cx 4945  (MedChemExpress)

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, Annexin V–FITC/propidium iodide (PI) apoptosis assay of SK-Mel-103 cells treated with CX-4945 (40 µM, 24 h) or DMSO. Scatterplots depict four different quadrant: viable cells (Annexin V⁻/PI⁻, Q4), early apoptotic (Annexin V⁺/PI⁻, Q3), late apoptotic/necrotic (Annexin V⁺/PI⁺, Q2), and necrotic (Annexin V⁻/PI⁺, Q1). b, Apoptosis DNA fragmentation analysis in SK-Mel-103 following CX-4945 treatment. c, Immunoblot analysis of caspase-3 cleavage in SK-Mel-103 cells treated with CX-4945 (5–40 µM) or DMSO; actin serves as loading control. d, Subcellular fractionation of SK-Mel-103 cells into cytosolic, nucleosolic and salt-extracted chromatin fractions (100, 250 and 450 mM NaCl), followed by immunoblotting for DEK. e, Immunoprecipitation of endogenous DEK from SK-Mel-103 cells treated with CX-4945 (40 µM, 24 h) or DMSO, followed by immunoblotting with a pan-phosphoserine antibody. f, Re-probing of the immunoprecipitated DEK membrane with a polyclonal anti-DEK antibody (K877). Clean-Blot IP Detection Reagent was used to minimize interference from immunoglobulin heavy and light chains. g, Representative LC–MS/MS spectra of DEK-derived phosphopeptides from SK-Mel-103 cells treated with DMSO or CX-4945. h, Summary of DEK phosphorylation sites identified by LC-MS/MS and schematic of DEK domains (top); site alignment is shown for endogenous DEK from SK-Mel-103 and HeLa S3 cells, and GFP–DEK expressed in HeLa S3 cells (bottom). i, Immunofluorescence of SK-Mel-103 cells after CK2 inhibition (CX-4945, 40 µM, 24 h) stained for DEK (scale bars:10µm).

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: Apoptosis Assay, Western Blot, Control, Fractionation, Immunoprecipitation, Membrane, Liquid Chromatography with Mass Spectroscopy, Derivative Assay, Phospho-proteomics, Immunofluorescence, Inhibition, Staining

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, Gels of immunoprecipitated DEK or GFP-DEK from HeLa S3 and SK-Mel-103 cells prepared for mass spectrometry analysis. Endogenous DEK or GFP-tagged DEK (GFP-DEK) was immunoprecipitated from HeLa S3 or SK-Mel-103 cells using DEK-specific antibodies or GFP-Trap beads, respectively. ( Left ) IP of endogenous DEK from HeLa S3 cells. ( Middle ) IP of DEK from SK-Mel-103 cells treated with DMSO or the CK2 inhibitor CX-4945. ( Right ) GFP-DEK immunoprecipitated from HeLa S3 cells expressing GFP-tagged DEK using GFP-Trap. All samples were resolved by SDS-PAGE and stained with Coomassie Brilliant Blue. The major DEK or GFP-DEK bands (highlight with red box) were excised for downstream mass spectrometry (MS) analysis to investigate phosphorylation sites. b , Mascot search results of DEK immunoprecipitates. Representative MASCOT search results from LC-MS/MS analysis of DEK protein treated with DMSO and CX-4945 from SK-Mel103, DEK and GFP-DEK from HeLa S3 cells, as well as GFP-DEK 12A mutant from 1E7. c , Phosphorylated DEK peptides detected in the indicated immunoprecipitates are shown, with modified residues and their positions in the DEK sequence annotated (S/T).

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: Immunoprecipitation, Mass Spectrometry, Expressing, SDS Page, Staining, Phospho-proteomics, Liquid Chromatography with Mass Spectroscopy, Mutagenesis, Modification, Sequencing

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, DEK ChIP-seq profiling in SK-Mel-103 cells treated with DMSO or CX-4945. Heatmap and principal component analysis (PCA) summarize DEK occupancy across samples (PC1 = 61%, PC2 = 30%). b, Differential DEK binding analysis between CX-4945 and DMSO conditions shown as a volcano plot (log2 fold change versus −log10 FDR); significantly differential regions are highlighted. c, Genomic annotation of CX-4945-specific DEK-bound regions. d, ChIP-qPCR validation of CX-4945–specific DEK occupancy at indicated loci (UFD1, RADIL, FBXL16, CSF3R and CALHM1) using DEK ChIP and IgG control; data are shown as percent input (mean ± s.d., n = 3). e, Association of DEK occupancy with active (H3K27ac) and repressive (H3K9me3) chromatin features. DEK ChIP-seq tags from DMSO- and CX-4945-reated cells were counted within ± 5kb windows centered on H3K27ac or H3K9me3 peak coordinates. f, Representative CX-4945-associated DEK peaks in ChIP-seq tracks (left). RT-qPCR of the corresponding genes showing reduced mRNA levels upon CX-4945 treatment (right; mean ± s.d., n = 3; two-tailed Student’s t-test, P < 0.05, ** P < 0.005).

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: ChIP-sequencing, Binding Assay, ChIP-qPCR, Biomarker Discovery, Control, Quantitative RT-PCR, Two Tailed Test

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, Replicate experiment relating to . Subcellular fractionation of SK-Mel-103 cells into cytosolic, nucleosolic and salt-extracted chromatin fractions (100, 250 and 450 mM NaCl), followed by immunoblotting for DEK. b , ChIP-qPCR validation was performed for CX-4945-specific DEK-accessible genes (UFD1, RADIL, FBXL16, CSF3R, and CALHM1) identified in SK-Mel-103 cells. ChIP was conducted in UACC-62 cells using antibodies against DEK and IgG as a negative control. This validation experiment was performed once to assess DEK enrichment at the corresponding loci . c. Representative genome browser tracks showing DEK ChIP – seq signal in HeLa S3 and FM232 cells at the TOP1 locus. d . Bar plot shows the number of DEK ChIP–seq peaks in human mammary epithelial cells (HMEC) and dermal fibroblasts.

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: Fractionation, Western Blot, ChIP-qPCR, Biomarker Discovery, Negative Control, ChIP-sequencing

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, Confocal imaging of nuclear chromatin morphology (DAPI) in SK-Mel-103 cells and DEK-depleted 1E7 cells following CX-4945 treatment; quantification of DAPI-positive nuclear area is shown (each dot represents one nucleus; n = 43, 50, 59, 60 as indicated; two-tailed Student’s t-test, P < 0.05, ** P < 0.005). Contrast-adjusted grayscale renderings of the DAPI channel are shown to aid visualization of chromatin compaction. Scale bar, 10 μm. b, RT-qPCR analysis of selected transcripts in DEK-depleted 1E7 cells versus controls following CX-4945 treatment (mean ± s.d., n = 3; two-tailed Student’s t-test, P < 0.05, ** P < 0.005). c, MNase digestion time course of nuclei isolated from DMSO-or CX-4945-treated SK-Mel-103 cells; purified DNA was resolved by agarose gel electrophoresis. d, Immunofluorescence staining for DEK in SK-Mel-103 cells following siRNA-mediated DEK knockdown and CX-4945 treatment, with DAPI counterstaining. Scale bar, 10 μm. e, ATAC-seq Metaprofiles centered on DMSO-specific (left) and CX-4945-specific (right) DEK binding sites (±5 kb) with DEK siRNA-mediated knockdown and control f, MNase accessibility assay following CX-4945 treatment in control and DEK knockdown SK-Mel-103 cells; DNA recovered from supernatant and pellet fractions was resolved by agarose gel electrophoresis.

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: Imaging, Two Tailed Test, Quantitative RT-PCR, Isolation, Purification, Agarose Gel Electrophoresis, Immunofluorescence, Staining, Knockdown, Binding Assay, Control

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, Additional representative confocal images of nuclear chromatin morphology in SK-Mel-103 cells and DEK-depleted 1E7 cells following treatment with DMSO or the CK2 inhibitor CX-4945 (40 μM), corresponding to . Shown are the DAPI channel, a contrast-adjusted grayscale rendering of the DAPI channel (for visualization of chromatin compaction), and DIC images. Scale bar, 10 μm. b, Additional representative immunofluorescence images of DEK staining in SK-Mel-103 cells following siRNA-mediated DEK knockdown and treatment with DMSO or CX-4945 (40 μM), corresponding to . DAPI marks nuclei and DIC images are shown. Scale bar, 10 μm.

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: Immunofluorescence, Staining, Knockdown