Journal: bioRxiv

Article Title: Chemical Probe Discovery for DEAD-box RNA Binding Protein DDX21 using Small Molecule Microarrays

doi: 10.1101/2025.04.18.649545

Figure Lengend Snippet: KI-DX-014 blocks release of P-TEFb from 7SK snRNP and causes developmental defects in zebrafish via Pol II phosphorylation. a . Schematic of P-TEFb release assay in the presence of KI-DX-014. Created with BioRender.com . b . Western blot analysis of released P-TEFb from HEXIM1 immunopurified 7SK snRNP upon addition of purified DDX21-FL and ATP in the presence of KI-DX-014. c . Schematic of in vivo treatment in zebrafish embryo model. KI-DX-014 or vehicle (DMSO) were microinjected to fertilized zebrafish embryos at 1 cell stage. Reference CDK9 inhibitor (Flavopiridol) or vehicle (DMSO) containing medium were treated to fertilized zebrafish embryos at 1 cell stage. After 24 h, zebrafish embryos were dechorionated for imaging and total protein extraction. Created with BioRender.com . d , Representative images of zebrafish embryos at 24 h.p.f. treated with KI-DX-014 and reference CDK9 inhibitors; scale bar, 200 µm. e , Western blot analysis of phospho-RNA Pol II CTD serine 2 and serine 5 levels in zebrafish embryos after 24 h treatment with KI-DX-014 and reference CDK9 inhibitors.

Article Snippet: The antibodies used in this study include CDK9 (C12F7) Rabbit mAb (Cell Signaling, 2316, 1:1000), Anti-HEXIM1 antibody (Abcam, ab25388, 1:1000), Purified anti-RNA Polymerase II RPB1 Antibody (H5) (BioLegend, 920204, 1:1000), Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody (Abcam, ab5131, 1:1000), Goat anti-Mouse IgG (H+L) Poly-HRP Secondary Antibody, HRP (Invitrogen, 32230, 1:5000), Goat anti-Rabbit IgG (H+L) Poly-HRP Secondary Antibody, HRP (Invitrogen, 32260, 1:5000), Peroxidase IgG Fraction Monoclonal Mouse Anti-Rabbit IgG, light chain specific (Jackson ImmunoResearch, 211-032-171, 1:5000)

Techniques: Phospho-proteomics, Release Assay, Western Blot, Purification, In Vivo, Imaging, Protein Extraction

Journal: bioRxiv

Article Title: Chemical Probe Discovery for DEAD-box RNA Binding Protein DDX21 using Small Molecule Microarrays

doi: 10.1101/2025.04.18.649545

Figure Lengend Snippet:

Article Snippet: The antibodies used in this study include CDK9 (C12F7) Rabbit mAb (Cell Signaling, 2316, 1:1000), Anti-HEXIM1 antibody (Abcam, ab25388, 1:1000), Purified anti-RNA Polymerase II RPB1 Antibody (H5) (BioLegend, 920204, 1:1000), Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody (Abcam, ab5131, 1:1000), Goat anti-Mouse IgG (H+L) Poly-HRP Secondary Antibody, HRP (Invitrogen, 32230, 1:5000), Goat anti-Rabbit IgG (H+L) Poly-HRP Secondary Antibody, HRP (Invitrogen, 32260, 1:5000), Peroxidase IgG Fraction Monoclonal Mouse Anti-Rabbit IgG, light chain specific (Jackson ImmunoResearch, 211-032-171, 1:5000)

Techniques:

Journal: Veterinary microbiology

Article Title: Transcriptome profiling reveals that the host BRD4 protein facilitates African swine fever virus infection and suppresses inflammatory cytokine expression by downregulating transcriptional regulatory signaling pathways.

doi: 10.1016/j.vetmic.2025.110498

Figure Lengend Snippet: Fig. 10. 3D4/21-BRD4-BD1/2 cells suppress the expression of transcription factors and inflammatory cytokines. A. 3D4/21-BRD4-BD1/2 suppresses the expression of transcription factors such as CDK9. B. Reduction in the expression of inflammatory cytokines such as IL-1β due to stable expression of BRD4-BD1/2. C. Suppression of the transcriptional levels of inflammatory cytokines, including IL-1β, by stable expression of BRD4-BD1/2.

Article Snippet: The following antibodies were procured: AntiDYKDDDK-tag rabbit antibody (CST, 14793S), anti-β-tubulin rabbit antibody (Proteintech, 10094–1-AP), anti-β-actin mouse monoclonal antibody (Proteintech, 66009–1), anti-NLRP3 rabbit antibody (CST, 15101S), anti-IL-1β rabbit antibody (CST, 12703S), anti-caspase-1 rabbit antibody (CST, 3866S), anti-ASC/TMS1 rabbit antibody (CST, 13833S), anti-NF-κB p65 mouse antibody (CST, 6956S), anti-phosphoNF-κB pp65 rabbit antibody (CST, 3033S), anti-CDK9 rabbit monoclonal antibody (CST, 2316), anti-phospho-Rpb1 CTD (Ser2/Ser5) rabbit monoclonal antibody (D1G3K) (CST, 13546 s), and anti-phospho-CDK9 rabbit monoclonal antibody (CST, 13546 s).

Techniques: Expressing

Journal: Veterinary microbiology

Article Title: Transcriptome profiling reveals that the host BRD4 protein facilitates African swine fever virus infection and suppresses inflammatory cytokine expression by downregulating transcriptional regulatory signaling pathways.

doi: 10.1016/j.vetmic.2025.110498

Figure Lengend Snippet: Fig. 10. 3D4/21-BRD4-BD1/2 cells suppress the expression of transcription factors and inflammatory cytokines. A. 3D4/21-BRD4-BD1/2 suppresses the expression of transcription factors such as CDK9. B. Reduction in the expression of inflammatory cytokines such as IL-1β due to stable expression of BRD4-BD1/2. C. Suppression of the transcriptional levels of inflammatory cytokines, including IL-1β, by stable expression of BRD4-BD1/2.

Article Snippet: The following antibodies were procured: AntiDYKDDDK-tag rabbit antibody (CST, 14793S), anti-β-tubulin rabbit antibody (Proteintech, 10094–1-AP), anti-β-actin mouse monoclonal antibody (Proteintech, 66009–1), anti-NLRP3 rabbit antibody (CST, 15101S), anti-IL-1β rabbit antibody (CST, 12703S), anti-caspase-1 rabbit antibody (CST, 3866S), anti-ASC/TMS1 rabbit antibody (CST, 13833S), anti-NF-κB p65 mouse antibody (CST, 6956S), anti-phosphoNF-κB pp65 rabbit antibody (CST, 3033S), anti-CDK9 rabbit monoclonal antibody (CST, 2316), anti-phospho-Rpb1 CTD (Ser2/Ser5) rabbit monoclonal antibody (D1G3K) (CST, 13546 s), and anti-phospho-CDK9 rabbit monoclonal antibody (CST, 13546 s).

Techniques: Expressing

Journal: bioRxiv

Article Title: Histone chaperone HIRA facilitates transcription elongation to regulate insulin sensitivity and obesity-associated adipose expansion

doi: 10.1101/2025.03.21.644577

Figure Lengend Snippet: 3T3-L1 white preadipocytes were infected with a lentiviral vector expressing human HIRA with C-terminal dTAG and HA double tags, followed by lentiviral CRISPR/Cas9- Hira gRNA to delete endogenous Hira . At D4 of adipogenesis, cells were treated with dTAG-13 for 6h. a , Pie charts depicting the genomic distribution of HIRA binding regions at D4. b , Heat maps were aligned around the center of HIRA binding sites on promoters (6,838), primed enhancers (1,998), active enhancers (AEs, 17,862) and other regions (1,751) at D4. c , Average binding profiles of HIRA-HA, H3K27ac, S5P-Pol II, S2P-Pol II, CDK9 and SPT6 around the center of HIRA + promoters and AEs. Normalized read counts are shown. d , Profiles of HIRA-HA, H3K27ac, S5P-Pol II, S2P-Pol II, CDK9 and SPT6 on gene bodies of HIRA + promoter-associated genes. g , ChIP–Seq profiles of HIRA-HA, H3K27ac, S5P-Pol II, S2P-Pol II, CDK9 and SPT6 were displayed on Adipoq , Mlxipl (ChREBP) and Fasn loci.

Article Snippet: Anti-S5P-Pol II (13523), anti-S2P-Pol II (13499S), anti-CDK9 (2316T) and anti-SPT6 (15616) were from Cell Signaling Technology.

Techniques: Infection, Plasmid Preparation, Expressing, CRISPR, Binding Assay, ChIP-sequencing

Journal: EMBO Reports

Article Title: Liquid–liquid phase separation of LARP7 restrains HIV-1 replication

doi: 10.1038/s44319-025-00421-9

Figure Lengend Snippet: Reagents and tools table

Article Snippet: Rabbit anti-CDK9 , Santa Cruz , Cat# sc-13130.

Techniques: Recombinant, Sequencing, Purification, SYBR Green Assay, Cell Isolation, Reporter Assay, Virus, Software