Journal: Journal of translational medicine

Article Title: METTL3 regulates Ambra1 expression in an m6A-YTHDF2-dependent manner to promote mantle cell lymphoma progression.

doi: 10.1186/s12967-025-06647-4

Figure Lengend Snippet: Fig. 8 METTL3/YTHDF2/Ambra1 promotes MCL progression. (A) Representative images of tumors from each group on day 28. (B-C) Changes in tumor size and weight in the indicated groups. (D) METTL3 and Ambra1 mRNA and protein expression in the tumor tissues of the indicated groups. (E) Immu noblots showing the expression of Bcl2, BAX, cleaved caspase-3, and PARP in the tumor tissues. (F-G) Representative IHC images showing expression of cyclin D1, CDK4, and CDK6 in the tumor tissues. n = 5, *P < 0.05 vs. sh-NC + sh-NC group, #P < 0.05 vs. sh-METTL3 + sh-NC group, &P < 0.05 vs. sh-NC + sh- Ambra1 group

Article Snippet: After blocking with 5% BSA, the sections were incubated overnight with rabbit polyclonal antibodies against cyclin D1 (AWA10518, Abiowell), CDK4 (11026-1-AP, ProteinTech), and CDK6 (14052-1-AP, ProteinTech) (dilution 1:200) at 4 °C.

Techniques: Expressing

Journal: bioRxiv

Article Title: CDKN1A (p21 Cip/Waf1 ) stabilizes Cyclin D3 by inhibiting its phosphorylation-dependent nuclear export following butyrate treatment

doi: 10.1101/2025.06.19.660543

Figure Lengend Snippet: Dose response to butyrate for cyclins D1 (CCND1), D3 (CCND3) and the cyclin-dependent-kinase (CDK) inhibitor CDKN1A protein, and CCNDs mRNA levels in HCT116 cells. Total “soluble” proteins were extracted from cells cultured during 16 hours in a medium containing initially different butyrate concentrations. (a) Representative western analysis; (b) quantitative analysis of the normalized western signal (level) ratios derived from 3 independent experiments; (c) Western analysis of phosphorylated cyclins D (same extracts as used in (a)). In (c), the sigmoidal fit for both CCND3 (R 2 = 0.9571) and CDKN1A (R 2 =0.8317) protein level ratios are shown. (d)(e) Dose response to butyrate treatment for transcript levels of CCND1 and CCND3 genes measured in HCT116 by RT-qPCR. Measurements issued from three different experiments were plotted. The graphical representation indicated a linear increase in CCND3 mRNA (P< 0.0001) while CCND1 mRNA level decreased (P=0.001).

Article Snippet: The anti-cyclin D3 rabbit polyclonal antibodies used in this study were purchased from Santa Cruz Biotechnology (sc-182) and Proteintech (26755-1-AP).

Techniques: Cell Culture, Western Blot, Derivative Assay, Quantitative RT-PCR

Journal: bioRxiv

Article Title: CDKN1A (p21 Cip/Waf1 ) stabilizes Cyclin D3 by inhibiting its phosphorylation-dependent nuclear export following butyrate treatment

doi: 10.1101/2025.06.19.660543

Figure Lengend Snippet: Structural comparison of the crystallographic (PDB ID: 6P8H) and AlphaFold2-predicted (AF2) CDKN1A–CCND1/3–CDK4 complexes. Each subunit (CDKN1A, CCND1/CCND3, and CDK4) was predicted separately by AF2 and then overlaid onto the experimentally determined partial complex. Shown are the reassembled AF2-predicted CDKN1A–CCND3–CDK4 (left) and CDKN1A–CCND1–CDK4 (right) structures, highlighting how unresolved intrinsically disordered regions (IDRs) and extended C-terminal tails differ from the crystal structure. Dashed boxes mark the spatial proximity between CDKN1A’s RRL motif (Arg19–Arg20–Leu21) and the conserved cyclin Thr residues (Thr283 in CCND3 or Thr286 in CCND1). The inset magnifies these residues (RRL in gray; Thr283 in red; Thr286 in yellow), showing side-chain orientations. Notably, AF2 predicts variation in the C-terminal tails, suggesting CCND1 and CCND3 may exhibit distinct molecular recognition features (MoRFs).

Article Snippet: The anti-cyclin D3 rabbit polyclonal antibodies used in this study were purchased from Santa Cruz Biotechnology (sc-182) and Proteintech (26755-1-AP).

Techniques: Comparison

Journal: bioRxiv

Article Title: CDKN1A (p21 Cip/Waf1 ) stabilizes Cyclin D3 by inhibiting its phosphorylation-dependent nuclear export following butyrate treatment

doi: 10.1101/2025.06.19.660543

Figure Lengend Snippet: Molecular dynamics (MD) ensembles of the final 100 ns of the CDKN1A–CCND1–CDK4 (top) and CDKN1A–CCND3–CDK4 (bottom) complexes. Each ensemble comprises 50 snapshots taken at 2 ns intervals, illustrating how CDKN1A (wheat) interacts distinctly with CCND1 (pink) versus CCND3 (blue); CDK4 is shown in green. A dashed rectangle highlights the region containing the RRL motif of CDKN1A (black) and the conserved cyclin Thr residues (Thr286 in CCND1, orange; Thr283 in CCND3, yellow), whose side chains are displayed. The right panels show zoomed-in views of these residues, with calculated solvent-accessible surface areas (SASA) indicating Thr286 is partially solvent-exposed (0.61 ± 0.16 Å 2 ), whereas Thr283 is nearly buried (0.09 ± 0.06 Å 2 ). In the CDKN1A–CCND1 complex, the RRL motif forms multiple hydrogen bonds with CCND1, orienting Thr286 outward and facilitating phosphorylation. By contrast, Thr283 in CCND3 remains solvent-inaccessible, suggesting that CDKN1A binding induces a locally folded conformation that hinders phosphorylation and promotes CCND3 stabilization.

Article Snippet: The anti-cyclin D3 rabbit polyclonal antibodies used in this study were purchased from Santa Cruz Biotechnology (sc-182) and Proteintech (26755-1-AP).

Techniques: Solvent, Phospho-proteomics, Binding Assay

Journal: bioRxiv

Article Title: CDKN1A (p21 Cip/Waf1 ) stabilizes Cyclin D3 by inhibiting its phosphorylation-dependent nuclear export following butyrate treatment

doi: 10.1101/2025.06.19.660543

Figure Lengend Snippet: Dose response to butyrate for cyclins D1 (CCND1), D3 (CCND3) and the cyclin-dependent-kinase (CDK) inhibitor CDKN1A protein, and CCNDs mRNA levels in HCT116 cells. Total “soluble” proteins were extracted from cells cultured during 16 hours in a medium containing initially different butyrate concentrations. (a) Representative western analysis; (b) quantitative analysis of the normalized western signal (level) ratios derived from 3 independent experiments; (c) Western analysis of phosphorylated cyclins D (same extracts as used in (a)). In (c), the sigmoidal fit for both CCND3 (R 2 = 0.9571) and CDKN1A (R 2 =0.8317) protein level ratios are shown. (d)(e) Dose response to butyrate treatment for transcript levels of CCND1 and CCND3 genes measured in HCT116 by RT-qPCR. Measurements issued from three different experiments were plotted. The graphical representation indicated a linear increase in CCND3 mRNA (P< 0.0001) while CCND1 mRNA level decreased (P=0.001).

Article Snippet: The anti-cyclin D3 rabbit polyclonal antibodies used in this study were purchased from Santa Cruz Biotechnology (sc-182) and Proteintech (26755-1-AP).

Techniques: Cell Culture, Western Blot, Derivative Assay, Quantitative RT-PCR

Journal: bioRxiv

Article Title: CDKN1A (p21 Cip/Waf1 ) stabilizes Cyclin D3 by inhibiting its phosphorylation-dependent nuclear export following butyrate treatment

doi: 10.1101/2025.06.19.660543

Figure Lengend Snippet: Structural comparison of the crystallographic (PDB ID: 6P8H) and AlphaFold2-predicted (AF2) CDKN1A–CCND1/3–CDK4 complexes. Each subunit (CDKN1A, CCND1/CCND3, and CDK4) was predicted separately by AF2 and then overlaid onto the experimentally determined partial complex. Shown are the reassembled AF2-predicted CDKN1A–CCND3–CDK4 (left) and CDKN1A–CCND1–CDK4 (right) structures, highlighting how unresolved intrinsically disordered regions (IDRs) and extended C-terminal tails differ from the crystal structure. Dashed boxes mark the spatial proximity between CDKN1A’s RRL motif (Arg19–Arg20–Leu21) and the conserved cyclin Thr residues (Thr283 in CCND3 or Thr286 in CCND1). The inset magnifies these residues (RRL in gray; Thr283 in red; Thr286 in yellow), showing side-chain orientations. Notably, AF2 predicts variation in the C-terminal tails, suggesting CCND1 and CCND3 may exhibit distinct molecular recognition features (MoRFs).

Article Snippet: The anti-cyclin D3 rabbit polyclonal antibodies used in this study were purchased from Santa Cruz Biotechnology (sc-182) and Proteintech (26755-1-AP).

Techniques: Comparison

Journal: bioRxiv

Article Title: CDKN1A (p21 Cip/Waf1 ) stabilizes Cyclin D3 by inhibiting its phosphorylation-dependent nuclear export following butyrate treatment

doi: 10.1101/2025.06.19.660543

Figure Lengend Snippet: Molecular dynamics (MD) ensembles of the final 100 ns of the CDKN1A–CCND1–CDK4 (top) and CDKN1A–CCND3–CDK4 (bottom) complexes. Each ensemble comprises 50 snapshots taken at 2 ns intervals, illustrating how CDKN1A (wheat) interacts distinctly with CCND1 (pink) versus CCND3 (blue); CDK4 is shown in green. A dashed rectangle highlights the region containing the RRL motif of CDKN1A (black) and the conserved cyclin Thr residues (Thr286 in CCND1, orange; Thr283 in CCND3, yellow), whose side chains are displayed. The right panels show zoomed-in views of these residues, with calculated solvent-accessible surface areas (SASA) indicating Thr286 is partially solvent-exposed (0.61 ± 0.16 Å 2 ), whereas Thr283 is nearly buried (0.09 ± 0.06 Å 2 ). In the CDKN1A–CCND1 complex, the RRL motif forms multiple hydrogen bonds with CCND1, orienting Thr286 outward and facilitating phosphorylation. By contrast, Thr283 in CCND3 remains solvent-inaccessible, suggesting that CDKN1A binding induces a locally folded conformation that hinders phosphorylation and promotes CCND3 stabilization.

Article Snippet: The anti-cyclin D3 rabbit polyclonal antibodies used in this study were purchased from Santa Cruz Biotechnology (sc-182) and Proteintech (26755-1-AP).

Techniques: Solvent, Phospho-proteomics, Binding Assay