REFERENCES
- Adelman, K., W. Wei, M. B. Ardehali, J. Werner, B. Zhu, D. Reinberg, and J. T. Lis. 2006. Drosophila Paf1 modulates chromatin structure at actively transcribed genes. Mol. Cell. Biol. 26:250–260.
- Agger, K., P. A. Cloos, J. Christensen, D. Pasini, S. Rose, J. Rappsilber, I. Issaeva, E. Canaani, A. E. Salcini, and K. Helin. 2007. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449:731–734.
- Barski, A., S. Cuddapah, K. Cui, T. Y. Roh, D. E. Schones, Z. Wang, G. Wei, I. Chepelev, and K. Zhao. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129:823–837.
- Boehm, A. K., A. Saunders, J. Werner, and J. T. Lis. 2003. Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock. Mol. Cell. Biol. 23:7628–7637.
- Cho, Y. W., T. Hong, S. Hong, H. Guo, H. Yu, D. Kim, T. Guszczynski, G. R. Dressler, T. D. Copeland, M. Kalkum, and K. Ge. 2007. PTIP associates with MLL3- and MLL4-containing histone H3 lysine 4 methyltransferase complex. J. Biol. Chem. 282:20395–20406.
- D'Andrea, L. D., and L. Regan. 2003. TPR proteins: the versatile helix. Trends Biochem. Sci. 28:655–662.
- De Santa, F., M. G. Totaro, E. Prosperini, S. Notarbartolo, G. Testa, and G. Natoli. 2007. The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. Cell 130:1083–1094.
- Eissenberg, J. C. 2006. Functional genomics of histone modification and non-histone chromosomal proteins using the polytene chromosomes of Drosophila. Methods 40:360–364.
- 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.
- Fischle, W., Y. Wang, S. A. Jacobs, Y. Kim, C. D. Allis, and S. Khorasanizadeh. 2003. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 17:1870–1881.
- Gerber, M., J. Ma, K. Dean, J. C. Eissenberg, and A. Shilatifard. 2001. Drosophila ELL is associated with actively elongating RNA polymerase II on transcriptionally active sites in vivo. EMBO J. 20:6104–6114.
- Gerber, M., K. Tenney, J. W. Conaway, R. C. Conaway, J. C. Eissenberg, and A. Shilatifard. 2005. Regulation of heat shock gene expression by RNA polymerase II elongation factor, Elongin A. J. Biol. Chem. 280:4017–4020.
- Goetting-Minesky, M. P., and K. D. Makova. 2006. Mammalian male mutation bias: impacts of generation time and regional variation in substitution rates. J. Mol. Evol. 63:537–544.
- Greenfield, A., L. Carrel, D. Pennisi, C. Philippe, N. Quaderi, P. Siggers, K. Steiner, P. P. Tam, A. P. Monaco, H. F. Willard, and P. Koopman. 1998. The UTX gene escapes X inactivation in mice and humans. Hum. Mol. Genet. 7:737–742.
- Guenther, M. G., S. S. Levine, L. A. Boyer, R. Jaenisch, and R. A. Young. 2007. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77–88.
- Issaeva, I., Y. Zonis, T. Rozovskaia, K. Orlovsky, C. M. Croce, T. Nakamura, A. Mazo, L. Eisenbach, and E. Canaani. 2007. Knockdown of ALR (MLL2) reveals ALR target genes and leads to alterations in cell adhesion and growth. Mol. Cell. Biol. 27:1889–1903.
- Jepsen, K., D. Solum, T. Zhou, R. J. McEvilly, H. J. Kim, C. K. Glass, O. Hermanson, and M. G. Rosenfeld. 2007. SMRT-mediated repression of an H3K27 demethylase in progression from neural stem cell to neuron. Nature 450:415–419.
- Klose, R. J., and Y. Zhang. 2007. Regulation of histone methylation by demethylimination and demethylation. Nat. Rev. Mol. Cell Biol. 8:307–318.
- Lan, F., P. E. Bayliss, J. L. Rinn, J. R. Whetstine, J. K. Wang, S. Chen, S. Iwase, R. Alpatov, I. Issaeva, E. Canaani, T. M. Roberts, H. Y. Chang, and Y. Shi. 2007. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449:689–694.
- 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.
- Lee, M. G., R. Villa, P. Trojer, J. Norman, K. P. Yan, D. Reinberg, L. Di Croce, and R. Shiekhattar. 2007. Demethylation of H3K27 regulates Polycomb recruitment and H2A ubiquitination. Science 318:447–450.
- 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.
- Lorincz, M. C., and D. Schubeler. 2007. RNA polymerase II: just stopping by. Cell 130:16–18.
- Ringrose, L., and R. Paro. 2004. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38:413–443.
- Schneider, J., and A. Shilatifard. 2006. Histone demethylation by hydroxylation: chemistry in action. ACS Chem. Biol. 1:75–81.
- 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.
- Shi, Y. 2007. Histone lysine demethylases: emerging roles in development, physiology and disease. Nat. Rev. Genet. 8:829–833.
- Shilatifard, A. 2006. Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu. Rev. Biochem. 75:243–269.
- Smith, E. R., C. D. Allis, and J. C. Lucchesi. 2001. Linking global histone acetylation to the transcription enhancement of X-chromosomal genes in Drosophila males. J. Biol. Chem. 276:31483–31486.
- Smith, E. R., A. Pannuti, W. Gu, A. Steurnagel, R. G. Cook, C. D. Allis, and J. C. Lucchesi. 2000. The Drosophila MSL complex acetylates histone H4 at lysine 16, a chromatin modification linked to dosage compensation. Mol. Cell. Biol. 20:312–318.
- Tenney, K., M. Gerber, A. Ilvarsonn, J. Schneider, M. Gause, D. Dorsett, J. C. Eissenberg, and A. Shilatifard. 2006. Drosophila Rtf1 functions in histone methylation, gene expression, and Notch signaling. Proc. Natl. Acad. Sci. USA 103:11970–11974.
- Xiang, Y., Z. Zhu, G. Han, H. Lin, L. Xu, and C. D. Chen. 2007. JMJD3 is a histone H3K27 demethylase. Cell Res. 17:850–857.