Journal: Nature Communications

Article Title: Regulation of NSL by TAF4A is critical for genome stability and quiescence of muscle stem cells

doi: 10.1038/s41467-025-64402-1

Figure Lengend Snippet: a Heat maps of centered TAF4A CUT&RUN peaks. The blue-to-red gradient indicates high-to-low counts in the corresponding region. b Genome-wide distribution of TAF4A peaks. c Bar plot representing TAF4A peaks at different types of promoters. d Detected SP1 and NF-YA binding site under TAF4A CUT&RUN peaks. e Taf4a and Nf-Ya expression in freshly isolated MuSCs (fiMuSCs) and muscle based on reads per exon kilobase per million (RPKM) values (unpaired two-tailed t test: * p = 0.0103, *** p = 0.0005 n = 3). f Co-IP of TAF4A and NF-YA/B in wildtype MuSCs. Blots were probed with antibodies against TAF4A and NF-YA or NF-YB ( n = 2). g Percentage of TAF4A CUT&RUN peaks overlapping either with NF-YA peaks or with SP1 binding motifs. h Venn diagram of overlapping TAF4A CUT&RUN (CnR) peaks, NF-YA CUT&RUN (CnR) peaks, and RNA-seq DEG in Taf4a sKO MuSCs. i TAF4A, NF-YA and H3K4me3 distribution in the proximal promoter region of the Kansl2 gene in WT MuSCs. 8-20-weeks-old males and females were used. Data are presented as mean ± SEM of biological replicates. Source data are provided in the Source Data file.

Article Snippet: In brief, 1 × 10 6 wild type in vitro cultured muscle stem cells (MuSCs) or 4 × 10 5 wild type and Taf4a sKO MuSCs were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories), permeated with 0.05% Digitonin (EMD Millipore), and incubated with TAF4A (Santa Cruz #sc-136093), KANSL2 (Proteintech #27261-1-AP), NF-YA (Santa Cruz #sc-17753) or mouse IgG (Millipore #12-371B) or rabbit IgG (Diagenode #C15410206) on a rotator with 1:100 dilution at 4 °C overnight on a rotator.

Techniques: Genome Wide, Binding Assay, Expressing, Isolation, Two Tailed Test, Co-Immunoprecipitation Assay, RNA Sequencing

Journal: Nature Communications

Article Title: Regulation of NSL by TAF4A is critical for genome stability and quiescence of muscle stem cells

doi: 10.1038/s41467-025-64402-1

Figure Lengend Snippet: a Representation of NSL complex functions. b Heat map of expression levels of NSL complex components in Taf4a sKO MuSCs compared to control MuSCs ( n = 3). c , d RT-qPCR analysis of Kansl2 ( c ) and Mcrs1 ( d ) expression in freshly isolated control and Taf4a sKO MuSCs. m36b4 was used as reference gene (unpaired two-tailed t test, ( c ) * p = 0.0161, ( d ) * p = 0.0417, n = 5). e Western blot analysis of H4K16ac in cultured MuSCs from control and Taf4a sKO mice. H3 was used as loading control (unpaired two-tailed t test: * p = 0.0280, n = 3). f Heat maps of CUT&RUN signals of KANSL2 at transcriptional start sites. The blue-to-red gradient indicates high-to-low counts in the corresponding region. g Genome-wide distribution of KANSL2 peaks. h Venn diagram of overlapping KANSL2 CUT&RUN peaks, up and down-regulated genes from RNA-seq data in Taf4a sKO MuSCs. i Heat map showing KANSL2 binding at promoters of downregulated epigenetic modifiers genes in Taf4a sKO MuSCs ( n = 3). j GO term analysis of genes with an overlap between KANSL2 CUT&RUN peaks and downregulated genes in Taf4a sKO MuSCs based on P-values using EnrichR (Fisher’s exact test, two-sided). The number of genes associated with each GO term is indicated in square brackets. 8–20-week-old males and females were used. MuSCs were isolated 4–6 weeks after tamoxifen administration. Data are presented as mean ± SEM of biological replicates. Source data are provided in the Source Data file.

Article Snippet: In brief, 1 × 10 6 wild type in vitro cultured muscle stem cells (MuSCs) or 4 × 10 5 wild type and Taf4a sKO MuSCs were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories), permeated with 0.05% Digitonin (EMD Millipore), and incubated with TAF4A (Santa Cruz #sc-136093), KANSL2 (Proteintech #27261-1-AP), NF-YA (Santa Cruz #sc-17753) or mouse IgG (Millipore #12-371B) or rabbit IgG (Diagenode #C15410206) on a rotator with 1:100 dilution at 4 °C overnight on a rotator.

Techniques: Expressing, Control, Quantitative RT-PCR, Isolation, Two Tailed Test, Western Blot, Cell Culture, Genome Wide, RNA Sequencing, Binding Assay

Journal: Nature Communications

Article Title: Regulation of NSL by TAF4A is critical for genome stability and quiescence of muscle stem cells

doi: 10.1038/s41467-025-64402-1

Figure Lengend Snippet: a DAPI staining of Taf4a sKO MuSCs. Quantification of relative micronuclei numbers. Scale bar: 5 µm (**** p < 0.0001, n = 6). b gH2A.X immunofluorescence in cultured control and Taf4a sKO MuSCs. Scale bar: 20 µm. Quantification of relative numbers of γH2A.X+ cells (*** p = 0.0008, n = 4). c Western blot of γH2A.X in control and Taf4a sKO MuSCs. Loading control: H3 ( n = 3). d Western blot of immunoprecipitated Lamin A/C in control and Taf4a sKO MuSCs. Acetylation signals were normalized to total Lamin A/C levels. Quantification of acetylation levels (*** p = 0.0006, n = 3). e Western blot of p-lamin A/C ser392 in cultured control and Taf4a sKO MuSCs. Loading control: GAPDH ( n = 2). f Stiffness measurements of control and Taf4a sKO MuSC nuclei by AFM. Data represent average medians of Young’s Modulus (Pa) normalized to control MuSCs (** p = 0.0017, n = 5). g RT-qPCR analysis of Kansl2 expression in scrambled control and Nf-ya knockdown MuSCs. Reference gene: m36b4 (*** p = 0.0004, *** p = 0.0007, n = 6). h LaminB staining and quantification of micronuclei-positive cells in untreated ( n = 6), scrambled control ( n = 3), Taf4a knockdown ( n = 3), Kansl2 knockdown ( n = 3), Nfya knockdown ( n = 3), and Mcrs1 knockdown ( n = 3) in cultured MuSCs (* p = 0.0214, *** p = 0.0001, **** p < 0.0001). Scale bar: 5 µm. i LaminB staining and quantification of micronuclei-positive cells in control, Kansl2 overexpressing control, Taf4a sKO and Kansl2 overexpressing Taf4a sKO MuSCs (** p = 0.0054 *** p = 0.0004 **** p < 0.0001, n = 4). Scale bar: 5 µm. j Stiffness measurements of control, Taf4a sKO and Kansl2 overexpressing Taf4a sKO MuSC nuclei by AFM. Data representation as in ( f ) (** p = 0.0026, * p = 0.0437 n = 4). k RT-qPCR analysis of Kansl2 expression in scrambled control, Nf-ya knockdown and Nf-ya knockdown in Kansl2 overexpressing MuSCs. Reference gene: m36b4 (** p = 0.0026, **** p < 0.0001, n = 3). l Quantification of micronuclei-containing cells in scrambled control, Nf-ya knockdown, and Nf-ya knockdown Kansl2 overexpressing MuSCs (**** p < 0.0001, n = 4) from 8-20 weeks old males and females, isolated 4–6 weeks after tamoxifen administration. Data are mean ± SEM of biological replicates. ( a , b , d , f , k ) unpaired two-tailed t test. ( g , h , l ) one-way ANOVA with Bonferroni’s multiple comparisons test. ( i ) one-way ANOVA with Tukey’s multiple comparisons test. ( j ) one-way ANOVA with Holm–Sidak’s multiple comparisons test. Source data are provided in the Source Data file.

Article Snippet: In brief, 1 × 10 6 wild type in vitro cultured muscle stem cells (MuSCs) or 4 × 10 5 wild type and Taf4a sKO MuSCs were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories), permeated with 0.05% Digitonin (EMD Millipore), and incubated with TAF4A (Santa Cruz #sc-136093), KANSL2 (Proteintech #27261-1-AP), NF-YA (Santa Cruz #sc-17753) or mouse IgG (Millipore #12-371B) or rabbit IgG (Diagenode #C15410206) on a rotator with 1:100 dilution at 4 °C overnight on a rotator.

Techniques: Staining, Immunofluorescence, Cell Culture, Control, Western Blot, Immunoprecipitation, Quantitative RT-PCR, Expressing, Knockdown, Isolation, Two Tailed Test

Journal: Nature Communications

Article Title: Regulation of NSL by TAF4A is critical for genome stability and quiescence of muscle stem cells

doi: 10.1038/s41467-025-64402-1

Figure Lengend Snippet: TAF4A drives expression of Kansl2 by interacting with the NF-Y complex. KANSL2 is a critical part of the NSL (non-specific lethal) complex, which also comprises the acetyl-transferase MOF. Decreased expression of Kansl2 prevents NSL-mediated acetylation of Lamin, increasing Lamin phosphorylation and solubility. Created in BioRender. Guo, X. (2025) https://BioRender.com/frmva1q .

Article Snippet: In brief, 1 × 10 6 wild type in vitro cultured muscle stem cells (MuSCs) or 4 × 10 5 wild type and Taf4a sKO MuSCs were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories), permeated with 0.05% Digitonin (EMD Millipore), and incubated with TAF4A (Santa Cruz #sc-136093), KANSL2 (Proteintech #27261-1-AP), NF-YA (Santa Cruz #sc-17753) or mouse IgG (Millipore #12-371B) or rabbit IgG (Diagenode #C15410206) on a rotator with 1:100 dilution at 4 °C overnight on a rotator.

Techniques: Expressing, Phospho-proteomics, Solubility