Functional dissection of IME1 transcription using quantitative promoter-reporter screening

Genetics

Volumn 186, Issue 3, 2010, Pages 829-841

  Kahana, Smadar ^a   Pnueli, Lilach ^a   Kainth, Pinay ^b,c   Sassi, Holly E ^b   Andrews, Brenda ^b,c   Kassir, Yona ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; PROTEIN SOK2; PROTEIN SUM1; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR IME1; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; FLUORESCENCE; GENETIC CONSERVATION; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; REGULATORY SEQUENCE; REPORTER GENE; SACCHAROMYCES; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; GENES, FUNGAL; GENES, REPORTER; GENES, SYNTHETIC; GENETIC TESTING; HIGH-THROUGHPUT SCREENING ASSAYS; MEIOSIS; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

SACCHAROMYCES; SACCHAROMYCETALES;

EID: 78951488810     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.122200     Document Type: Article

References (39)

1. ANDREWS, B. J., and I. HERSKOWITZ, 1989 Identification of a DNA binding factor involved in cell-cycle control of the yeast HO gene. Cell 57: 21-29.
2. BADIS, G., E. T. CHAN, H. VAN BAKEL, L. PENA-CASTILLO, D. TILLO et al., 2008 A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol. Cell 32: 878-887.
3. BERGER, M. F., and M. L. BULYK, 2006 Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins. Methods Mol. Biol. 338: 245-260.
4. BREEDEN, L., and K. NASMYTH, 1987 Cell cycle control of the yeast HO gene: cis- and trans-acting regulators. Cell 48: 389-397.
5. CHELLAPPA, R., P. KANDASAMY, C. S. OH, Y. JIANG, M. VEMULA et al., 2001 The membrane proteins, Spt23p and Mga2p, play distinct roles in the activation of Saccharomyces cerevisiae OLE1 gene expression. Fatty acid-mediated regulation of Mga2p activity is independent of its proteolytic processing into a soluble transcription activator. J. Biol. Chem. 276: 43548-43556.
6. CHUA, G., Q. D. MORRIS, R. SOPKO, M. D. ROBINSON, O. RYAN et al., 2006 Identifying transcription factor functions and targets by phenotypic activation. Proc. Natl. Acad. Sci. USA 103: 12045-12050.
7. CLIFTEN, P. F., L. W. HILLIER, L. FULTON, T. GRAVES, T. MINER et al., 2001 Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 11: 1175-1186.
8. CLIFTEN, P., P. SUDARSANAM, A. DESIKAN, L. FULTON, B. FULTON et al., 2003 Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
9. COVITZ, P. A., and A. P.MITCHELL, 1993 Repression by the yeast meiotic inhibitor RME1. Genes Dev. 7: 1598-1608.
10. DAVIDSON, E. H., J. P. RAST, P. OLIVERI, A. RANSICK, C. CALESTANI et al., 2002 A genomic regulatory network for development. Science 295: 1669-1678.
11. FILLINGHAM, J., P. KAINTH, J. P. LAMBERT, H. VAN BAKEL, K.TSUI et al., 2009 Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. Mol. Cell 35: 340-351.
12. GORNER, W., E. DURCHSCHLAG, M. T.MARTINEZ-PASTOR, F. ESTRUCH, G. AMMERER et al., 1998 Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev. 12: 586-597.
13. GRANOT, D., J. P. MARGOLSKEE and G. SIMCHEN, 1989 A long region upstream of the IME1 gene regulates meiosis in yeast. Mol. Gen. Genet. 218: 308-314.
14. GRAY, M., M. KUPIEC and S. M. HONIGBERG, 2004 Site-specific genomic (SSG) and random domain-localized (RDL) mutagenesis in yeast. BMC Biotechnol. 4: 7.
15. GUREVICH, V., Y. KASSIR, 2010 A switch from a gradient to a threshold mode in the regulation of a transcriptional cascade promotes robust execution of meiosis in budding yeast. PLoS ONE 5: e11005.
16. HARBISON, C. T., D. B. GORDON, T. I. LEE, N. J.RINALDI, K.D.MACISAAC et al., 2004 Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
17. KAINTH, P., H. E. SASSI, L. PENA-CASTILLO, G. CHUA, T. R. HUGHES et al., 2009 Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast. Methods 48: 258-264.
18. KASSIR, Y., and G. SIMCHEN, 1991 Monitoring meiosis and sporulation in Saccharomyces cerevisiae. Methods Enzymol. 194: 94-110.
19. KASSIR, Y., D. GRANOT and G. SIMCHEN, 1988 IME1, a positive regulator gene of meiosis in S. cerevisiae. Cell 52: 853-862.
20. KASSIR, Y., N. ADIR, E. BOGER-NADJA, N. GUTTMANN-RAVIV, I. RUBIN-BEJERANO et al., 2003 Transcriptional regulation of meiosis in budding yeast. Int. Rev. Cytol. 224: 111-171.
21. KUNOH, T., Y. KANEKO and S. HARASHIMA, 2000 YHP1 encodes a new homeoprotein that binds to the IME1 promoter in Saccharomyces cerevisiae. Yeast 16: 439-449.
22. LAPIDOT,M., O.MIZRAHI-MAN and Y. PILPEL, 2008 Functional characterization of variations on regulatory motifs. PLoS Genet. 4: e1000018.
23. LINDGREN, A., D. BUNGARD, M. PIERCE, J. XIE, A. VERSHON et al., 2000 The pachytene checkpoint in Saccharomyces cerevisiae requires the Sum1 transcriptional repressor. EMBOJ. 19: 6489-6497.
24. MACISAAC, K. D., T.WANG, D.B.GORDON, D.K.GIFFORD, G. D. STORMO et al., 2006 An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7: 113.
25. MILLER, J., 1972 Experiments in Molecular Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
26. PNUELI, L., I. EDRY, M. COHEN and Y. KASSIR, 2004 Glucose and nitrogen regulate the switch from histone deacetylation to acetylation for expression of early meiosis-specific genes in budding yeast. Mol. Cell. Biol. 24: 5197-5208.
27. ROTH, F. P., J. D. HUGHES, P. W. ESTEP and G. M. CHURCH, 1998 Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16: 939-945.
28. RUBIN-BEJERANO, I., S. SAGEE, O. FRIEDMAN, L. PNUELI and Y. KASSIR, 2004 The in vivo activity of Ime1, the key transcriptional activator of meiosis-specific genes in Saccharomyces cerevisiae, is inhibited by the cyclic AMP/protein kinase A signal pathway through the glycogen synthase kinase 3-beta homolog Rim11. Mol. Cell. Biol. 24: 6967-6979.
29. RUBINSTEIN, A., V. GUREVICH, Z. KASULIN-BONEH, L. PNUELI, Y. KASSIR et al., 2007 Faithful modeling of transient expression and its application to elucidating negative feedback regulation. Proc. Natl. Acad. Sci. USA 104: 6241-6246.
30. SAGEE, S., A. SHERMAN, G. SHENHAR, K. ROBZYK, N. BEN-DOY et al., 1998 Multiple and distinct activation and repression sequences mediate the regulated transcription of IME1, a transcriptional activator of meiosis-specific genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 18: 1985-1995.
31. SHENHAR, G., and Y. KASSIR, 2001 A positive regulator of mitosis, Sok2, functions as a negative regulator of meiosis in Saccharomyces cerevisiae. Mol. Cell. Biol. 21: 1603-1612.
32. SHIMIZU, M., W. LI, P. A. COVITZ, M. HARA, H. SHINDO et al., 1998 Genomic footprinting of the yeast zinc finger protein Rme1p and its roles in repression of the meiotic activator IME1. Nucleic Acids Res. 26: 2329-2336.
33. SIKORSKI, R. S., and P. HIETER, 1989 A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
34. SOUSSI-BOUDEKOU, S., S. VISSERS, A. URRESTARAZU, J. C. JAUNIAUX and B. ANDRE, 1997 Gzf3p, a fourth GATA factor involved in nitrogen-regulated transcription in Saccharomyces cerevisiae. Mol. Microbiol. 23: 1157-1168.
35. TIROSH, I., J. BERMAN and N. BARKAI, 2007 The pattern and evolution of yeast promoter bendability. Trends Genet. 23: 318-321.
36. TONG, A. H., M. EVANGELISTA, A. B. PARSONS, H. XU, G. D. BADER et al., 2001 Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368.
37. WARD, M. P., C. J. GIMENO, G. R. FINK and S. GARRETT, 1995 SOK2 may regulate cyclic AMP-dependent protein kinase-stimulated growth and pseudohyphal development by repressing transcription. Mol. Cell. Biol. 15: 6854-6863.
38. XIE, J., M. PIERCE, V. GAILUS-DURNER, M. WAGNER, E. WINTER et al., 1999 Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae. EMBO J. 18: 6448-6454.
39. YUAN, G. C., Y. J. LIU, M. F. DION, M. D. SLACK, L. F. WU et al., 2005 Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630.