Transcriptome profiling in preadipocytes identifies long noncoding RNAs as Sam68 targets

Abstract

The KH-type RNA binding protein Sam68 is required for adipogenesis. We have previously shown that Sam68-deficient mice have a lean phenotype and are protected against dietary-induced obesity due to defects in mTOR and S6K1 alternative splicing. Herein we profiled the transcriptome of Sam68 wild type and deficient 3T3-L1 mouse preadipocytes. We identified 652 protein-coding genes and 9 ncRNAs that were significantly altered with the loss of Sam68. As expected, downregulated genes were significantly associated with GO terms linked to cell migration, motility, and fat cell differentiation, while upregulated genes were mostly associated with GO terms linked to neurogenesis. Of the lncRNAs, we identified <i>Hotair</i>, <i>Mir155hg</i>, as well as two new lncRNAs (<i>SR-lncRNA-1</i> and <i>SR-lncRNA-2</i>) that were regulated by Sam68, and contained consensus Sam68 binding sites. RNA stability assays showed that Sam68-deficiency decreased the half-life of <i>Hotair,</i> and increased the half-lives of <i>Mir155hg</i> and <i>SR-lncRNA-2</i>, while the stability of <i>SR-lncRNA-1</i> was unaffected. Depletion of <i>Hotair</i> and <i>SR-lncRNA-1</i> in wild type 3T3-L1 cells led to defects in adipogenesis, whereas depletion of <i>SR-lncRNA-2</i> in Sam68-deficient 3T3-L1 cells partially rescued the adipogenesis defect observed in these cells. Collectively, our findings define a new role for Sam68 as a regulator of lncRNAs during adipogenic differentiation.