β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture

Abstract

β-actin is a crucial component of several chromatin remodeling complexes that control chromatin structure and accessibility. The mammalian Brahma-associated factor (BAF) is one such complex that plays essential roles in development and differentiation by regulating the chromatin state of critical genes and opposing the repressive activity of polycomb repressive complexes (PRCs). While previous work has shown that β-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in β-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of β-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that β-actin levels can affect the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2 in a dosage-dependent manner. Our results show that changes in β-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversible changes in 3D genome architecture. Our findings support a novel role for β-actin-dependent chromatin remodeling in shaping the chromatin landscape and regulating genes involved in development and differentiation. METHODSCell culture: WT, KO and HET mouse embryonic fibroblasts (MEFs) (from the lab of Dr. Christophe Ampe, University of Gent, Belgium) were maintained and cultured with Dulbecco's modified Eagle medium (DMEM) with high glucose, 10% fetal bovine serum (FBS) and 100 units/mL penicillin and 100 μg/mL streptomycin, in a humidified incubator with 5% CO2 at 37⁰C. The KO(Mm) and KO(Hs) cells with GFP and NLS-β actin re-introduced into KO cells were generated by retroviral transduction as described in (2). ATAC-Seq:Samples with 50,000 cells per condition were shipped in frozen medium (DMEM with 50 % FBS and 10% DMSO) on dry ice to Novogene (Beijing, China). All subsequent processing was performed by Novogene using standard DNA extraction and library preparation protocols. Cell nuclei were isolated, mixed with Tn5 Transposase with two adapters and tagmentation was performed for 30 minutes at 37⁰C. The fragmented DNA was purified and amplified with limited PCR cycle using index primers. Libraries were prepared according to recommended Illumina NovaSeq6000 protocols. All ATAC-Seq processing was performed by Novogene (Beijing, China). ChIP-Seq:ChIP-Seq for BRG1, H3K9me3 and H3K27me3 was performed as described in (2). For EZH2 ChIP-Seq, Mouse Embryonic fibroblasts were crosslinked using 1% formaldehyde (Sigma cat. No. F8775) for 10 minutes followed by quenching with 0.125 M Glycine for 5 minutes and lysis with lysis buffer 1 -LB1-(50 mM Hepes KOH pH 7.5, 10 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100). Nuclei were pelleted, collected and washed using lysis buffer 2 -LB2-(10 mM Tris HCl pH 8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA). This was followed by lysis using lysis buf...

Regulation of oxidative phosphorylation by Nuclear myosin 1 protects cells from metabolic reprogramming and tumorigenesis in mice

“…The nuclear genome is hierarchically organized into A and B compartments which respectively correlate with open and closed chromatin or euchromatin and heterochromatin (Fortin and Hansen, 2015). We recently reported that loss of nuclear actin leads to compartment switching, in turn leading to differential expression of genes present within these compartments (Mahmood et al, 2021). Mitochondrial genes tend to cluster together and are often found in the pericentromeric and subtelomeric regions, which are characterized by lesser chromatin accessibility and heterochromatinization (Moon et al, 2008).…”

“…The nuclear genome is hierarchically organized into A and B compartments which respectively correlate with open and closed chromatin or euchromatin and heterochromatin (Fortin and Hansen, 2015). We recently reported that loss of nuclear actin leads to compartment switching, in turn leading to differential expression of genes present within these compartments (Mahmood et al, 2021).…”

The prolyl-isomerase PIN1 is essential for nuclear Lamin-B structure and function and protects heterochromatin under mechanical stress

“…Because jasplakinolide also directly affects nuclear actin, which is required for HC dynamics (Mahmood et al, 2020;Xie et al, 2018aXie et al, , 2018b, we generated a genetic model of mechanical stress based on cytoplasmic F-actin hyperpolymerization by Actin capping protein-b (Cpb) knockdown. In fly brains, neuronspecific cpb RNAi caused cytoplasmic F-actin hyperpolymerization (Figure 5D), and, similar to knockout of its ortholog Capzb in mice (Pocaterra et al, 2019), was associated with actomyosin hypercontraction, as shown by phosphorylation of Spaghetti squash (Sqh; the ortholog of MLC-2 [myosin light chain-2]) (Figure S5F), leaving Dodo protein levels unaffected (Figure S5G).…”

Regulation of nuclear actin levels and MRTF/SRF target gene expression during PC6.3 cell differentiation

“…Actin could be one possible candidate to regulate these global changes in chromatin organization during differentiation. Indeed, mouse embryonic fibroblasts (MEFs) lacking the β-actin gene display altered 3D genome architecture (Mahmood et al, 2021) and are defective in their reprogramming capacity towards osteoblast-like cells (Gjorgjieva et al, 2020), adipocytes (Al-Sayegh et al, 2020) and chemical-induced neurons. In this latter case, β-actin deficiency is linked to loss of chromatin-binding of Brg1, an ATPase of the BAF chromatin remodeling complex.…”