Journal: Nature Communications

Article Title: EPOP restricts PRC2.1 targeting to chromatin by directly modulating enzyme complex dimerization

doi: 10.1038/s41467-025-68280-5

Figure Lengend Snippet: a Re-expression of WT and mutant EPOP in mESCs. Representative of two biological replicates . b Co-IP assay of re-expressed EPOP. The re-expressed 3 × FLAG-EPOP-HA protein was used as the bait, and the bound endogenous SUZ12 was detected. Representative of two replicates. c Schematic of the EpiLC differentiation. Some parts of the figure were created in BioRender. Liu, X. (2026) ( https://biorender.com/gvraoqv ). d Heatmaps of ChIP-seq replicates. Using the FDR < 0.05 threshold, the gain-of-signal MTF2 (purple) and H3K27me3 (green) peaks from individual replicates (WT-1, WT-2, D5-1, and D5-2) are shown in the heatmaps. The centers of the consensus binding sites are aligned. The number of the consensus binding sites is labeled. e Metaplots of ChIP-seq replicates. The mean ChIP-seq signal of the differential MTF2 (upper panel) and H3K27me3 (lower panel) peaks shown in ( d ) is plotted. The individual replicates are color-coded. f Genome browser tracks of selected gene loci. Tracks were generated by SparK ( https://github.com/harbourlab/SparK ). Genomic coordinates are provided. The difference between the replicates, calculated as the standard deviation, is indicated as the shaded areas surrounding the tracks. g Scatter plots of MTF2 and H3K27me3. MTF2 (left panel) and H3K27me3 (right panel) reads were normalized by the total reads. The mean read concentration corresponding to log2 (normalized ChIP-seq reads with input reads subtracted) was calculated by DiffBind.

Article Snippet: Antibodies used in this study are listed below: SUZ12 antibody (CST, Cat. # 3737S), MTF2 antibody (Proteintech, Cat. # 162081AP), EPOP antibody (Active Motif, Cat. # 61753), JARID2 antibody (CST, Cat. # 13594S), AEBP2 antibody (CST, Cat. # 14129S), Elongin B antibody (Abcam, Cat. # ab168836), EZH2 antibody (CST, Cat. # 5246S), FLAG antibody (Sigma, Cat. # F1804), Myc antibody (CST, Cat. # 2276S), H3 antibody (CST, Cat. # 9715S), H3K27me3 antibody (CST, Cat. # 9733S), β-Tubulin antibody (CST, Cat. # 2128S).

Techniques: Expressing, Mutagenesis, Co-Immunoprecipitation Assay, ChIP-sequencing, Binding Assay, Labeling, Generated, Standard Deviation, Concentration Assay

Journal: Nature Communications

Article Title: EPOP restricts PRC2.1 targeting to chromatin by directly modulating enzyme complex dimerization

doi: 10.1038/s41467-025-68280-5

Figure Lengend Snippet: a Volcano plot of differential gene expression. RNA-seq results of the EPOP D5 EpiLCs in triplicates were compared to those of the EPOP WT EpiLCs. The number of upregulated and downregulated genes is indicated. Data passing the FDR < 0.05, FC > 1.5, and average TPM of WT or mutant > 0.5 thresholds were analyzed. b Correlation of RNA-seq and ChIP-seq. One ChIP-seq replicate is shown here, and the other replicate is shown in the supplemental materials. The differential gene expression was aligned with the differential MTF2 enrichment around the transcription start site (TSS). The corresponding H3K27me3 signals are also displayed. Compared to the WT counterpart, 130 genes in the EPOP D5 EpiLCs were downregulated and associated with enhanced MTF2 signals around the TSS. The other 318 downregulated genes were not associated with EPOP-regulated MTF2 targeting. 187 upregulated genes are shown as well. c Gene ontology analysis. The PRC2.1-repressed, EPOP-maintained genes were subjected to gene ontology analysis on the DAVID server. The top 5 overrepresented terms in molecular function are shown. The p -value is one-tail Fisher Exact probability value used for gene-enrichment analysis by the DAVID server. d Schematic model of developmental gene repression by PRC2. On the left, the transient intrinsic dimer of the PRC2 core complex is illustrated. In the middle, distinct oligomerization states of various PRC2.1 and PRC2.2 holocomplexes are highlighted. MTF2 mediates direct chromatin binding, and it also stabilizes the intrinsic dimer, promoting chromatin targeting of the dimeric PRC2.1, likely via an avidity effect. EPOP disrupts the dimeric architecture of PRC2.1, containing MTF2, restricts PRC2.1 targeting, and thereby maintains the limited expression of PRC2.1-repressed developmental regulators. On the right, the PRC2.1-dependent role of EPOP in early development is illustrated. Black solid curve: during the ESC differentiation, a set of key gene regulators is repressed by PRC2.1, with limited expression being maintained by the EPOP-mediated inhibition of PRC2.1 targeting, which is followed by upregulation of the same set of gene regulators, leading to cell fate 1, e.g., PGCLCs. Gray dotted curve: the absence of EPOP results in the over-repression of these gene regulators by PRC2.1, which may change stem cell differentiation trajectories and result in an alternative cell fate 2. Some parts of the figure were created in BioRender. Liu, X. (2026) ( https://biorender.com/l3ji249 ).

Article Snippet: Antibodies used in this study are listed below: SUZ12 antibody (CST, Cat. # 3737S), MTF2 antibody (Proteintech, Cat. # 162081AP), EPOP antibody (Active Motif, Cat. # 61753), JARID2 antibody (CST, Cat. # 13594S), AEBP2 antibody (CST, Cat. # 14129S), Elongin B antibody (Abcam, Cat. # ab168836), EZH2 antibody (CST, Cat. # 5246S), FLAG antibody (Sigma, Cat. # F1804), Myc antibody (CST, Cat. # 2276S), H3 antibody (CST, Cat. # 9715S), H3K27me3 antibody (CST, Cat. # 9733S), β-Tubulin antibody (CST, Cat. # 2128S).

Techniques: Gene Expression, RNA Sequencing, Mutagenesis, ChIP-sequencing, Binding Assay, Expressing, Inhibition, Cell Differentiation

Journal: Oncotarget

Article Title: KDM1A promotes tumor cell invasion by silencing TIMP3 in non-small cell lung cancer cells.

doi: 10.18632/oncotarget.8563

Figure Lengend Snippet: Figure 5: KDM1A removes H3K4me2 at the TIMP3 promoter and represses its promoter activity. (A) WB detection of the H3K4me2 level in PC9 and A549 cells expressing the control shRNA (sh-Control) or KDM1A shRNA (sh-KDM1A). Total histone H3 serves as a loading control. (B) Schematic drawing of the TIMP3 promoter region and ChIP-qPCR primer set locations (–685, –506, –345, –180, –43, and +65), relative to the TSS (transcriptional start site). TSS is assigned as the “+1” position. (C, D) ChIP-qPCR was performed in PC9 cells expressing the control shRNA (sh-Control) or KDM1A shRNA (sh-KDM1A) using an anti-H3K4me2 antibody (C) or an anti-KDM1A antibody (D). Bar graphs show percentages of fold enrichment of H3K4me2 (C) or KDM1A (D) at different locations of the TIMP3 promoter region, relative to IgG immunoprecipitation. (E) Schematic drawing of the TIMP3 promoter luciferase reporter construct (TIMP3pro-Luc plasmid). TIMP3 promoter region spanning from –1000 bp to 500 bp with respect to the TSS was cloned into luciferase reporter vector (pGL3). (F) TIMP3pro-Luc plasmid was co-transfected with either KDM1A overexpression plasmid (KDM1A) or the control plasmid (Control) into PC9 cells stably expressing KDM1A shRNA, and relative luciferase activity was measured 72 hours later. Each condition was performed in six replicates. Data are represented as mean (SD).

Article Snippet: The following primary antibodies were used: KDM1A (CST, #2184), TIMP3 (Santa Cruz, #6836), MMP2 (Santa Cruz, #13594), H3K4me2 (CST, #9725), total histone H3 (CST, #4499), SAPK/JNK(CST, #9252), Phospho-SAPK/JNK (Thr183/Tyr185) (CST, #9251), MAO-A/B (Santa Cruz, #50333), caspase 3 (CST, #9665), and PARP (CST, #9542), GAPDH (Sigma-Aldrich, #G9545), p-EGFR (Tyr1068) (CST #3777), EGFR (CST #4267), β-Actin (CST, #4970).

Techniques: Activity Assay, Expressing, Control, shRNA, ChIP-qPCR, Immunoprecipitation, Luciferase, Construct, Plasmid Preparation, Clone Assay, Transfection, Over Expression, Stable Transfection

Journal: Oncotarget

Article Title: KDM1A promotes tumor cell invasion by silencing TIMP3 in non-small cell lung cancer cells.

doi: 10.18632/oncotarget.8563

Figure Lengend Snippet: Figure 7: 2-PCPA treatment inhibits cell proliferation, invasion, and migration in NSCLC cells. (A) PC9 and A549 cells were treated with 2-PCPA at various concentrations (0, 2, 4, 10, 15, 20 µM), and subjected for cell proliferation assay, at given time points (0, 1, 2, 3, or 4 days). (B, C) PC9 and A549 cells were treated with either DMSO or 2-PCPA (4, 10, or 20 µM), and subjected to cell invasion assay (B), and cell migration assays (C). The red line indicates the edge of migrating cells at a given time point. (D) PC9 and A549 cells were treated with either DMSO or 2-PCPA (4, 10, or 20 µM), and subjected to cell apoptosis assay using BD Annexin V FITC kit. The bar graph represents percentages of cells expressing early (Annexin V) or late (PI) apoptosis markers. (E) Normalized KDM1A and TIMP3 expressions in PC9 and A549 cells treated with 0 or 4 µM 2-PCPA for 2 days, detected by real time RT-PCR. Each condition was performed in triplicates. Data are represented as mean (SD). (F-G) PC9 and A549 cells were treated with 2-PCPA at various concentrations (0, 0.5, 1, 2, 5, and 15 µM (F), and 0, 2, 4, 5, 10, and 15 µM (G), and subjected to WB, to detect the following protein expressions: KDM1A, TIMP3, H3K4me2 (F), P-JNK, and T-JNK (G). GAPDH, Actin, and total histone H3 serve as loading controls. (H, I,) Growth curve of PC9 cells derived xenograft tumors (H) and mice body weight (I) with either PBS (control) or 2-PCPA treatment. (J) Image of dissected xenograft tumors (left panel). Tumor weight comparison of two treatment groups by t test (right panel).

Article Snippet: The following primary antibodies were used: KDM1A (CST, #2184), TIMP3 (Santa Cruz, #6836), MMP2 (Santa Cruz, #13594), H3K4me2 (CST, #9725), total histone H3 (CST, #4499), SAPK/JNK(CST, #9252), Phospho-SAPK/JNK (Thr183/Tyr185) (CST, #9251), MAO-A/B (Santa Cruz, #50333), caspase 3 (CST, #9665), and PARP (CST, #9542), GAPDH (Sigma-Aldrich, #G9545), p-EGFR (Tyr1068) (CST #3777), EGFR (CST #4267), β-Actin (CST, #4970).

Techniques: Migration, Proliferation Assay, Invasion Assay, Apoptosis Assay, Expressing, Quantitative RT-PCR, Derivative Assay, Control, Comparison