Histone H3 K4 Demethylation during Activation and Attenuation of GAL1 Transcription in Saccharomyces cerevisiae

REFERENCES

• Briggs, S. D., M. Bryk, B. D. Strahl, W. L. Cheung, J. K. Davie, S. Y. Dent, F. Winston, and C. D. Allis. 2001. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev. 15:3286–3295.
   PubMed Web of Science ®Google Scholar
• Burke, D., D. Dawson, and T. Stearns. 2000. Methods in yeast genetics: a Cold Spring Harbor Laboratory course manual, p. 149–154. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
   Google Scholar
• Christensen, J., K. Agger, P. A. Cloos, D. Pasini, S. Rose, L. Sennels, J. Rappsilber, K. H. Hansen, A. E. Salcini, and K. Helin. 2007. RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 128:1063–1076.
   PubMed Web of Science ®Google Scholar
• Cloos, P. A., J. Christensen, K. Agger, A. Maiolica, J. Rappsilber, T. Antal, K. H. Hansen, and K. Helin. 2006. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442:307–311.
   PubMed Web of Science ®Google Scholar
• Collart, M. A., and S. Oliviero. 1996. Preparation of yeast RNA, p. 13.12.1–13.12.2. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. A. Seidman, and K. Struhl (ed.), Current protocols in molecular biology, vol. 2. John Wiley & Sons, Hoboken, NJ.
   Google Scholar
• Cuthbert, G. L., S. Daujat, A. W. Snowden, H. Erdjument-Bromage, T. Hagiwara, M. Yamada, R. Schneider, P. D. Gregory, P. Tempst, A. J. Bannister, and T. Kouzarides. 2004. Histone deimination antagonizes arginine methylation. Cell 118:545–553.
   PubMed Web of Science ®Google Scholar
• Eissenberg, J. C., M. G. Lee, J. Schneider, A. Ilvarsonn, R. Shiekhattar, and A. Shilatifard. 2007. The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase. Nat. Struct. Mol. Biol. 14:344–346.
   PubMed Web of Science ®Google Scholar
• Fang, J., G. J. Hogan, G. Liang, J. D. Lieb, and Y. Zhang. 2007. The Saccharomyces cerevisiae histone demethylase Jhd1 fine-tunes the distribution of H3K36me2. Mol. Cell. Biol. 27:5055–5065.
   PubMedGoogle Scholar
• Fodor, B. D., S. Kubicek, M. Yonezawa, R. J. O'Sullivan, R. Sengupta, L. Perez-Burgos, S. Opravil, K. Mechtler, G. Schotta, and T. Jenuwein. 2006. Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev. 20:1557–1562.
   PubMed Web of Science ®Google Scholar
• Gallagher, S., S. E. Winston, S. A. Fuller, and J. G. R. Hurrell. 2004. Immunoblotting and immunodetection, p. 10.8.1–10.8.17. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. A. Seidman, and K. Struhl (ed.), Current protocols in molecular biology, vol. 2. John Wiley & Sons, Hoboken, NJ.
   Google Scholar
• Gallagher, S. R. 2006. One-dimensional SDS gel electrophoresis of proteins, p. 10.2.1–10.2.35. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. A. Seidman, and K. Struhl (ed.), Current protocols in molecular biology, vol. 2. John Wiley & Sons, Hoboken, NJ.
   Google Scholar
• Henry, K. W., A. Wyce, W. S. Lo, L. J. Duggan, N. C. Emre, C. F. Kao, L. Pillus, A. Shilatifard, M. A. Osley, and S. L. Berger. 2003. Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 17:2648–2663.
   PubMed Web of Science ®Google Scholar
• Huarte, M., F. Lan, T. Kim, M. W. Vaughn, M. Zaratiegui, R. A. Martienssen, S. Buratowski, and Y. Shi. 2007. The fission yeast jmj2 reverses histone h3 lysine 4 trimethylation. J. Biol. Chem. 282:21662–21670.
   PubMedGoogle Scholar
• Iwase, S., F. Lan, P. Bayliss, L. de la Torre-Ubieta, M. Huarte, H. H. Qi, J. R. Whetstine, A. Bonni, T. M. Roberts, and Y. Shi. 2007. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128:1077–1088.
   PubMed Web of Science ®Google Scholar
• Kim, T., and S. Buratowski. 2007. Two Saccharomyces cerevisiae JmjC domain proteins demethylate histone H3 Lys36 in transcribed regions to promote elongation. J. Biol. Chem. 282:20827–20835.
   PubMedGoogle Scholar
• Klose, R. J., K. Yamane, Y. Bae, D. Zhang, H. Erdjument-Bromage, P. Tempst, J. Wong, and Y. Zhang. 2006. The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442:312–316.
   PubMed Web of Science ®Google Scholar
• Klose, R. J., Q. Yan, Z. Tothova, K. Yamane, H. Erdjument-Bromage, P. Tempst, D. G. Gilliland, Y. Zhang, and W. G. Kaelin, Jr. 2007. The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 128:889–900.
   PubMed Web of Science ®Google Scholar
• Kouzarides, T. 2002. Histone methylation in transcriptional control. Curr. Opin. Genet. Dev. 12:198–209.
   PubMed Web of Science ®Google Scholar
• Krogan, N. J., J. Dover, S. Khorrami, J. F. Greenblatt, J. Schneider, M. Johnston, and A. Shilatifard. 2002. COMPASS, a histone H3 (lysine 4) methyltransferase required for telomeric silencing of gene expression. J. Biol. Chem. 277:10753–10755.
   PubMed Web of Science ®Google Scholar
• Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685.
   PubMed Web of Science ®Google Scholar
• Lee, M. G., J. Norman, A. Shilatifard, and R. Shiekhattar. 2007. Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein. Cell 128:877–887.
   PubMed Web of Science ®Google Scholar
• Lee, M. G., C. Wynder, N. Cooch, and R. Shiekhattar. 2005. An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 437:432–435.
   PubMed Web of Science ®Google Scholar
• Lee, N., J. Zhang, R. J. Klose, H. Erdjument-Bromage, P. Tempst, R. S. Jones, and Y. Zhang. 2007. The trithorax-group protein Lid is a histone H3 trimethyl-Lys4 demethylase. Nat. Struct. Mol. Biol. 14:341–343.
   PubMedGoogle Scholar
• Liang, G., R. J. Klose, K. E. Gardner, and Y. Zhang. 2007. Yeast Jhd2p is a histone H3 Lys4 trimethyl demethylase. Nat. Struct. Mol. Biol. 14:243–245.
   PubMedGoogle Scholar
• Longtine, M. S., A. McKenzie III, D. J. Demarini, N. G. Shah, A. Wach, A. Brachat, P. Philippsen, and J. R. Pringle. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14:953–961.
   PubMed Web of Science ®Google Scholar
• Margueron, R., P. Trojer, and D. Reinberg. 2005. The key to development: interpreting the histone code? Curr. Opin. Genet. Dev. 15:163–176.
   PubMed Web of Science ®Google Scholar
• Martin, C., and Y. Zhang. 2005. The diverse functions of histone lysine methylation. Nat. Rev. Mol. Cell Biol. 6:838–849.
   PubMed Web of Science ®Google Scholar
• Morillon, A., N. Karabetsou, A. Nair, and J. Mellor. 2005. Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. Mol. Cell 18:723–734.
   PubMedGoogle Scholar
• Nagy, P. L., J. Griesenbeck, R. D. Kornberg, and M. L. Cleary. 2002. A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3. Proc. Natl. Acad. Sci. USA 99:90–94.
   PubMedGoogle Scholar
• Ng, H. H., F. Robert, R. A. Young, and K. Struhl. 2003. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell 11:709–719.
   PubMed Web of Science ®Google Scholar
• Roguev, A., D. Schaft, A. Shevchenko, W. W. Pijnappel, M. Wilm, R. Aasland, and A. F. Stewart. 2001. The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4. EMBO J. 20:7137–7148.
   PubMed Web of Science ®Google Scholar
• Santos-Rosa, H., R. Schneider, A. J. Bannister, J. Sherriff, B. E. Bernstein, N. C. Emre, S. L. Schreiber, J. Mellor, and T. Kouzarides. 2002. Active genes are tri-methylated at K4 of histone H3. Nature 419:407–411.
   PubMed Web of Science ®Google Scholar
• Schneider, J., A. Wood, J. S. Lee, R. Schuster, J. Dueker, C. Maguire, S. K. Swanson, L. Florens, M. P. Washburn, and A. Shilatifard. 2005. Molecular regulation of histone H3 trimethylation by COMPASS and the regulation of gene expression. Mol. Cell 19:849–856.
   PubMed Web of Science ®Google Scholar
• Secombe, J., L. Li, L. Carlos, and R. N. Eisenman. 2007. The trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth. Genes Dev. 21:537–551.
   PubMed Web of Science ®Google Scholar
• Seward, D. J., G. Cubberley, S. Kim, M. Schonewald, L. Zhang, B. Tripet, and D. L. Bentley. 2007. Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat. Struct. Mol. Biol. 14:240–242.
   PubMedGoogle Scholar
• Shi, Y., F. Lan, C. Matson, P. Mulligan, J. R. Whetstine, P. A. Cole, R. A. Casero, and Y. Shi. 2004. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941–953.
   PubMed Web of Science ®Google Scholar
• Shi, Y. J., C. Matson, F. Lan, S. Iwase, T. Baba, and Y. Shi. 2005. Regulation of LSD1 histone demethylase activity by its associated factors. Mol. Cell 19:857–864.
   PubMed Web of Science ®Google Scholar
• Shilatifard, A. 2006. Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu. Rev. Biochem. 75:243–269.
   PubMed Web of Science ®Google Scholar
• Sims, R. J., III, K. Nishioka, and D. Reinberg. 2003. Histone lysine methylation: a signature for chromatin function. Trends Genet. 19:629–639.
   PubMed Web of Science ®Google Scholar
• Stols, L., M. Gu, L. Dieckman, R. Raffen, F. R. Collart, and M. I. Donnelley. 2002. A new vector for high throughput, ligation independent cloning encoding a TEV protease cleavage site. Protein Expr. Purif. 25:8–15.
   PubMed Web of Science ®Google Scholar
• Taverna, S. D., S. Ilin, R. S. Rogers, J. C. Tanny, H. Lavender, H. Li, L. Baker, J. Boyle, L. P. Blair, B. T. Chait, D. J. Patel, J. D. Aitchison, A. J. Tackett, and C. D. Allis. 2006. Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol. Cell 24:785–796.
   PubMed Web of Science ®Google Scholar
• Tsukada, Y., J. Fang, H. Erdjument-Bromage, M. E. Warren, C. H. Borchers, P. Tempst, and Y. Zhang. 2006. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439:811–816.
   PubMed Web of Science ®Google Scholar
• Tu, S., E. M. Bulloch, L. Yang, C. Ren, W. C. Huang, P. H. Hsu, C. H. Chen, C. L. Liao, H. M. Yu, W. S. Lo, M. A. Freitas, and M. D. Tsai. 2007. Identification of histone demethylases in Saccharomyces cerevisiae. J. Biol. Chem. 282:14262–14271.
   PubMed Web of Science ®Google Scholar
• Wang, Y., J. Wysocka, J. Sayegh, Y. H. Lee, J. R. Perlin, L. Leonelli, L. S. Sonbuchner, C. H. McDonald, R. G. Cook, Y. Dou, R. G. Roeder, S. Clarke, M. R. Stallcup, C. D. Allis, and S. A. Coonrod. 2004. Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 306:279–283.
   PubMed Web of Science ®Google Scholar
• Whetstine, J. R., A. Nottke, F. Lan, M. Huarte, S. Smolikov, Z. Chen, E. Spooner, E. Li, G. Zhang, M. Colaiacovo, and Y. Shi. 2006. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125:467–481.
   PubMed Web of Science ®Google Scholar
• Yamane, K., C. Toumazou, Y. Tsukada, H. Erdjument-Bromage, P. Tempst, J. Wong, and Y. Zhang. 2006. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125:483–495.
   PubMed Web of Science ®Google Scholar