Ubiquitination of Histone H2B by Rad6 Is Required for Efficient Dot1-mediated Methylation of Histone H3 Lysine 79

著者: Huck‐Hui Ng, Rui-Ming Xu, Yi Zhang, Kevin Struhl - Journal of Biological Chemistry 2002 被引用: 440

Dot1 is a non-SET domain protein that methylates histone H3 at lysine 79, a surface-exposed residue that lies within the globular domain. In the context of a nucleosome, H3 lysine 79 is located in close proximity with lysine 123 of histone H2B, a major site for ubiquitination by Rad6. Here we show that Rad6-mediated ubiquitination of H2B lysine 123 is important for efficient methylation of lysine 79, but not lysine 36, of histone H3. In contrast, lysine 79 methylation of H3 is not required for ubiquitination of H2B. Our study provides a new example of trans-histone regulation between modifications on different histones. In addition, it suggests that Rad6 affects telomeric silencing, at least in part, by influencing methylation of histone H3. Dot1 is a non-SET domain protein that methylates histone H3 at lysine 79, a surface-exposed residue that lies within the globular domain. In the context of a nucleosome, H3 lysine 79 is located in close proximity with lysine 123 of histone H2B, a major site for ubiquitination by Rad6. Here we show that Rad6-mediated ubiquitination of H2B lysine 123 is important for efficient methylation of lysine 79, but not lysine 36, of histone H3. In contrast, lysine 79 methylation of H3 is not required for ubiquitination of H2B. Our study provides a new example of trans-histone regulation between modifications on different histones. In addition, it suggests that Rad6 affects telomeric silencing, at least in part, by influencing methylation of histone H3. Histones are subjected to post-translational modifications such as acetylation, phosphorylation, ubiquitination, and methylation. Methylation on specific lysine or arginine residues is carried out by distinct classes of enzymes. The CARM1/PRMT1 class of enzymes mediates arginine methylation, while the SET domain-containing enzymes mediate lysine methylation (1Zhang Y. Reinberg D. Genes Dev. 2001; 15: 2343-2360Crossref PubMed Scopus (1222) Google Scholar, 2Lachner M. Jenuwein T. Curr. Opin. Cell Biol. 2002; 14: 286-298Crossref PubMed Scopus (688) Google Scholar). In Saccharomyces cerevisiae, arginine methylation of histones has not been described, but the N-terminal tail of histone H3 is methylated at lysines 4 and 36. Set1 is the lysine 4 methylase because lysine 4 methylation is abolished in a set1 deletion strain and the Set1 complex methylates lysine 4 in vitro (3Briggs S.D. Bryk M. Strahl B.D. Cheung W.L. Davie J.K. Dent S.Y. Winston F. Allis C.D. Genes Dev. 2001; 15: 3286-3295Crossref PubMed Scopus (473) Google Scholar, 4Roguev A. Schaft D. Shevchenko A. Pijnappel W.W. Wilm M. Aasland R. Stewart A.F. EMBO J. 2001; 20: 7137-7148Crossref PubMed Scopus (453) Google Scholar, 5Krogan N. Dover J. Khorrami S. Greenblatt J.F. Schneider J. Johnston M. Shilatifard A. J. Biol. Chem. 2002; 277: 10753-10755Abstract Full Text Full Text PDF PubMed Scopus (312) Google Scholar, 6Nagy P.L. Griesenbeck J. Kornberg R.D. Cleary M.L. Proc. Natl. Acad. Sci. U. S. A. 2002; 99: 90-94Crossref PubMed Scopus (263) Google Scholar). Set1 methylation of H3 lysine 4 is important for rDNA silencing (3Briggs S.D. Bryk M. Strahl B.D. Cheung W.L. Davie J.K. Dent S.Y. Winston F. Allis C.D. Genes Dev. 2001; 15: 3286-3295Crossref PubMed Scopus (473) Google Scholar, 7Bryk M. Briggs S.D. Strahl B.D. Curcio M.J. Allis C.D. Winston F. Curr. Biol. 2002; 12: 165-170Abstract Full Text Full Text PDF PubMed Scopus (168) Google Scholar). Lysine 36 methylation of H3 is mediated by Set2, and artificial recruitment of Set2 to a promoter results in transcriptional repression (8Strahl B.D. Grant P.A. Briggs S.D. Sun Z.W. Bone J.R. Caldwell J.A. Mollah S. Cook R.G. Shabanowitz J. Hunt D.F. Allis C.D. Mol. Cell. Biol. 2002; 22: 1298-1306Crossref PubMed Scopus (426) Google Scholar). Unlike the case in higher eukaryotes, methylation of histone H3 at lysines 9 and 27 and methylation of histone H4 at lysine 20 are not observed inS. cerevisiae (1Zhang Y. Reinberg D. Genes Dev. 2001; 15: 2343-2360Crossref PubMed Scopus (1222) Google Scholar, 9Fang J. Feng Q. Ketel C.S. Wang H. Cao R. Xia L. Erdjument-Bromage H. Tempst P. Simon J.A. Zhang Y. Curr. Biol. 2002; 12: 1086-1099Abstract Full Text Full Text PDF PubMed Scopus (265) Google Scholar, 10Nishioka K. Rice J.C. Sarma K. Erdjument-Bromage H. Werner J. Wang Y. Chuikov S. Valenzuela P. Tempst P. Steward R. Lis J.T. Allis C.D. Reinberg D. Mol. Cell. 2002; 9: 1201-1213Abstract Full Text Full Text PDF PubMed Scopus (459) Google Scholar).Recently S. cerevisiae Dot1 and the related human protein have been identified as histone methylases that specifically methylate lysine 79 within the globular domain of histone H3 (11van Leeuwen F. Gafken P.R. Gottschling D.E. Cell. 2002; 109: 745-756Abstract Full Text Full Text PDF PubMed Scopus (664) Google Scholar, 12Ng H.H. Feng Q. Wang H. Erdjument-Bromage H. Tempst P. Zhang Y. Struhl K. Genes Dev. 2002; 16: 1518-1527Crossref PubMed Scopus (421) Google Scholar, 13Feng Q. Wang H., Ng, H.H. Erdjument-Bromage H. Tempst P. Struhl K. Zhang Y. Curr. Biol. 2002; 12: 1052-1058Abstract Full Text Full Text PDF PubMed Scopus (623) Google Scholar, 14Lacoste N. Utley R.T. Hunter J. Poirier G.G. Cote J. J. Biol. Chem. 2002; 277: 30421-30424Abstract Full Text Full Text PDF PubMed Scopus (228) Google Scholar). These studies demonstrate that histone H3 can be methylated outside the tail region, and they provide the first example of a non-SET domain protein that mediates lysine methylase activity. Based on the crystal structure of a nucleosome, lysine 79 is a surface-exposed residue that is located within loop 1 between helix 1 and helix 2 of histone H3 (15Luger K. Mader A.W. Richmond R.K. Sargent D.F. Richmond T.J. Nature. 1997; 389: 251-260Crossref PubMed Scopus (6795) Google Scholar). Dot1 methylates lysine 79 only in the context of nucleosomes, indicating that a certain structural feature of the nucleosome is required for enzymatic activity (11van Leeuwen F. Gafken P.R. Gottschling D.E. Cell. 2002; 109: 745-756Abstract Full Text Full Text PDF PubMed Scopus (664) Google Scholar, 12Ng H.H. Feng Q. Wang H. Erdjument-Bromage H. Tempst P. Zhang Y. Struhl K. Genes Dev. 2002; 16: 1518-1527Crossref PubMed Scopus (421) Google Scholar). A similar requirement for the nucleosomal configuration has been reported for Set2 and SET8/PR-SET7 (8Strahl B.D. Grant P.A. Briggs S.D. Sun Z.W. Bone J.R. Caldwell J.A. Mollah S. Cook R.G. Shabanowitz J. Hunt D.F. Allis C.D. Mol. Cell. Biol. 2002; 22: 1298-1306Crossref PubMed Scopus (426) Google Scholar, 9Fang J. Feng Q. Ketel C.S. Wang H. Cao R. Xia L. Erdjument-Bromage H. Tempst P. Simon J.A. Zhang Y. Curr. Biol. 2002; 12: 1086-1099Abstract Full Text Full Text PDF PubMed Scopus (265) Google Scholar, 10Nishioka K. Rice J.C. Sarma K. Erdjument-Bromage H. Werner J. Wang Y. Chuikov S. Valenzuela P. Tempst P. Steward R. Lis J.T. Allis C.D. Reinberg D. Mol. Cell. 2002; 9: 1201-1213Abstract Full Text Full Text PDF PubMed Scopus (459) Google Scholar).In yeast cells, either loss or overexpression of Dot1 results in impaired telomeric silencing (16Singer M.S. Kahana A. Wolf A.J. Meisinger L.L. Peterson S.E. Goggin C. Mahowald M. Gottschling D.E. Genetics. 1998; 150: 613-632Crossref PubMed Google Scholar). Telomeric silencing is also disrupted by mutations of lysine 79 of histone H3 or by mutations that abolish the catalytic activity of Dot1, suggesting that Dot1 influences telomeric silencing largely through methylation of lysine 79 (11, 12). This defect in telomeric silencing might reflect an interaction between Sir proteins and lysine 79 because dot1 and lysine 79 mutations weaken the interaction of Sir2 and Sir3 with the telomeric region in vivo (11van Leeuwen F. Gafken P.R. Gottschling D.E. Cell. 2002; 109: 745-756Abstract Full Text Full Text PDF PubMed Scopus (664) Google Scholar, 12Ng H.H. Feng Q. Wang H. Erdjument-Bromage H. Tempst P. Zhang Y. Struhl K. Genes Dev. 2002; 16: 1518-1527Crossref PubMed Scopus (421) Google Scholar).In S. cerevisiae, histone H2B is monoubiquitinated at lysine 123 by Rad6 (17Robzyk K. Recht L. Osley M.A. Science. 2000; 287: 501-504Crossref PubMed Scopus (520) Google Scholar), and Rad6 is important for telomeric silencing (18Huang H. Kahana A. Gottschling D.E. Prakash L. Liebman S.W. Mol. Cell. Biol. 1997; 17: 6693-6699Crossref PubMed Scopus (111) Google Scholar). Unlike higher eukaryotes, ubiquitination of histone H2A has not been reported (19Swerdlow P.S. Schuster T. Finley D. Mol. Cell. Biol. 1990; 10: 4905-4911Crossref PubMed Scopus (42) Google Scholar), and mutations of the putative H2A ubiquitination site have no phenotypic effect (17Robzyk K. Recht L. Osley M.A. Science. 2000; 287: 501-504Crossref PubMed Scopus (520) Google Scholar). Interestingly, Rad6-mediated ubiquitination of H2B lysine 123 is required for methylation of H3 at lysine 4, a phenomenon termed trans-regulation (20Sun Z.W. Allis C.D. Nature. 2002; 418: 104-108Crossref PubMed Scopus (822) Google Scholar, 21Dover J. Schneider J. Tawiah-Boateng M.A. Wood A. Dean K. Johnston M. Shilatifard A. J. Biol. Chem. 2002; 277: 28368-28371Abstract Full Text Full Text PDF PubMed Scopus (421) Google Scholar). Here we provide a second and related example oftrans-histone regulation of histone modifications by showing that Rad6-mediated ubiquitination of H2B is also important for Dot1-mediated methylation of H3 lysine 79. A similar conclusion was reported in a recent paper that appeared while this manuscript was in preparation (22Briggs S.D. Xiao T. Sun Z.-W. Caldwell J.A. Shabanowitz J. Hunt D.F. Allis C.D. Strahl B.D. Nature. 2002; 418: 498Crossref PubMed Scopus (391) Google Scholar). Histones are subjected to post-translational modifications such as acetylation, phosphorylation, ubiquitination, and methylation. Methylation on specific lysine or arginine residues is carried out by distinct classes of enzymes. The CARM1/PRMT1 class of enzymes mediates arginine methylation, while the SET domain-containing enzymes mediate lysine methylation (1Zhang Y. Reinberg D. Genes Dev. 2001; 15: 2343-2360Crossref PubMed Scopus (1222) Google Scholar, 2Lachner M. Jenuwein T. Curr. Opin. Cell Biol. 2002; 14: 286-298Crossref PubMed Scopus (688) Google Scholar). In Saccharomyces cerevisiae, arginine methylation of histones has not been described, but the N-terminal tail of histone H3 is methylated at lysines 4 and 36. Set1 is the lysine 4 methylase because lysine 4 methylation is abolished in a set1 deletion strain and the Set1 complex methylates lysine 4 in vitro (3Briggs S.D. Bryk M. Strahl B.D. Cheung W.L. Davie J.K. Dent S.Y. Winston F. Allis C.D. Genes Dev. 2001; 15: 3286-3295Crossref PubMed Scopus (473) Google Scholar, 4Roguev A. Schaft D. Shevchenko A. Pijnappel W.W. Wilm M. Aasland R. Stewart A.F. EMBO J. 2001; 20: 7137-7148Crossref PubMed Scopus (453) Google Scholar, 5Krogan N. Dover J. Khorrami S. Greenblatt J.F. Schneider J. Johnston M. Shilatifard A. J. Biol. Chem. 2002; 277: 10753-10755Abstract Full Text Full Text PDF PubMed Scopus (312) Google Scholar, 6Nagy P.L. Griesenbeck J. Kornberg R.D. Cleary M.L. Proc. Natl. Acad. Sci. U. S. A. 2002; 99: 90-94Crossref PubMed Scopus (263) Google Scholar). Set1 methylation of H3 lysine 4 is important for rDNA silencing (3Briggs S.D. Bryk M. Strahl B.D. Cheung W.L. Davie J.K. Dent S.Y. Winston F. Allis C.D. Genes Dev. 2001; 15: 3286-3295Crossref PubMed Scopus (473) Google Scholar, 7Bryk M. Briggs S.D. Strahl B.D. Curcio M.J. Allis C.D. Winston F. Curr. Biol. 2002; 12: 165-170Abstract Full Text Full Text PDF PubMed Scopus (168) Google Scholar). Lysine 36 methylation of H3 is mediated by Set2, and artificial recruitment of Set2 to a promoter results in transcriptional repression (8Strahl B.D. Grant P.A. Briggs S.D. Sun Z.W. Bone J.R. Caldwell J.A. Mollah S. Cook R.G. Shabanowitz J. Hunt D.F. Allis C.D. Mol. Cell. Biol. 2002; 22: 1298-1306Crossref PubMed Scopus (426) Google Scholar). Unlike the case in higher eukaryotes, methylation of histone H3 at lysines 9 and 27 and methylation of histone H4 at lysine 20 are not observed inS. cerevisiae (1Zhang Y. Reinberg D. Genes Dev. 2001; 15: 2343-2360Crossref PubMed Scopus (1222) Google Scholar, 9Fang J. Feng Q. Ketel C.S. Wang H. Cao R. Xia L. Erdjument-Bromage H. Tempst P. Simon J.A. Zhang Y. Curr. Biol. 2002; 12: 1086-1099Abstract Full Text Full Text PDF PubMed Scopus (265) Google Scholar, 10Nishioka K. Rice J.C. Sarma K. Erdjument-Bromage H. Werner J. Wang Y. Chuikov S. Valenzuela P. Tempst P. Steward R. Lis J.T. Allis C.D. Reinberg D. Mol. Cell. 2002; 9: 1201-1213Abstract Full Text Full Text PDF PubMed Scopus (459) Google Scholar). Recently S. cerevisiae Dot1 and the related human protein have been identified as histone methylases that specifically methylate lysine 79 within the globular domain of histone H3 (11van Leeuwen F. Gafken P.R. Gottschling D.E. Cell. 2002; 109: 745-756Abstract Full Text Full Text PDF PubMed Scopus (664) Google Scholar, 12Ng H.H. Feng Q. Wang H. Erdjument-Bromage H. Tempst P. Zhang Y. Struhl K. Genes Dev. 2002; 16: 1518-1527Crossref PubMed Scopus (421) Google Scholar, 13Feng Q. Wang H., Ng, H.H. Erdjument-Bromage H. Tempst P. Struhl K. Zhang Y. Curr. Biol. 2002; 12: 1052-1058Abstract Full Text Full Text PDF PubMed Scopus (623) Google Scholar, 14Lacoste N. Utley R.T. Hunter J. Poirier G.G. Cote J. J. Biol. Chem. 2002; 277: 30421-30424Abstract Full Text Full Text PDF PubMed Scopus (228) Google Scholar). These studies demonstrate that histone H3 can be methylated outside the tail region, and they provide the first example of a non-SET domain protein that mediates lysine methylase activity. Based on the crystal structure of a nucleosome, lysine 79 is a surface-exposed residue that is located within loop 1 between helix 1 and helix 2 of histone H3 (15Luger K. Mader A.W. Richmond R.K. Sargent D.F. Richmond T.J. Nature. 1997; 389: 251-260Crossref PubMed Scopus (6795) Google Scholar). Dot1 methylates lysine 79 only in the context of nucleosomes, indicating that a certain structural feature of the nucleosome is required for enzymatic activity (11van Leeuwen F. Gafken P.R. Gottschling D.E. Cell. 2002; 109: 745-756Abstract Full Text Full Text PDF PubMed Scopus (664) Google Scholar, 12Ng H.H. Feng Q. Wang H. Erdjument-Bromage H. Tempst P. Zhang Y. Struhl K. Genes Dev. 2002; 16: 1518-1527Crossref PubMed Scopus (421) Google Scholar). A similar requirement for the nucleosomal configuration has been reported for Set2 and SET8/PR-SET7 (8Strahl B.D. Grant P.A. Briggs S.D. Sun Z.W. Bone J.R. Caldwell J.A. Mollah S. Cook R.G. Shabanowitz J. Hunt D.F. Allis C.D. Mol. Cell. Biol. 2002; 22: 1298-1306Crossref PubMed Scopus (426) Google Scholar, 9Fang J. Feng Q. Ketel C.S. Wang H. Cao R. Xia L. Erdjument-Bromage H. Tempst P. Simon J.A. Zhang Y. Curr. Biol. 2002; 12: 1086-1099Abstract Full Text Full Text PDF PubMed Scopus (265) Google Scholar, 10Nishioka K. Rice J.C. Sarma K. Erdjument-Bromage H. Werner J. Wang Y. Chuikov S. Valenzuela P. Tempst P. Steward R. Lis J.T. Allis C.D. Reinberg D. Mol. Cell. 2002; 9: 1201-1213Abstract Full Text Full Text PDF PubMed Scopus (459) Google Scholar). In yeast cells, either loss or overexpression of Dot1 results in impaired telomeric silencing (16Singer M.S. Kahana A. Wolf A.J. Meisinger L.L. Peterson S.E. Goggin C. Mahowald M. Gottschling D.E. Genetics. 1998; 150: 613-632Crossref PubMed Google Scholar). Telomeric silencing is also disrupted by mutations of lysine 79 of histone H3 or by mutations that abolish the catalytic activity of Dot1, suggesting that Dot1 influences telomeric silencing largely through methylation of lysine 79 (11, 12). This defect in telomeric silencing might reflect an interaction between Sir proteins and lysine 79 because dot1 and lysine 79 mutations weaken the interaction of Sir2 and Sir3 with the telomeric region in vivo (11van Leeuwen F. Gafken P.R. Gottschling D.E. Cell. 2002; 109: 745-756Abstract Full Text Full Text PDF PubMed Scopus (664) Google Scholar, 12Ng H.H. Feng Q. Wang H. Erdjument-Bromage H. Tempst P. Zhang Y. Struhl K. Genes Dev. 2002; 16: 1518-1527Crossref PubMed Scopus (421) Google Scholar). In S. cerevisiae, histone H2B is monoubiquitinated at lysine 123 by Rad6 (17Robzyk K. Recht L. Osley M.A. Science. 2000; 287: 501-504Crossref PubMed Scopus (520) Google Scholar), and Rad6 is important for telomeric silencing (18Huang H. Kahana A. Gottschling D.E. Prakash L. Liebman S.W. Mol. Cell. Biol. 1997; 17: 6693-6699Crossref PubMed Scopus (111) Google Scholar). Unlike higher eukaryotes, ubiquitination of histone H2A has not been reported (19Swerdlow P.S. Schuster T. Finley D. Mol. Cell. Biol. 1990; 10: 4905-4911Crossref PubMed Scopus (42) Google Scholar), and mutations of the putative H2A ubiquitination site have no phenotypic effect (17Robzyk K. Recht L. Osley M.A. Science. 2000; 287: 501-504Crossref PubMed Scopus (520) Google Scholar). Interestingly, Rad6-mediated ubiquitination of H2B lysine 123 is required for methylation of H3 at lysine 4, a phenomenon termed trans-regulation (20Sun Z.W. Allis C.D. Nature. 2002; 418: 104-108Crossref PubMed Scopus (822) Google Scholar, 21Dover J. Schneider J. Tawiah-Boateng M.A. Wood A. Dean K. Johnston M. Shilatifard A. J. Biol. Chem. 2002; 277: 28368-28371Abstract Full Text Full Text PDF PubMed Scopus (421) Google Scholar). Here we provide a second and related example oftrans-histone regulation of histone modifications by showing that Rad6-mediated ubiquitination of H2B is also important for Dot1-mediated methylation of H3 lysine 79. A similar conclusion was reported in a recent paper that appeared while this manuscript was in preparation (22Briggs S.D. Xiao T. Sun Z.-W. Caldwell J.A. Shabanowitz J. Hunt D.F. Allis C.D. Strahl B.D. Nature. 2002; 418: 498Crossref PubMed Scopus (391) Google Scholar). We thank Fred Winston for yeast strains and plasmid DNAs.