung KS. 2011. Nuclear localization of the meiosis-specific transcription factor Ndt80 is regulated by the pachytene checkpoint. Mol. Biol. Cell 22:1878–1886.
  • Xie J, et al. 1999. Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae. EMBO J. 18:6448–6454.
  • Xu L, Ajimura M, Padmore R, Klein C, Kleckner N. 1995. NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae. Mol. Cell. Biol. 15:6572–6581.
  • Zhang L, Ma H, Pugh BF. 2011. Stable and dynamic nucleosome states during a meiotic developmental process. Genome Res. 21:875–884.

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