Journal: EMBO Reports

Article Title: A CRISPR-Cas9 screen reveals genetic determinants of the cellular response to decitabine

doi: 10.1038/s44319-025-00385-w

Figure Lengend Snippet: Reagents and tools table

Article Snippet: GSK3484862 , TargetMol , T11469.

Techniques: Recombinant, Sequencing, Software, Cloning, Proliferation Assay, In Situ

Journal: Nature Communications

Article Title: Mechanisms of gene regulation by SRCAP and H2A.Z

doi: 10.1038/s41467-026-70087-x

Figure Lengend Snippet: a SRCAP-YPet-AID genomic mapping by CUT&RUN at H2A.Z peaks in control SYAT (left panel) and active (19,308) and bivalent (8763) TSS (right panel). b Left panel: Microscopy snapshots of SYAT cells, treated with IAA or control for 2 h and stained with DAPI. Right panel: Quantification of total SRCAP-YA signal in interphase and mitotic cells treated with IAA or control. N = 50 cells per condition. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. c Genome tracks of H2A.Z and H2A ChIP-Seq in SYAT cells treated with IAA. d ChIP-Seq profiles of H2A.Z and H2A at H2A.Z peaks (143561 peaks) in SYAT cells treated with IAA. e , f H2A.Z enrichment at active and bivalent promoters ( e ) and enhancers ( f ) upon SRCAP degradation. Black line: changes in median values. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. g ChIP-seq metaplots and heatmaps of H2A.Z enrichment around the TSS of active (19308), bivalent (8763), and inactive (35247) genes. h Z-score enrichment of different DNA-binding proteins for the different H2A.Z turnover groups. p values were determined by a two-sided pairwise Wilcoxon test and are indicated on the graphs.

Article Snippet: For DNMT1 inhibition, SYAT cells were treated with 2 μM GSK-3484862 (MedChemExpress #HY-135146) for 5 days before performing ATAC-seq.

Techniques: Control, Microscopy, Staining, ChIP-sequencing, DNA Binding Assay

Journal: Nature Communications

Article Title: Mechanisms of gene regulation by SRCAP and H2A.Z

doi: 10.1038/s41467-026-70087-x

Figure Lengend Snippet: a Heatmaps and metaplots of H2A.Z enrichment centered on the summit of H2A.Z peaks across the cell cycle. b Mean-normalized H2A.Z enrichment calculated from H2A.Z-scores across the cell cycle in promoters or enhancers containing H2A.Z peaks, classified according to their activity. Black line: changes in median values. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. p values are indicated in Supplementary Data . c H2A.Z enrichment in promoter peaks in regions where mitotic H2A.Z was decreased, stable or increased with respect to G2 and EG1 phases. d H2A.Z enrichment around H2A.Z peaks in the clusters shown in ( c ). e Exon counts of genes regulated by each of the three promoter clusters. RNA-Seq data from SYAT control samples, performed in two biological replicates were used. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. f Heatmaps and metaplots of acH2A.Z enrichment centered on the summit of acH2A.Z peaks in asynchronous versus mitotic cells. g Heatmap of H2A.Z enrichment centered on the summit of H2A.Z peaks in mitotic or asynchronous SYAT cells treated for 1 h with IAA. h H2A.Z enrichment in promoters of mitotic or asynchronous SYAT cells treated for 1 h with IAA. Black line: changes in median values. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. p values were determined by a two-sided pairwise Wilcoxon test, **** p < 0.0001, ns nonsignificant.

Article Snippet: For DNMT1 inhibition, SYAT cells were treated with 2 μM GSK-3484862 (MedChemExpress #HY-135146) for 5 days before performing ATAC-seq.

Techniques: Activity Assay, RNA Sequencing, Control

Journal: Nature Communications

Article Title: Mechanisms of gene regulation by SRCAP and H2A.Z

doi: 10.1038/s41467-026-70087-x

Figure Lengend Snippet: a Fold-change of intronic reads and Benjamini–Hochberg (BH) adjusted p value (computed from Wald test performed by DESeq2) for SYAT cells treated for 2, 4, 6, and 8 h with IAA. Numbers: genes significantly downregulated (blue) or upregulated (red) with a threshold of |log2FC| >0.5 and adjusted p value <0.05. b Fold-change of intronic reads and BH-adjusted p value (DESeq2 default Wald test) for SYAT cells treated for 6 h with IAA. Genes regulated by a bivalent promoter are colored. c Top 15 GO terms enri c hed for genes upregulated at 6 h with the category “molecular function”. d Fold-change of intronic reads and adjusted p value for SYAT cells treated for 6 h with IAA. Ubiquitously-expressed genes are colored. e Number (left panel) and strength (right panel) of promoter-enhancer loops formed for genes found to be downregulated or upregulated at any time point. Data from ref. . p values were determined by a two-sided Welch two-sample t -test, and are indicated on the plots. f Changes in proteome composition in SYAT cells treated with IAA for 4 h compared to control. Numbers: proteins enriched (blue) or depleted (red) from the proteome upon IAA treatment with a threshold of |log2FC| >0.5 and p value <0.05. p values were determined using a two-sided Student’s t -test. g , h Fold-change of intronic reads, for SYAT cells treated for 1 h with IAA and sorted in EG1 ( g ) or LG1 ( h ). Numbers: genes significantly downregulated (blue) or upregulated (red) with a threshold of |log2FC| >0.25 and p value <0.05. p values were determined using the DESeq2 default Wald test.

Article Snippet: For DNMT1 inhibition, SYAT cells were treated with 2 μM GSK-3484862 (MedChemExpress #HY-135146) for 5 days before performing ATAC-seq.

Techniques: Control

Journal: Nature Communications

Article Title: Mechanisms of gene regulation by SRCAP and H2A.Z

doi: 10.1038/s41467-026-70087-x

Figure Lengend Snippet: a Percentage of different types of genomic regions with increased, stable or decreased H3K4me3, H3K27me3 and H2AK119ub1 marks. b H3K4me3 enrichment at active and bivalent promoters, in SYAT cells treated with control or IAA for 4, 6, and 8 h. Black line: changes in median values. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. c Scatterplot of intronic reads of genes controlled by active promoters as a function of H3K4me3 enrichment changes between 6 h of IAA treatment and control. Upper right corner: Pearson correlation coefficient. d , e H3K27me3 ( d ) and H2AK119ub1 ( e ) enrichment at bivalent and inactive promoters in SYAT cells treated with control or IAA for 4, 6, and 8 h. Black line: changes in median values. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. f Nucleosome occupancy at promoters in SYAT cells as a function of H2A.Z levels, in control or after 4 h of IAA treatment. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. Exact p values are provided in Supplementary Data . Numbers of nucleosomes analyzed are indicated in supplementary Data . g MNase-Seq fragment densities in SYAT cells treated with control or IAA for 4 h, as a function of H2A.Z enrichment and the class of promoter where nucleosomes are localized. h Fragile nucleosomes in nucleosomes of different types of promoters, as a function of H2A.Z levels. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. Exact p values are provided in supplementary Data . Numbers of nucleosomes analyzed are indicated in supplementary Data . p values comparing H2A.Z levels in boxplots were determined by a pairwise two-sided Wilcoxon test. p values comparing CTRL and IAA conditions in the boxplot were determined by a two-sided Welch two-sample t -test. p values comparing fragment length distributions were determined by a Kolmogorov–Smirnov test. **** p < 0.0001; *** p < 0.001; ** p < 0.01; * p < 0.05, ns nonsignificant.

Article Snippet: For DNMT1 inhibition, SYAT cells were treated with 2 μM GSK-3484862 (MedChemExpress #HY-135146) for 5 days before performing ATAC-seq.

Techniques: Control

Journal: Nature Communications

Article Title: Mechanisms of gene regulation by SRCAP and H2A.Z

doi: 10.1038/s41467-026-70087-x

Figure Lengend Snippet: a Chromatin accessibility changes in SYAT cells treated with control or IAA for 2, 4, 6, and 8 h. Exact p values are provided in supplementary Data . Black line: changes in median values. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. b Percentage of different types of genomic regions in accessible regions belonging to accessibility classes defined in ( a ). c Fold-change of TF footprinting calculated using TOBIAS in SYAT cells treated for 4 h with IAA versus control. Numbers: TF motifs losing (blue) or gaining (red) binding upon IAA treatment with |FC| >0.05 and p value <0.0001 ( p value provided by TOBIAS). d Percentage of occurrence of all motifs, for TFs predicted to gain or lose binding upon IAA treatment, for different genomic regions. e Fold-change of TF footprinting calculated using TOBIAS in SYAT cells at the end of mitosis (left panel) or EG1 (right panel). Numbers: TF motifs predicted to lose (blue) or gain (red) binding upon IAA treatment with |FC| >0.05 and p value <0.0001 ( p value provided by TOBIAS). Colors: Predicted TF footprinting changes in SYAT treated 4 h with IAA versus control. f Chromatome analysis. Turquoise: TFs; red: members of SRCAP complex; purple: H2A.Z. Numbers: proteins enriched (blue) or depleted (red) from the chromatome upon IAA treatment with |log2FC| >0.5 and p value <0.05. p values were determined using a two-sided Student’s t -test. g Numbers of peaks with an increased or decreased TF ChIP-seq enrichment after 4 h of IAA treatment in SYAT cells. h Fold-change in TF binding determined by ChIP-seq, chromatome, and TOBIAS prediction analysis. i Chromatin accessibility changes upon IAA treatment for TF motifs predicted to gain or lose binding. Exact p values are provided in Supplementary Data . j Number of motifs containing at least one CpG, in motifs predicted by TOBIAS to lose or gain binding upon SRCAP depletion. k Numbers of motifs enriched in H2A.Z peaks located in promoters or enhancers and displaying cytosine hyper- or hypomethylation upon SRCAP/H2A.Z loss. Unless indicated otherwise, p values were determined by a two-sided pairwise Wilcoxon test; **** p < 0.0001; *** p < 0.001; ns nonsignificant.

Article Snippet: For DNMT1 inhibition, SYAT cells were treated with 2 μM GSK-3484862 (MedChemExpress #HY-135146) for 5 days before performing ATAC-seq.

Techniques: Control, Footprinting, Binding Assay, ChIP-sequencing

Journal: Nature Communications

Article Title: Mechanisms of gene regulation by SRCAP and H2A.Z

doi: 10.1038/s41467-026-70087-x

Figure Lengend Snippet: a Experimental procedure for dox-induced wtSRCAP and cdSRCAP expression and cell sorting. b H2A.Z enrichment in rescued peaks (44769 peaks) upon overexpression of wtSRCAP or cdSRCAP treated with control or IAA for 4 h. Boxes: interquartile range (IQR); whiskers: 1.5xIQR; dots: outlier points. c Heatmap of normalized intronic read counts ranked according to H2A.Z and SRCAP levels and k-means-clustered. When SRCAP and H2A.Z display opposite effects, the dominant effect is written in bold. d Fold-change of intronic reads from two independent biological replicates and adjusted p value for SYAT cells treated for 4 h with IAA versus control, in the six gene clusters determined in ( c ). Colored dots: genes significantly downregulated (blue) or upregulated (red) with a threshold of |log2FC| >0.5 and adjusted p value <0.05. e The number of genes downregulated or upregulated by H2A.Z or SRCAP. f Fold-change of intronic reads between cdSRCAP and wtSRCAP and adjusted p value in control (left) or IAA condition (right). Numbers: genes significantly lower (blue) or higher (red) in cdSRCAP with a threshold of |log2FC|>0.5 and adjusted p value <0.05. g Fold-change in intronic reads in the six clusters defined in ( c ) for SYAT cells treated for 1 h with IAA or control and sorted in EG1. h Heatmap of TOBIAS footprinting scores ranked according to H2A.Z and SRCAP levels and k-means-clustered. When SRCAP and H2A.Z display opposite effects, the dominant effect is indicated in bold. i Fold-change of TF footprinting calculated using TOBIAS in SYAT cells treated for 4 h with IAA versus control for the six clusters determined in ( h ). Colored dots: TF motifs predicted to lose (blue) or gain (red) binding upon IAA treatment with a threshold of |FC| >0.05 < 0.0001. j Numbers of TF motifs with binding increased or decreased by H2A.Z or SRCAP. p values for comparison of mean H2A.Z levels in ChIP-Seq were determined by two-sided Welch two-sample t -tests. **** p < 0.0001.

Article Snippet: For DNMT1 inhibition, SYAT cells were treated with 2 μM GSK-3484862 (MedChemExpress #HY-135146) for 5 days before performing ATAC-seq.

Techniques: Expressing, FACS, Over Expression, Control, Footprinting, Binding Assay, Comparison, ChIP-sequencing

Journal: Nature Communications

Article Title: Mechanisms of gene regulation by SRCAP and H2A.Z

doi: 10.1038/s41467-026-70087-x

Figure Lengend Snippet: a Left panel. Cryo-EM structure of human SRCAP determined by ref. , DNA is displayed in blue, histones in yellow, SRCAP subunit in purple, and all other subunits of the SRCAP complex in gray (structure pdb_00008x1c deposited on RCSB PDB, figure created using Mol* . Right panel. Surface of the DNA accessible to molecules of different radii calculated from the Cryo-EM structure. b SRCAP enrichment determined by CUT&RUN, centered on NANOG peaks where SRCAP peaks are also detected (8578 peaks). c Nanog enrichment at binding sites of both NANOG and SRCAP (8578 peaks) in SYAT cells treated with different doses of IAA for 2 h. d Images of single Halo-NANOG molecules in a cell nucleus at the indicated time points, and corresponding tracks (colored). Scale bar: 3 µm. e Absolute fraction of Halo-NANOG molecules bound longer than 50 s, calculated from data displayed in Fig. S7f–j, l–n, with the statistics provided there. For CTRL, 2813 tracks in 16 cells, for IAA, 1121 tracks in 26 cells, for cdSRCAP IAA, 4624 cells in 47 cells, for cdSRCAP IAA + DOX, 1623 tracks in 16 cells, for wtSRCAP IAA + DOX, 2571 tracks in 34 cells. Data were represented as calculated mean values ± standard deviation. f Binding frequency of Halo-NANOG molecules calculated from data displayed in Fig. S7f–j, l–n, with the statistics provided there. Data, from the same number of tracks as in 7e, are represented as calculated mean values ± standard deviation of 500 resamplings with randomly selected 80% of the data and error propagation.

Article Snippet: For DNMT1 inhibition, SYAT cells were treated with 2 μM GSK-3484862 (MedChemExpress #HY-135146) for 5 days before performing ATAC-seq.

Techniques: Cryo-EM Sample Prep, Binding Assay, Standard Deviation

Journal: Science Advances

Article Title: Select EZH2 inhibitors enhance viral mimicry effects of DNMT inhibition through a mechanism involving NFAT:AP-1 signaling

doi: 10.1126/sciadv.adk4423

Figure Lengend Snippet: ( A ) Approach for generating an in-cell endogenous SFRP1 -NLuc reporter assay in HCT116 cells with hypomorphic DNMT1. IRES, internal ribosomal entry site. ( B ) Reactivation of the silenced SFRP1 locus small interfering RNA (siRNA)–mediated DNMT1 knockdown (left) or DAC treatment (right). Relative luminescence units (RLU) are shown as fold change (FC) over control at the first time point. siNTC, siRNA nontargeting control; Veh, vehicle. Data are representative of three biological replicates, and the means ± SD of technical triplicates from a single experiment is shown. Statistical significance calculated using two-way analysis of variance (ANOVA) (**** P < 0.0001). ns, not significant. ( C and D ) NLuc reporter activity measurements following 72-hour treatment with the indicated EZH2is alone (C) or in combination (D) with a fixed concentration of DAC. RLU are normalized to relative fluorescence units (RFU) from CellTiter-Fluor cell viability assay to account for cell number. Data are representative of three biological replicates, and the means ± SD of technical triplicates from a single experiment is shown. Dashed black lines denote scaling difference between (C) and (D). ( E ) NLuc reporter activity measurements following 72-hour treatment with the DNMTis DAC or GSK3484862 alone (dashed lines) or in combination with a fixed concentration of TAZ (solid lines). RLU are normalized to RFU from CellTiter-Fluor cell viability assay. Data are representative of three biological replicates, and the means ± SD of technical triplicates from a single experiment is shown. ( F ) Surface plot and Bliss synergy score of DAC + TAZ dose-response curves derived from the SFRP1 -NLuc reporter assay after 72-hour treatment. Data presented are representative results of two biological replicates. See also fig. S1.

Article Snippet: TAZ (Selleck Chemicals, S7128, and Cayman Chemical, 16174), CPI-1205 (Selleck Chemicals, S8353), EPZ0011989 (Selleck Chemicals, S7805), EPZ005687 (Cayman Chemical, 13966), GSK126 (Selleck Chemicals, S7061, and Cayman Chemical, 15415), GSK343 (Selleck Chemicals, S7164), GSK503 (Cayman Chemical, 18531), UNC1999 (Caymen Chemical, 14621), GSK3484862 (Chemietek, CT-CSKMI-714), CsA (Selleck Chemicals, S2286), LCK inhibitor (Cayman Chemical, 15135), and ionomycin (Cayman Chemical, 11932) were dissolved in dimethyl sulfoxide (DMSO) and stored at −20°C.

Techniques: Reporter Assay, Small Interfering RNA, Knockdown, Control, Activity Assay, Concentration Assay, Fluorescence, Viability Assay, Derivative Assay