β‐Actin‐dependent global chromatin organization and gene expression programs control cellular identity

Abstract

During differentiation and development, cell fate and identity are established by waves of genetic reprogramming. Although the mechanisms are largely unknown, during these events, dynamic chromatin reorganization is likely to ensure that multiple genes involved in the same cellular functions are coregulated, depending on the nuclear environment. In this study, using high-content screening of embryonic fibroblasts from a β-actin knockout (KO) mouse, we found major chromatin rearrangements and changes in histone modifications, such as methylated histone (H)3-lysine-(K)9. Genome-wide H3K9 trimethylation-(Me)3 landscape changes correlate with gene up- and down-regulation in β-actin KO cells. Mechanistically, we found loss of chromatin association by the Brahma-related gene ( Brg)/Brahma-associated factor (BAF) chromatin remodeling complex subunit Brg1 in the absence of β-actin. This actin-dependent chromatin reorganization was concomitant with the up-regulation of sets of genes involved in angiogenesis, cytoskeletal organization, and myofibroblast features in β-actin KO cells. Some of these genes and phenotypes were gained in a β-actin dose-dependent manner. Moreover, reintroducing a nuclear localization signal-containing β-actin in the knockout cells affected nuclear features and gene expression. Our results suggest that, by affecting the genome-wide organization of heterochromatin through the chromatin-binding activity of the BAF complex, β-actin plays an essential role in the determination of gene expression programs and cellular identity.-Xie, X., Almuzzaini, B., Drou, N., Kremb, S., Yousif, A., Östlund Farrants, A.-K., Gunsalus, K., Percipalle, P. β-Actin-dependent global chromatin organization and gene expression programs control cellular identity.

Elevated transforming growth factor β signaling activation in β‐actin‐knockout mouse embryonic fibroblasts enhances myofibroblast features

“…Our recent study shows that β-actin KOs display myofibroblast features, including enhanced abilities to produce and contract ECM (Xie et al, 2017). Since Nox4 induced by TGF-β mediates myofibroblast differentiation (Hecker et al, 2009;Jiang et al, 2014), we next and DPI (0.5 µM; see Supporting Information Figure S2 for MTT cytotoxicity assay), there was no difference of gel contraction ability between WT and KO cells although the contractility of both WT and KO cells were impaired (Figure 3a,b).…”

“…We recently reported major alterations in the cell surface mechanical properties of β‐actin −/− KO cells in comparison to WT cells (Xie et al, ). The KO cells, with reorganized actin cytoskeleton, also upregulate several integrin genes (Xie et al, ). Therefore, we conclude that the KO cells activate and consume the latent TGF‐β in the medium more efficiently than WT cells, leading to elevated TGF‐β signaling and the upregulation of its target genes.…”

Mechano‐modulation of nuclear events regulating oligodendrocyte progenitor gene expression

“…Actin was shown to co‐immunoprecipitate with both the LINC complex and the repressive H3K9me3 histone mark in protein extracts from white matter tracts (Hernandez et al, ). This was of particular interest, especially since ablation of actin in other cell types (i.e., fibroblasts) led to aberrant genome‐wide localization of H3K9me3 (Xie et al, ). Therefore, these studies conducted in oligodendrocyte lineage cells suggest that nuclear actin in this glial lineage may play an important role in regulating the repressive histone marks that are necessary for heterochromatin formation and for OPC differentiation (Liu et al, ).…”

“…In addition to establishing heterochromatin, it is worth exploring the role of nuclear actin in mediating gene activation in OPCs, as actin has been shown to associate with all three RNA polymerases (Hofmann et al, ; Hu et al, ; Kukalev et al, ; Philimonenko et al, ). Ablation of actin in fibroblasts results in a dramatic reduction of genome‐wide BRG1 binding (Xie et al, ). Given the role of BRG1 in activating pro‐differentiation genes during OPC differentiation (Yu et al, ), it is conceivable that actin might also regulate gene activation in the oligodendrocyte lineage through BRG1.…”

Actomyosin contraction during cellularization is regulated in part by Src64 control of Actin 5C protein levels

“…Depletion of cytoplasmic γ-actin also leads to increased expression of smooth muscle actin (Patrinostro et al, 2017). The actin compensation mechanism for β-actin involves chromatin remodeling, transcriptional regulation as well as translational regulation and RNA processing (Almuzzaini et al, 2016;Percipalle, 2013;Vedula & Kashina, 2018;Xie et al, 2018). Thus, it is likely that the same molecular mechanisms are involved in the compensate for the reduction of Actin 5C and Actin 42A in Drosophila.…”