Nuclear matrix-associated protein SMAR1 regulates alternative splicing via HDAC6-mediated deacetylation of Sam68

Abstract

Pre-mRNA splicing is a complex regulatory nexus modulated by various trans-factors and their posttranslational modifications to create a dynamic transcriptome through alternative splicing. Signalinduced phosphorylation and dephosphorylation of trans-factors are known to regulate alternative splicing. However, the role of other posttranslational modifications, such as deacetylation/acetylation, methylation, and ubiquitination, that could modulate alternative splicing in either a signal-dependent or -independent manner remain enigmatic. Here, we demonstrate that Scaffold/matrix-associated region-binding protein 1 (SMAR1) negatively regulates alternative splicing through histone deacetylase 6 (HDAC6)-mediated deacetylation of RNA-binding protein Sam68 (Src-associated substrate during mitosis of 68 kDa). SMAR1 is enriched in nuclear splicing speckles and associates with the snRNAs that are involved in splice site recognition. ERK-MAPK pathway that regulates alternative splicing facilitates ERK-1/2-mediated phosphorylation of SMAR1 at threonines 345 and 360 and localizes SMAR1 to the cytoplasm, preventing its interaction with Sam68. We showed that endogenously, SMAR1 through HDAC6 maintains Sam68 in a deacetylated state. However, knockdown or ERK-mediated phosphorylation of SMAR1 releases the inhibitory SMAR1-HDAC6-Sam68 complex, facilitating Sam68 acetylation and alternative splicing. Furthermore, loss of heterozygosity at the Chr.16q24.3 locus in breast cancer cells, wherein the human homolog of SMAR1 (BANP) has been mapped, enhances Sam68 acetylation and CD44 variant exon inclusion. In addition, tail-vein injections in mice with human breast cancer MCF-7 cells depleted for SMAR1 showed increased CD44 variant exon inclusion and concomitant metastatic propensity, confirming the functional role of SMAR1 in regulation of alternative splicing. Thus, our results reveal the complex molecular mechanism underlying SMAR1-mediated signal-dependent and -independent regulation of alternative splicing via Sam68 deacetylation.ewly synthesized pre-mRNAs undergo multiple posttranscriptional gene-regulatory events, such as capping, splicing, cleavage, and polyadenylation. Of these, splicing is most stringently regulated, because it is a prerequisite for spatiotemporal generation of splice variants observed in 95% of human genes (1). Accuracy of alternative splicing (AS) is modulated by cis-regulatory elements that include splice enhancers and silencers and/or trans-acting factors, viz. the serine-arginine (SR)-rich family proteins, heteronuclear ribonucleoproteins (hnRNPs) and various chromatin modifiers (2, 3). The majority of these trans-factors are distributed along the nuclear matrix (NM), which is a fibro-granular structural framework, organized as chromatin and ribonucleoprotein (RNP) domains. Chromatin domains are involved in replication and transcription, whereas RNP domains are actively associated with cotranscriptional and posttranscriptional gene-regulatory events (4, 5). Thus, NM is considered to be the site for pre-mRN...

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Histone Deacetylase 3 Inhibition Overcomes BIM Deletion Polymorphism–Mediated Osimertinib Resistance in EGFR-Mutant Lung Cancer

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Roles of Splicing Factors in Hormone-Related Cancer Progression

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