Mitochondrial stress deregulates the expression of Brahma, a chromatin - remodeling factor that controls transcription and splicing of genes involved in axon growth and guidance

The human protein Brahma (Brm), encoded by the SMARCA2 gene, is one of the two mutually exclusive ATPase subunits of the mammalian SWI/SNF-BAF chromatin-remodelling complex. Brm-containing BAF complexes are enriched in neurons, where they play crucial roles in the regulation of genes involved in neuronal differentiation. Moreover, it has been reported that Brm associates with components of the spliceosome to regulate the inclusion of alternative internal exons. While investigating with splicing-sensitive microarrays the gene expression changes triggered by mitochondrial stress, I found that Brm is strongly downregulated in SH-SY5Y human neuroblastoma cells overexpressing the SOD1 (G93A) protein, one of the genetic causes of Amyotrophic Lateral Sclerosis (ALS). I found that this downregulation is due to a mitochondrial stress-induced impairment in the SMARCA2 promoter activity. Among the genes deregulated at the splicing level by SOD1 (G93A) expression, I identified several targets that are regulated by alternative 3’ terminal exon usage in a Brm-dependent manner. Specifically, I found that Brm promotes the skipping of the proximal terminal exon in five out of six genes that were analyzed. In order to define the molecular mechanism that allow to Brm to modulate the choice of alternative 3’ terminal exons, I used one of these genes, RPRD1A, as a model. I found that Brm inhibits the choice of the proximal RPRD1A last exon by directly localizing in its genomic region. In turn, the absence of Brm at the level of the proximal last exon is concomitant with a change in the processivity of the RNA Polymerase II, an observation consistent with the “terminal exon pausing” event. I hypothesized a model where Brahma may recruit the Bard1-Cstf complex on the RPRD1A proximal last exon, a complex known to inhibit the 3’ end processing of the pre-mRNA. These observations suggest an inhibitory role for Brm, which is exerted both at the level of the cotranscriptional choice of the proximal last exon and at the level of the 3’ end pre-mRNA processing.