β-actin mediated H3K27ac changes demonstrate the link between compartment switching and enhancer-dependent transcriptional regulation

Abstract

Background Recent work has demonstrated that three-dimensional genome organization is directly affected by changes in the levels of nuclear cytoskeletal proteins such as β-actin. The mechanisms which translate changes in 3D genome structure into changes in transcription, however, are not fully understood. Here, we use a comprehensive genomic analysis of cells lacking nuclear β-actin to investigate the mechanistic links between compartment organization, enhancer activity, and gene expression. Results Using HiC-Seq, ATAC-Seq, and RNA-Seq, we first demonstrate that transcriptional and chromatin accessibility changes observed upon β-actin loss are highly enriched in compartment-switching regions. Accessibility changes within compartment switching genes, however, are mainly observed in non-promoter regions which potentially represent distal regulatory elements. Our results also show that β-actin loss induces widespread accumulation of the enhancer-specific epigenetic mark H3K27ac. Using the ABC model of enhancer annotation, we then establish that these epigenetic changes have a direct impact on enhancer activity and underlie transcriptional changes observed upon compartment switching. A complementary analysis of fibroblasts undergoing reprogramming into pluripotent stem cells further confirms that this relationship between compartment switching and enhancer-dependent transcriptional change is not specific to β-actin knockout cells but represents a general mechanism linking compartment-level genome organization to gene expression. Conclusions We demonstrate that enhancer-dependent transcriptional regulation plays a crucial role in driving gene expression changes observed upon compartment-switching. Our results also reveal a novel function of nuclear β-actin in regulating enhancer function by influencing H3K27 acetylation levels.

Nuclear actin-dependent Meg3 expression suppresses metabolic genes by affecting the chromatin architecture at sites of elevated H3K27 acetylation levels

“…β-actin regulates enhancer function by influencing H3K27 acetylation levels, presumably by controlling HDAC recruitment [13, 14]. Results from this study provide first mechanistic links between compartment organization, enhancer activity, and gene expression [15] and further support a role of the nuclear actin pool in the compartmentalization of gene expression. Indeed, nuclear actin is enriched at chromosomal transcription sites and it is required for transcription in complex with several factors, including heterogeneous nuclear ribonucleoproteins (hnRNPs) as part of ribonucleoprotein complexes [16, 17], chromatin remodeling complexes and epigenetic regulators.…”

“…Using HiC-Seq, ATAC-Seq, and RNA-Seq, we recently demonstrated that accessibility changes within compartment switching genes upon β-actin depletion are primarily observed in non-promoter regions such as distal regulatory elements [15]. The finding that β-actin loss induces widespread accumulation of H3K27ac [15] and that this enrichment happens at sites of Meg3 enrichment suggest that Meg3 may be involved in regulating transcription of certain metabolic genes at the level of promoter-enhancer interaction.…”

“…Nuclear actin has been shown to control acetylation levels by regulating HDAC 1 and 2 recruitment [43], which might explain a potential increase in histone acetylation levels and histone acetyl transferase activity upon β-actin depletion. Indeed, increased levels of H3K27ac were observed in β-actin KO MEFs and were shown to accompany compartment switching and enhancer-dependent transcriptional regulation [15]. To find out if these actin-dependent changes in H3K27ac levels correlate functionally with changes in Meg3 association with the genome at gene regulatory regions, either promoter or enhancer sites, we next focused on those genes that are commonly involved in the Chondroitin, Heparan and Dermatan biosynthesis and phospholipases pathways and are the most significantly overrepresented pathways in the KO condition.…”

“…Enhanced TGF-β signaling has an overall impact on chromatin accessibility with increased H3K27 acetylation at enhancers [29]. Enhanced TGF-β signaling is also downstream effect of nuclear β-actin depletion when extensive genetic reprogramming results from genome re-organization and alterations in promoter-enhancer interactions due to increased H3K27 acetylation [12, 15, 30]. However, the functional significance of a possible association of lncRNAs with increased H3K27 acetylation and their impact on genome organization upon β-actin depletion is not known.…”

Working a second job: Cell adhesion proteins that moonlight in the nucleus

“…Myosin directly binds to DNA through its cargo binding domain to regulate these functions ( Fili et al, 2017 ). Similarly, Nuclear β-actin regulates enhancer function by influencing H3K27 acetylation levels ( Mahmood et al, 2023 ); while association of nuclear Tubulin with chromatin was known as early as the 1980s ( Menko and Tan, 1980 ). It is therefore easy to envision existing interactions with cell adhesion proteins being used for additional functions such as transcriptional regulation within the nuclear milieu.…”