SET domains

In addition to histone deacetylation, histone lysine methylation can also lead to gene silencing which is not blocked by the HDAC inhibitors [6, 51], Several lines of evidence have suggested a connection between cancer and histone lysine methyltrans-ferases (HKMTs) [52], HKMTs catalyze the transfer of methyl group(s) from the cofactor. S -adenosyI-methionine (AdoMet) to some specific lysine residues in the N-terminal histone tails [53, 54], With one exception of Dotl [55], all known HKMTs contain the SET domain which represents a novel structural fold [53, 56], Among SET-domain HKMTs, SET7/9 is one of the best characterized experimentally. It is a... 

Xiao B, Wilson JR, Gamblin SJ (2003) Set domains and histone methylation. Curr Opin Struct Biol 13 699-705... 

Min J, Feng Q, Li Z, Zhang Y, Xu R (2003) Structure of the catalytic domain of human dotll, a non-set domain nucleosomal histone methyltransferase. Cell 112 711—723... 

Yeates TO (2002) Structures of set domain proteins protein lysine methyltransferases make their mark. Cell 111 5-7... 

Trievel RC, Beach BM, Dirk LMA, Houtz RL, Hurley JH (2002) Structure and catalytic mechanism of a set domain protein methyltransferase. Cell 111 91—103... 

Three-dimensional X-ray crystal structures of the SET domains of >10 PMTs and the catalytic domain of DOT1L have been reported to date [25-27]. These structures, either in the apo-state or when bound to the cofactor product S-adenosyl-L-homocysteine (SAH), a histone peptide, or an inhibitor, yield key structural insights into enzyme/substrate/cofactor/inhibitor interactions and inform approaches to further inhibitor design. 

RIZl was originally isolated as a molecule associating with the retinoblastoma protein, Rb (Buyse et al, 1995). RIZl is classified as a member of the PR-domain family (PRDM-2) (the PR-domain family is now a sub-family of the SET-domain family proteins). It exerts H3K9 methyltransferase activity (Derunes et al, 2005). 

There is a school of thought, which believes that HMTases are tumor suppressors especially the lysine methyltransferases because of the loss of SET domain proteins in tumor conditions, exceptions do exist like Ezh2. The well-known example of the above is RIZl, which interacts with Rb protein (again the same tumor suppressor). RIZ-1 is in chromosome lp36 region, which is commonly deleted, in more than a dozen different types of human cancers. Riz-1 expression is commonly silenced in many tumors including breast cancer, liver cancer, colon cancer, neuroblastoma, melanoma, lung cancer and osteosarcoma (Kim et al, 2003). 

Yet another SET domain protein, which is directly related to cancers, is SMYD3 that gets upregulated in colorectal cancer and hepatocellular carcinoma, a leading cause of death in developed countries (Hamamoto et al, 2004). 

Lys-9 methyltransferase, DIMS, is similar in sequence to Clr4 and Su(var)3-9 and has a SET domain flanked by cysteine rich elements [191]. Murine ESET (ERG-associated protein with SET domain) has these domains and methylates free H3 [192]. This murine methyltransferase, which has high sequence similarity to human SETDBl (SET domain, bifurcated 1), interacts with the transcription factor ERG. SETBl, a specific H3 Lys-9 methyltransferase, interacts with KAP-1 copressor, which binds to KRAB domain zinc-finger proteins [193]. SETBl methylates Lys-9 when Lys-4 is methylated but enzymatic activity is inhibited when Ser-10 is phosphorylated or when Lys-14 is acetylated. 

Mammalian G9a is a SET-domain histone methyltransferase that methylated H3 at Lys-9 and Lys-27 in vitro and at Lys-9 in vivo [196]. The consensus sequence for G9a appears to be TKXXARKS. G9a is dilferent from Suv39hl is several ways. G9a nuclear localization is distinct from that of Suv39hl, which locate to heterochromatic foci [197]. Suv39hlj2 double mutant mice lose H3 Lys-9 methylation at pericentromeric heterochromatic regions but broad methylation of chromatin remains. It is the latter that is lost in GPa-deficient cells [196]. G9a, molecular mass about 100 kDa, methylates free H3 and nucleosomal H3 with a preference for the former however, the presence of H1 stimulates the methylation of chromatin substrates. Suv39hl, molecular mass about 650 kDa, methylates free H3 and H3 in nucleosomes with equivalent efficiency, but when HI is present, methylation of chromatin substrates is lessened [198]. 

Human Set9 is a 50 kDa H3 methyltransferase that methylates Lys-4 of H3. The enzyme methylated free H3 but not H3 in chromatin substrates. There is evidence that Set9 may stimulate activated transcription [198]. Set9 has the SET domain but lacks the cysteine-rich (pre-SET and post-SET) domains. Disruption of Saccharomyces cerevisiae and Saccharomyces pombe Setl obliterates H3 methyl Lys-4 [199]. Thus this SET domain containing protein appears to be a H3 Lys-4 methyltransferase, catalyzing both di- and tri-methylation of H3 Lys-4 [155]. However, studies with recombinant Setl failed to show histone methyltransferase activity. It has been suggested that other associated proteins may be required for the Setl to be catalytically active [139,200]. Indeed, Setl is associated with several... 

MLL (also named ALL-1, HRX, and HTRX), the human homolog of Drosophila trithorax, is a SET domain protein that methylates H3 at Lys-4. The enzymatic activity was enhanced with H3 acetylated at Lys-9 or Lys-14. MLL is a component of a large multiprotein complex composed of greater than 29 proteins, including TFIID, SWI/SNF remodeling complex and NuRD, a histone deacetylase complex. MLL binds to the promoter of Hox genes and regulates their expression [202,203]. 

Ashl, a member of the trithorax group of epigenetic activators, methylates H3 at Lys-4 and Lys-9 and H4 at Lys-20. Ashl is a SET domain protein that contains both pre- and post-SET domains [216]. 

In fact, the cross-talk between histone methylation and DNA methylation has been experimentally demonstrated for the first time in Neurospora [145] (see commentary by Bird [146]) and proved the second scenario. Using the power of Neurospora genetics, Tamaru and Selker [145] have identified a gene which, when mutated, abolishes methylation of all tested DNA sequences. This gene, dim-5, is different from dim-2, the previously identified gene that encodes the only DNA methyltransferase in Neurospora responsible for all known cytosine methylation in this fungus. The dim-5 gene encodes a histone H3 methyltransferase the deduced polypeptide sequence contains a SET domain with sequence similarity to some known histone methyltransferases moreover, the recombinant DIM-5 protein exhibits histone methyltransferase activity in vitro. Additional in vivo experiments... 

Histone lysine (K) methyltransferase (HKMTs) may lead to mono, di- and trimethy-lation of the E-amino group and the extent of modification at a specific site controls the recruitment of the effector proteins. Two unequally populated folds are presently known the SET domain-containing family and the Dotl family (for a recent review, see Ref. [70])... 

S ETdomain containing H KMTs have been classified according to the presence or absence and the nature of the sequences surrounding the SET domain that are conserved within families [71, 72]. The SET domain has a unique structural fold classified as class V AdoMet-dependent methyltransferase (MTase) [69], characterized by four highly-conserved signature sequences, namely motif I... 

Figure 2.5 Representative examples of two SET domain-containing structures, (a) Human SET7/9 in complex with SAH and a histone peptide cofactor (PDB code lo9s). The N-SET (shown in light blue), SET (p strands shown in yellow and helices in red) and C-SET (shown in magenta) domains in SET7/9 are indicated. The bound SAH molecule is shown in a stick model, together with the lysine side-chain of the bound histone peptide (the rest of the peptide is not shown).

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