arca cap analog  (Jena Bioscience)

Journal: Journal of Biochemistry

Article Title: DAXX promotes SUMOylation of chromatin-trapped DNMT1

doi: 10.1093/jb/mvag011

Figure Lengend Snippet: Xenopus egg extract recapitulates 5-aza-dCTP-induced SUMOylated DNMT1 accumulation on chromatin. (A) Xenopus sperm nuclei were incubated in egg extracts supplemented with or without 50 μM 5-aza-dCTP for indicated periods. Isolated chromatins were analyzed by immunoblotting with the indicated antibodies. (B) Immunoblotting results using indicated antibodies following DNMT1 immunoprecipitation of chromatin treated or untreated with 5-aza-dCTP for 60 min. The input results were shown in the lower panels.

Article Snippet: For DNMT1 inhibition, egg extracts were incubated with 50 μM 5-aza-dCTP (Jena Bioscience) or with 100 μM GSK-3484862 (MedChemExpress).

Techniques: Incubation, Isolation, Western Blot, Immunoprecipitation

Journal: Journal of Biochemistry

Article Title: DAXX promotes SUMOylation of chromatin-trapped DNMT1

doi: 10.1093/jb/mvag011

Figure Lengend Snippet: DAXX accumulates on DNMT1-trapped chromatin in a SUMO-dependent manner identified by CHROMASS. (A) Volcano plot showing chromatin mass spectrometry analysis of protein recruitment to chromatins treated with or without 5-aza-dCTP ( n = 3 technical replicates). Proteins highlighted in blue were identified in the comparison between 5-aza-dCTP+UBC9-DN and control groups and represent factors whose accumulation on chromatin is associated with SUMOylation. (B) Scatter plot showing protein abundance ratios derived from indicated comparisons in the axis titles.

Article Snippet: For DNMT1 inhibition, egg extracts were incubated with 50 μM 5-aza-dCTP (Jena Bioscience) or with 100 μM GSK-3484862 (MedChemExpress).

Techniques: Mass Spectrometry, Comparison, Control, Quantitative Proteomics, Derivative Assay

Journal: Journal of Biochemistry

Article Title: DAXX promotes SUMOylation of chromatin-trapped DNMT1

doi: 10.1093/jb/mvag011

Figure Lengend Snippet: DAXX interacts with SUMOylated DNMT1 on chromatin through SIMs. (A) The multiple sequence alignment of DAXX from different indicated species. DAXX contains SUMO-interacting motifs (SIMs), four-helix bundle (4HB), histone binding domain (HBD) and acidic residue-rich domain ( ad ). (B) Xenopus sperm nuclei were incubated in egg extracts supplemented with buffer, 5-aza-dCTP or 5-aza-dCTP and SUMO inhibitor ML-792. Isolated chromatin was analyzed by immunoblotting with indicated antibodies. (C) Xenopus sperm nuclei were incubated in mock-depleted or DNMT1-depleted extracts in the presence of buffer or 5-aza-dCTP. Isolated chromatin was analyzed by immunoblotting with indicated antibodies. (D) 3× FLAG-tagged xDAXX WT, 3× FLAG-tagged xDAXX SIM1 mutants (I7AI8A point mutant or 1–14 deletion mutant) or 3× FLAG-tagged xDAXX SIM2 mutants (V911A/I912A point mutant or 909–916 deletion mutant) were added to DAXX-depleted extracts. (E) Xenopus sperm nuclei were incubated in mock-depleted or DAXX-depleted extracts supplemented with xDAXX WT, xDAXX SIM1 mutants or xDAXX SIM2 mutants in the presence of buffer or 5-aza-dCTP.

Article Snippet: For DNMT1 inhibition, egg extracts were incubated with 50 μM 5-aza-dCTP (Jena Bioscience) or with 100 μM GSK-3484862 (MedChemExpress).

Techniques: Sequencing, Binding Assay, Residue, Incubation, Isolation, Western Blot, Mutagenesis

Journal: Journal of Biochemistry

Article Title: DAXX promotes SUMOylation of chromatin-trapped DNMT1

doi: 10.1093/jb/mvag011

Figure Lengend Snippet: DAXX promotes SUMOylation of chromatin-trapped DNMT1. (A) Immunoblotting results of egg extracts using indicated antibodies. 3× FLAG-tagged xDAXX WT was added to xDAXX-depleted egg extracts. (B) Chromatin fractions were isolated from mock-depleted or xDAXX-depleted egg extracts treated or untreated with 5-aza-dCTP for the indicated times, with or without adding 3× FLAG-tagged xDAXX. DNMT1 SUMOylation was assessed by immunoblotting using anti-DNMT1 antibodies.

Article Snippet: For DNMT1 inhibition, egg extracts were incubated with 50 μM 5-aza-dCTP (Jena Bioscience) or with 100 μM GSK-3484862 (MedChemExpress).

Techniques: Western Blot, Isolation

Journal: bioRxiv

Article Title: Dual Pathways of Extracellular ATP Action in Cancer Cells: Purinergic Signaling–Driven Senescence and Macropinocytic ATP Internalization

doi: 10.64898/2026.04.23.720363

Figure Lengend Snippet: (A–B) Short-time interval ATP concentration assay (minutes). Intracellular ATP (iATP, % of control) for A549 (A) and A549STC1KO (B) cells measured at the indicated induction times between 30-120 minutes. (C–D) Long-time interval ATP concentration assay (hours). iATP (%) for A549 WT (C) and STC1-KO (D) across induction times between 2-4 hours. (E) Immunofluorescence/confocal imaging of macropinocytosis. A549 WT, A549 STC1-KO (two independent clones), and NL20 control cells were stained with NHF-ATP (green; ATP analog), High molecular weight dextran (red-macropinosome marker), and DAPI (blue; cell nuclei). Merged images show colocalization (yellow). STC1-KO cells display visibly reduced FITC-dextran uptake relative to WT based on gene expression reduction, while NL20 shows minimal uptake. Scale bars: 20 µm (A549 and STC1-KO), 10 µm (NL20). Data is representation for one set of biological replicates as mean ± SD for (n ≥ 5 technical replicates). Colors denote the eATP dose as indicated in the in-plot legend. One-way ANOVA with post-hoc multiple-comparisons; *P < 0.05,**P < 0.01,***P < 0.001, ****P < 0.0001.

Article Snippet: For fluorescence microscopy, NHF-ATP was obtained from Jena Bioscience (NU-810-488), ProLong TM Gold Antifade Mountant with DAPI from Thermo Fisher and high molecular weight fluorescent TMR-dextran (HMWFD) 70,000 Daltons MW, Neutral (no electric charge) from Invitrogen (D818).

Techniques: Concentration Assay, Control, Immunofluorescence, Imaging, Clone Assay, Staining, High Molecular Weight, Marker, Gene Expression

Journal: bioRxiv

Article Title: Dual Pathways of Extracellular ATP Action in Cancer Cells: Purinergic Signaling–Driven Senescence and Macropinocytic ATP Internalization

doi: 10.64898/2026.04.23.720363

Figure Lengend Snippet: Tumor xenografts were established by subcutaneous injection of 1×10 –5×10 cells into the right flank of 3–4-week-old male NU/J nude mice. When tumors reached ∼200–500 mm³, tumors were injected intratumorally with DMEM control, HMWFD tracer, or HMWFD plus NHF-ATP (100 μM) in a total volume of 50 μL using 27G needles. Tumors were harvested within ∼7–8 minutes post-injection, embedded in OCT, and cryosectioned (10 μm). Sections were ethanol-fixed, PBS-washed, and mounted with antifade medium containing DAPI. Images were acquired using a Nikon NiU epifluorescence microscope with identical exposure settings across groups and processed using Nikon NIS-Elements software. A-H. NHF-ATP and HMWFD colocalize in HT29 (A), PANC1 (B), MCF7 (C), SK-HEP1 (D), HOP-92 (E), H1299 (F), and A549 (G) and A375 (H). respectively. Color: Blue:DAPI (nuclei), Red: HMWFD, Green: NHF-ATP, Yellow: Co-localization. Scale bar: 10 µm, 100x magnification.

Article Snippet: For fluorescence microscopy, NHF-ATP was obtained from Jena Bioscience (NU-810-488), ProLong TM Gold Antifade Mountant with DAPI from Thermo Fisher and high molecular weight fluorescent TMR-dextran (HMWFD) 70,000 Daltons MW, Neutral (no electric charge) from Invitrogen (D818).

Techniques: Injection, Control, Microscopy, Software