Since SWI/SNF complexes can promote both gene activation and repression by nucleosome disruption and reconstruction [5
], it is formally possible that they mediate both processes to coordinate gene expression and repression during skeletal myogenesis. While current data indicate a prominent role of SWI/SNF in the activation of muscle-gene expression, the physical and functional interactions reported in other cell types between SWI/SNF and other chromatin modifiers (see below) suggest a more complicated picture.
The ability of MyoD to promote myogenic conversion when ectopically introduced in non-muscle cells reflects the concerted activity of the associated epigenetic machinery that remodels the chromatin in the regulatory regions of target gene [16
]. Of note, the composition of this machinery is extremely heterogeneous and dynamic, with a stage-specific association of distinct enzymatic complexes that execute different functions in myoblasts vs myotubes. In undifferentiated myoblasts, muscle-specific gene activation is precluded by the recruitment of transcriptional corepressors, such as histone deacetylases (HDACs) and histone methyltransferases, which contribute to generate the epigenetic marks associated with silent chromatin — H3–K9 dimethylation, H3K27 trimethylation and local hypoacetylation [12
]. Upon differentiation cues, the chromatin at muscle promoters undergoes massive structural changes that reflect the elimination of HDACs and repressive methyltransferases, such as Suv39h1 and Polycomb complex [21
], in favor of the recruitment and functional activation of positive regulators, such as histone acetyltransferases (HATs), arginine methyltransferases and SWI/SNF complexes. The result of these modifications is the deletion of pre-existing marks of transcriptional repression and the deposition of positive epigenetic modifications, such as H3–K4 trimethylation [12
]. Whether these two processes occur simultaneously or sequentially is currently unknown. Likewise, the functional relationship between repressive and activatory chromatin-associated enzymatic complexes, which has been reported in other cell types, has not been yet investigated in muscle cells. In this regard, increasing interest is now directed toward the function of specific histone demethylases of the Jumonj family, as crucial effectors of the epigenetic switch during myoblast-to-myotube transition [24
]. Moreover, other events, such as histone exchange, are likely involved in the switching of the epigenetic signature.
How do SWI/SNF complexes contribute to the epigenetic switch that occurs at muscle genes during the transition from myoblasts to myotubes?
A number of reported interactions between SWI/SNF and other chromatin-modifying complexes suggest that these interactions can be involved in some of the molecular events underlying the changes in chromatin architecture at muscle loci during myoblast differentiation.
An indirect link between SWI/SNF and other histone-modifying complexes was first established based on the increased affinity of the bromodomain-containing proteins for acetylated histones [25
]. Bromodomains are present in the enzymatic sub-units of the SWI/SNF complex, Brg1 and Brm. As such, it has been proposed that interactions between Brg1 and Brm and acetylated histones contribute to stabilize SWI/SNF binding to hyperacetylated chromatin within the regulatory sequences of muscle genes. According to this model, HDAC-mediated histone deacetylation counters while HAT-dependent hyperacetylation promotes SWI/SNF recruitment to muscle genes. Other studies have illustrated a functional hierarchy in the recruitment of HATs and SWI/SNF complexes that is imposed by two intracellular cascades activated by regeneration cues — the MKK6>p38 and IGF1>Pi3K>AKT pathways. The IGF1 signaling promotes the recruitment of p300/CBP and PCAF HATs on the chromatin of muscle genes, thereby generating local hyperacetylation, which contribute to nucleosome disruption, possibly by cooperation with SWI/SNF activity [26
]. Interestingly, the chromatin recruitment of SWI/SNF on muscle genes can be observed also in experimental conditions that prevent hyperacetylation — e.g. pharmacological blockade of the IGF1 signaling to HATs. Under these conditions, the p38 signaling appears sufficient to promote SWI/SNF recruitment on the chromatin of muscle genes, despite the local hypoacetylation; however, the chromatin-remodeling ability of SWI/SNF can only be detected once muscle-gene promoters are hyperacetylated in response to the IGF1 signaling to HATs. This evidence indicates a further level of functional relationship between SWI/SNF and HATs in response to external cues, whereby IGF1-mediated local hyperacetylation at muscle genes is required for the remodeling activity of the SWI/SNF complex, which is recruited in response to activation of the p38 signaling [26
Independent studies have identified a multistep recruitment of the SWI/SNF complexes on muscle promoters. On myogenin promoter, the SWI/SNF recruitment is dependent on a prior association of MyoD with constitutively bound Pbx1 on a promoter region juxtaposed to, but not buried by, the nucleosome [17
]. MyoD–Pbx1 complex mediates an initial recruitment of SWI/SNF complex possibly to displace the nucleosome, thereby allowing the full access of MyoD to the canonical Eboxes in the productive conformation for activation of gene expression — that is the heterodimer formed by MyoD and the E2A gene products, and the associated myogenic transcriptosome [12
]. Moreover, SWI/SNF complexes can sequentially interact with two arginine methyltransferases, Prmt5 and CARM1, at early and late promoter respectively [27
]. Interactions of the SWI/SNF complexes with other components of the muscle transcriptosome are regulated by chromatin-associated p38 alpha/beta kinases, which are activated in response to differentiation cues [28
]. p38 signaling appears to promote multiple interactions within the muscle transcriptosome, including SWI/SNF recruitment, via BAF60 phosphorylation [4
], formation of MyoD/E47 heterodimer, via E47 phosphorylation [29
], and recruitment of the Ash2L-containing mixed-lineage leukemia (MLL) methyltransferases, via phosphorylation of MEF2D [30
Other studies performed in different cell types reported on the functional interactions between SWI/SNF complexes and proteins implicated in repression of gene transcription, such as heterochromatin protein 1 (HP1) [31
] and the Polycomb group proteins [32