Role of Protein Methylation in Chromatin Remodeling and Transcriptional Regulation
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Oncogene (2001) 20, 3014 ± 3020 ã 2001 Nature Publishing Group All rights reserved 0950 ± 9232/01 $15.00 www.nature.com/onc Role of protein methylation in chromatin remodeling and transcriptional regulation Michael R Stallcup*,1,2 1Department of Pathology, University of Southern California, Los Angeles, California, CA 90089, USA; 2Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California, CA 90089, USA Recent ®ndings suggest that lysine and arginine-speci®c Types of protein methylation and their possible roles in methylation of histones may cooperate with other types of various signaling pathways post-translational histone modi®cation to regulate chro- matin structure and gene transcription. Proteins that Protein methylation involves transfer of a methyl methylate histones on arginine residues can collaborate group from S-adenosylmethionine to acceptor groups with other coactivators to enhance the activity of speci®c on substrate proteins. Proteins can be methylated on transcriptional activators such as nuclear receptors. Lysine lysine, arginine, histidine, or carboxyl residues (Aletta methylation of histones is associated with transcriptionally et al., 1998). In addition, when some aspartate residues active nuclei, regulates other types of histone modi®ca- in proteins spontaneously convert to isoaspartate as a tions, and is necessary for proper mitotic cell divisions. The result of protein aging, a methylation mechanism is fact that some transcription factors and proteins involved used in cells to reverse this process (Najbauer et al., in RNA processing can also be methylated suggests that 1996). Speci®c roles for carboxy-methylation of protein methylation may also contribute in other ways to proteins such as Ras and protein phosphatase 2A have regulation of transcription and post-transcriptional steps been identi®ed in various signaling pathways, and in gene regulation. In future work, it will be important to recent evidence has implicated arginine-speci®c protein develop methods for evaluating the precise roles of protein methyltransferases in several signaling pathways, methylation in the regulation of native genes in physiolo- although in most of these cases the speci®c roles of gical settings, e.g. by using chromatin immunoprecipita- protein methylation and the relevant protein substrates tion assays, dierentiating cell culture systems, and have not been identi®ed (Aletta et al., 1998; Gary and genetically altered cells and animals. It will also be Clarke, 1998; Lin et al., 1996; Abramovitch et al., important to isolate additional protein methyltransferases 1997). Arginine methylation is important for nuclear by molecular cloning and to characterize new methyl- export of some hnRNP proteins (Shen et al., 1998; transferase substrates, the regulation of methyltransferase Nichols et al., 2000; Gary and Clarke, 1998). The activities, and the roles of new methyltransferases and major arginine methyltransferase in mammalian cells, substrates. Oncogene (2001) 20, 3014 ± 3020. PRMT1 (Tang et al., 2000a), is required for very early stages of mouse development, suggesting a funda- Keywords: protein methylation; coactivators; histones; mental role in development (Pawlak et al., 2000). transcriptional regulation; chromatin Evidence for dynamic histone methylation DNA methylation is well known to play roles in the regulation of chromatin structure and regulation of The lysine and arginine-rich N-terminal tails of transcription (Bird and Wole, 1999). However, a histones are the sites of many types of post-transla- surprising convergence of recent work in a number of tional modi®cations such as methylation, acetylation, laboratories indicates that protein methylation also and phosphorylation (Strahl and Allis, 2000; van contributes to the complex web of mechanisms that Holde, 1989). In nucleosomes, these N-terminal histone govern chromatin remodeling and gene transcription. tails extend beyond the DNA double helix which is This review will focus on recent evidence that wrapped around the nucleosome core formed by the C- methylation of histones and perhaps other proteins terminal regions of eight (two of each type) histone on lysine and arginine residues cooperates with other molecules. In their unmodi®ed form the N-terminal types of post-translational modi®cations, such as histone tails are positively charged and interact with histone acetylation and phosphorylation, in the regula- the negatively charged DNA backbone or core histone tion of transcription. regions on the same or neighboring nucleosomes; this interaction contributes to chromatin compaction (Luger et al., 1997; Luger and Richmond, 1998). Neutralization of the positive charge of the N-terminal *Correspondence: MR Stallcup, Department of Pathology, HMR 301, University of Southern California, 2011 Zonal Avenue, Los tails by acetylation of lysines and phosphorylation of Angeles, California, CA 90089-9092, USA serines weakens the binding of the N-terminal tail with Protein methylation in transcriptional regulation MR Stallcup 3015 the negative regions of nucleosomes and thus con- metabolism; PRMT1 substrates include ®brillarin, tributes to chromatin remodeling. nucleolin, several hnRNPs, and histone H4 (Najbauer Lysine methylation of histones in vivo is well et al., 1993; Gary and Clarke, 1998; Chen et al., 1999a). documented: histone H3 is methylated on lysines 4, 9, Yeast RMT1 also eciently methylates arginines in 27 and 36, although the speci®c pattern of residues glycine rich regions of proteins (Gary and Clarke, methylated may vary among species; histone H4 is 1998). However, CARM1 has little or no activity with methylated on lysine 20 (van Holde, 1989; Strahl and the substrates preferred by PRMT1 and RMT1. To Allis, 2000). In contrast to lysine methylation, in vivo date the best substrate reported for CARM1 is histone methylation of arginine residues in histones is less well H3 (Chen et al., 1999a), and the methylation is not in documented. Arginine methylation has been dicult to glycine rich regions (BT Schurter et al., 2001, detect in native mammalian histones (Gary and Clarke, submitted). JBP1 can methylate histones H2A and H4 1998), but has been reported in Drosophila (Desrosiers and myelin basic protein (Pollack et al., 1999). Both and Tanguay, 1988). The latter study found changes in PRMT1 and PRMT3 methylated poly(A)-binding lysine and arginine methylation of histone H3 and in protein II, but the two enzymes produced dierent the N-terminal methylation of histone H2B after heat patterns of methylated proteins in a cell extract (Smith shock of cultured Drosophila cells, suggesting that et al., 1999; Tang et al., 1998). Substrates for PRMT2 arginine methylation of histones not only exists but is a have not yet been reported. dynamically regulated process. Subsequent studies in Symmetric dimethylarginine has been found in mammalian and avian cells provided further evidence myelin basic protein (Gary and Clarke, 1998) and for association of dynamic histone methylation with human spliceosomal Sm proteins D1 and D3, which active (i.e. acetylated) chromatin, although it was not are components of some of the small nuclear determined whether the methylation was on lysine or ribonucleoprotein complexes (Brahms et al., 2000), arginine residues (Annunziato et al., 1995; Hendzel and but the enzymes responsible for methylating these Davie, 1991). The eect of lysine or arginine methyla- proteins have not yet been isolated. tion on chromatin structure is currently unknown. Lysines may accept one, two, or three methyl groups on the terminal amine group of the lysine side chain. Histone H3 lysine methyltransferase activity has been Families of lysine and arginine-speci®c protein observed in several proteins containing SET domains methyltransferases (Rea et al., 2000; O'Carroll et al., 2000). The mammalian SET domain protein SUV39H1 methylates Arginine methylation occurs on either or both of the lysine 9 of histone H3, and the SET domain was two terminal guanidino nitrogen atoms, resulting in important for this activity. The ability to methylate three possible products: monomethylarginine; NG,NG- histones was observed in some but not all SET domain dimethylarginine, in which both methyl groups are on proteins. It remains to be determined whether the the same nitrogen (asymmetric dimethylarginine); and inactive SET domain proteins lack catalytic activity or NG,N'G-dimethylarginine, in which each nitrogen atom require undetermined non-histone proteins as sub- receives one methyl group (symmetric dimethylargi- strates, and whether SET domains are common nine) (Aletta et al., 1998; Gary and Clarke, 1998). features of lysine methyltransferases. cDNA clones for ®ve genetically distinct but related mammalian arginine methyltransferases have been isolated: PRMT1 (Lin et al., 1996), PRMT2/ Recent evidence implicating histone methylation in HRMT1L1 (Scott et al., 1998), PRMT3 (Tang et al., transcriptional regulation 1998), CARM1 (Chen et al., 1999a), and JBP1 (Pollack et al., 1999). A clone for one yeast protein, Hmt1 or Arginine methylation RMT1, belonging to this family has also been identi®ed (Henry and Silver, 1996; Gary et al., 1996). While the Recent studies on the mechanism of transcriptional overall length of these polypeptide chains varies from regulation by the nuclear hormone receptors led to the 348 ± 608 amino acids, they all share a highly conserved identi®cation of many proteins that may serve as central domain encoding