Cell proliferation and differentiation are coordinated by synchronized patterns of gene expression. The regulation of these patterns is achieved, in part, through epigenetic mechanisms that affect the nature of DNA packaging into chromatin [1
]. Specifically, post-translational covalent modifications to histone tails impact the structural dynamics of the nucleosome, thereby affecting DNA accessibility to transcriptional complexes [2
]. Common modifications to histones include methylation, acetylation, phosphorylation, and ubiquitination [5
]. Importantly, alterations in global levels of histone methylation and acetylation are connected to the biology of cancerous lesions and their clinical outcome [6
]. A number of histone lysine methyltransferases (HKMTs) are disrupted in a variety of cancer types [7
]. How histone methylation mechanistically contributes to the oncogenic state is poorly understood.
All known HKMTs, with one exception [5
], catalyze methyl transfer via the SET domain, a module encoded within many proteins that regulate diverse processes, including those critical for development and proper progression of the cell cycle [2
]. Histone lysine methylation on specific residues typically correlates with distinct states of gene expression [5
]. Histone 3 (H3) contains most of the known targeted lysines of histone methyltransferases and thereby serves as a conduit of such epigenetic regulation. In general, lysine methylation on H3K9, H3K27, and H4K20 corresponds with gene silencing, whereas methylation of H3K4, H3K36, or H3K79 is associated with actively transcribed genes [5
]. Methylation of H3K36 (H3K36me) is tightly associated with actively transcribed genes [11
], and appears to correspond primarily within the coding region. H3K36 methylation by Set2 in yeast was recently observed to recruit an Rpd3-mediated histone deacetylase complex through direct recognition of H3K36me by the chromodomain of Eaf3 [13
]. Rpd3 is a histone deacetylase (HDAC) that has well-established functions as a transcriptional repressor [13
]. Rpd3 associates into several co-repressor complexes, including one that contains Pho23, Sds3, Sap30, Ume1, Cti6/Rxt1, and Sin3 [13
]. However, recent evidence suggests that HDACs may also play a role during active transcription. As such, methylation of H3K36 is directly linked to histone deacetylation via Rpd3-Sin3 that in turn functions to maintain chromatin structure during active transcription [13
]. These findings reveal a new level of complexity with respect to histone modifications, and demonstrate our need to better understand the enzymes that catalyze these modifications.
Here we describe a subfamily of SET domain containing proteins with a unique domain architecture. This family of proteins is defined by a SET domain that is split into two segments by an MYND domain, followed by a cysteine-rich post SET domain [16
] (Fig. ). Members of this family may be important developmental regulators, as targeted disruption of the Smyd1 gene results in impaired cardiomyocyte maturation, flawed cardiac morphogenesis, and embryonic lethality [17
]. Functionally, Smyd1 is thought to regulate gene expression via its association with histone deacetylase activity [17
]. Smyd3 has been noted for its involvement in cancer cell proliferation [8
]. It is over-expressed in most hepatocellular and colorectal carcinomas, and its exogenous over-expression in NIH3T3 cells significantly augmented growth [8
]. Similar to Smyd1, Smyd3 modulates chromatin structure through its intrinsic H3K4-specific HKMT activity [8
]. Although Smyd2 is highly conserved with Smyd1 and Smyd3, nothing is known about its biochemical or functional activities. Here, we demonstrate that Smyd2 contains SET-domain dependent H3K36 HKMT activity. Smyd2 specifically associates with the Sin3A histone deacetylase complex, suggesting a link between two independent chromatin modification activities. Moreover, we observe that over-expression of Smyd2 in NIH3T3 cells significantly suppresses their growth. We propose that Smyd2-mediated chromatin modification regulates specific gene expression that has important implications for normal and neoplastic cell proliferation.
Figure 1 Alignment of the mammalian Smyd family proteins, and Smyd2 localization. (A) Schematic representation of the five mammalian Smyd proteins. The split SET domain is shown in light gray; the MYND domain is represented in black and the cysteine-rich post-SET (more ...)