RNA-seq for wild type and beta-actin KO MEFs in presence and in KD of Meg3

In eukaryotic cells, beta-actin is crucial for nuclear functions. It influences genome organization and regulates promoter-enhancer interactions as part of the BAF (SWI/SNF) chromatin remodeling complex. beta-actin also binds to the hyperphosphorylated carboxy-terminal domain (CTD) of RNA polymerase II. A lack of beta-actin results in altered gene expression, affecting key cellular processes such as differentiation. This study examined whether beta-actin regulates long non-coding RNA (lncRNA) levels. Using bulk RNA-seq and qPCR analyses on total RNA from WT mouse embryonic fibroblasts (MEFs), beta-actin heterozygous (HET) MEFs, and beta-actin knockout (KO) MEFs, we found that the expression of several lncRNAs is influenced by beta-actin depletion. Notably, the lncRNA Meg3 showed increased expression in a dosage-dependent manner. ChIRP-seq analysis revealed changes in Meg3 genomic association and its enrichment at or near enhancer sites following beta-actin depletion, along with increased H3K27 acetylation. These changes led to disrupted promoter-enhancer interactions, as indicated by the Activity by Contact (ABC) model, due to a sponging effect by Meg3. This resulted in the repression of genes involved in the metabolic biosynthetic pathways for chondroitin, heparan, dermatan sulfate, and phospholipases, affecting their synthesis. We suggest that Meg3 disrupts local genome organization (or DNA looping) and negatively impacts gene expression through its chromatin sponging effect, interfering with promoter-enhancer interactions.