cdk7  (Bethyl)

Journal: Nucleic Acids Research

Article Title: CDK7–CDK11 axis in spliceosome regulation and pre-mRNA splicing

doi: 10.1093/nar/gkaf1343

Figure Lengend Snippet: CDK7 transiently binds CDK11. ( A ) Schematic representation of proteomic BioID experiment for identification of proteins proximal to CDK11. The N-terminus of CDK11 fused to biotin ligase (BirA) biotinylates nearby proteins in cells. The biotinylated proteins are purified and identified by mass spectrometry. ( B ) Volcano plot of proteins identified in CDK11 BioID. Splicing factors are marked in orange, components of the CDK11 complex in blue, CDK7 in cyan and other proteins in green. ( C ) Immunoblot analysis of immunoprecipitations of endogenous CDK11 after 4 h treatment with 50 nM SY-351 in HCT116 cells. Detected proteins are indicated on the right. IgG = antibody control.

Article Snippet: Blocking was done with 3% fetal bovine serum (FBS) in PBS for 1 h. Subsequently, cells were incubated with primary antibodies (P-CDK11 Ab1, P-CDK11 Ab2, 1:100 dilution), SF3B1 (MBL, MB-D221-3, 1:300 dilution), CDK11 (Abcam, ab19393, 1:400 dilution), and CDK7 (Bethyl, A300-405A, 1:400 dilution) for 1 h and washed 3 × 5 min with PBS.

Techniques: Purification, Mass Spectrometry, Western Blot, Control

Journal: Nucleic Acids Research

Article Title: CDK7–CDK11 axis in spliceosome regulation and pre-mRNA splicing

doi: 10.1093/nar/gkaf1343

Figure Lengend Snippet: CDK11 is phosphorylated on canonical activating Thr595 in cells. ( A ) Amino acid sequence of T-loop of CDK11B. Activating Thr595 is in red. Peptide sequences used for the production of three (Ab1, Ab2, and Ab3) phospho-specific Thr595 antibodies are indicated by black bars. ( B ) Multiple protein sequence alignment of T-loop of CDKs. Activating Thr residues are highlighted in red, Ser corresponding to Ser164 in CDK7 is in orange. xDFG and APE motifs are indicated. ( C ) Immunoblot analysis of CDK11 in HCT116 cells upon treatment with control or CDK11 siRNAs for 40 h. Bands corresponding to CDK11 110 and P-CDK11 220 (monitored by Ab3) are marked on the right with arrows. “Long” and “short” corresponds to long and short exposure of the film. Asterisk denotes nonspecific bands. ( D ) Immunoblot analysis of CDK11 in HCT116 cells upon treatment with 50 nM SY-351 or control DMSO for 4 h. See Fig. for the legend. ( E ) Immunofluorescence microscopy of HCT116 cells using DAPI stain and the P-CDK11 220 (Ab2) and SF3B1 antibodies upon 100 nM treatment with SY-351 or control DMSO for 4 h; scale bar = 10 µm. ( F ) Quantification of P-CDK11 intensity (monitored by Ab2) in Fig. . Box plots represent median and IQR, whiskers extend to the furthest value inside 1.5 × IQR, asterisk: P < 0.05.

Article Snippet: Blocking was done with 3% fetal bovine serum (FBS) in PBS for 1 h. Subsequently, cells were incubated with primary antibodies (P-CDK11 Ab1, P-CDK11 Ab2, 1:100 dilution), SF3B1 (MBL, MB-D221-3, 1:300 dilution), CDK11 (Abcam, ab19393, 1:400 dilution), and CDK7 (Bethyl, A300-405A, 1:400 dilution) for 1 h and washed 3 × 5 min with PBS.

Techniques: Sequencing, Western Blot, Control, Immunofluorescence, Microscopy, Staining

Journal: Nucleic Acids Research

Article Title: CDK7–CDK11 axis in spliceosome regulation and pre-mRNA splicing

doi: 10.1093/nar/gkaf1343

Figure Lengend Snippet: CDK7 is required for the formation of P-CDK11 220 and active spliceosomes. ( A ) Immunoblot analyses of indicated proteins in HCT116 cells treated with control DMSO or 50 nM SY-351 for 2 h and separated into cytoplasmic (cyto), nucleoplasm (nucl), and chromatin (chrom) fractions. Bands corresponding to CDK11 110 and P-CDK11 220 (monitored by Ab3) are marked on the right with arrows. CCNL1 is marked on the right with an arrow. “Long” and “short” corresponds to long and short exposure of the film. Asterisk denotes a nonspecific band. ( B ) Immunoblot analyses of indicated proteins in nucleoplasm and chromatin fractions (from Fig. ) separated by ultracentrifugation in 10%–40% glycerol gradient. Bands corresponding to CDK11 110 and P-CDK11 220 (monitored by Ab3) are marked on the right with arrows. Asterisks denote nonspecific bands. ( C ) Metagene analyses of P-CDK11 ChIP-Seq (using Ab2) on 8090 genes in cells treated with either control DMSO or 50 nM SY-351 for 2 h. Each transcript was divided into two parts with fixed length [transcription start site (TSS) −3 kb to +1.5 kb and transcription termination site (TTS) −1.5 kb to +20 kb] and a central part with variable length corresponding to the rest of gene body (shown in %). Each part was binned into a fixed number of bins (90/180/215), average coverage normalized to sequencing depth was calculated for each bin for each transcript in each sample and then averaged first across genes and second across samples. The color track at the bottom indicates the significance of paired Wilcoxon tests comparing the normalized transcript coverages for each bin between DMSO and SY-351 treatment. P ‐values are adjusted for multiple testing with the Bonferroni method within each subfigure; color code: red = adjusted P ‐value ≤ 10 −15 , orange = adjusted P ‐value ≤ 10 −10 , yellow = adjusted P ‐value ≤ 10 −3 . ( D ) IGV genome browser view of P-CDK11 220 ChIP-Seq on EZR gene in HCT116 cells treated with either control DMSO or 50 nM SY-351 for 2 h. SF3B1 and P-SF3B1 ChIP-seq on EZR gene in cells treated with control DMSO are shown below. noAb = control without antibody, R1, R2 = replicate 1, 2. T211 and T235 Ab = antibodies against P-Thr211 and P-Thr235 in SF3B1, respectively. Y -axis scale is denoted in square brackets.

Article Snippet: Blocking was done with 3% fetal bovine serum (FBS) in PBS for 1 h. Subsequently, cells were incubated with primary antibodies (P-CDK11 Ab1, P-CDK11 Ab2, 1:100 dilution), SF3B1 (MBL, MB-D221-3, 1:300 dilution), CDK11 (Abcam, ab19393, 1:400 dilution), and CDK7 (Bethyl, A300-405A, 1:400 dilution) for 1 h and washed 3 × 5 min with PBS.

Techniques: Western Blot, Control, ChIP-sequencing, Sequencing

Journal: Nucleic Acids Research

Article Title: CDK7–CDK11 axis in spliceosome regulation and pre-mRNA splicing

doi: 10.1093/nar/gkaf1343

Figure Lengend Snippet: Onset of splicing deficiency after CDK7 inhibition correlates with P-CDK11 220 dephosphorylation. ( A ) Immunoblot analyses of proteins after treatment of HCT116 cells with control DMSO or 50 nM SY-351 for the indicated times. Bands corresponding to CDK11 110 and P-CDK11 220 are marked on the right with arrows. ( B ) DNA gel-visualised RT-PCR analyses of splicing of ARRDC4, CCNL1 , and RIOK1 transcripts after treatment of HCT116 cells with 100 nM SY-351 for the indicated times. Schema of unspliced and spliced transcripts, including order of the tested exons in each transcript, are depicted on the right. DNA represents control RT-PCR product from genomic DNA. ( C ) Graph shows ratio of unspliced to spliced transcripts of six genes measured by RT-qPCR in HCT116 cells treated with 50 nM SY-351 for indicated times. mRNA levels were normalised to PPIA mRNA and expression in control DMSO condition was set as 1. Error bars = SD, n = 3.

Article Snippet: Blocking was done with 3% fetal bovine serum (FBS) in PBS for 1 h. Subsequently, cells were incubated with primary antibodies (P-CDK11 Ab1, P-CDK11 Ab2, 1:100 dilution), SF3B1 (MBL, MB-D221-3, 1:300 dilution), CDK11 (Abcam, ab19393, 1:400 dilution), and CDK7 (Bethyl, A300-405A, 1:400 dilution) for 1 h and washed 3 × 5 min with PBS.

Techniques: Inhibition, De-Phosphorylation Assay, Western Blot, Control, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Expressing

Journal: Nucleic Acids Research

Article Title: CDK7–CDK11 axis in spliceosome regulation and pre-mRNA splicing

doi: 10.1093/nar/gkaf1343

Figure Lengend Snippet: Working Model. ( A ) CDK7 activity in normal cell. CDK7, as part of the TFIIH complex, phosphorylates the CTD of RNAPII to regulate promoter escape and normal transcription. CDK7, probably as part of the CAK complex, is also required for the onset of P-CDK11 220 , which is needed for the phosphorylation of SF3B1 (P-SF3B1) and activation of the spliceosome and normal splicing. ( B ) Consequences of short (<2 h) CDK7 inhibition with SY-351. Short inhibition blocks promoter escape, which results in a strong decrease in transcription, with some RNAPII slowly transcribing into the gene body. ( C ) Consequences of long (>2 h) CDK7 inhibition with SY-351. After a longer inhibition, the transcription is rescued by other transcriptional CDKs that phosphorylate the CTD of RNAPII . This results in faster elongation and synthesis of nascent RNA. The RNA is not spliced, because ongoing CDK7 inhibition blocks the formation of P-CDK11 220 and subsequent SF3B1 phosphorylation, which results in an inactive spliceosome and nonfunctional splicing.

Article Snippet: Blocking was done with 3% fetal bovine serum (FBS) in PBS for 1 h. Subsequently, cells were incubated with primary antibodies (P-CDK11 Ab1, P-CDK11 Ab2, 1:100 dilution), SF3B1 (MBL, MB-D221-3, 1:300 dilution), CDK11 (Abcam, ab19393, 1:400 dilution), and CDK7 (Bethyl, A300-405A, 1:400 dilution) for 1 h and washed 3 × 5 min with PBS.

Techniques: Activity Assay, Phospho-proteomics, Activation Assay, Inhibition

Journal: mBio

Article Title: Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans

doi: 10.1128/mbio.02898-25

Figure Lengend Snippet: Phylogenetic/guide trees obtained following multiple amino acid sequence alignment of the CDK7, cyclin H, and Mat1 homologs from C. neoformans ( Cn ), Homo sapiens ( Hs ), S. cerevisiae ( Sc ), and S. pombe ( Sp ). The trees show that Cn CDK7 and Cn Mat1 proteins cluster with the human homologs. Cn CDK7 (CNAG_06445 and XP_012053336.1 ), Hs CDK7 ( NP_001790.1 ), Sc CDK7/ Sc Kin28 ( NP_010175.1 ), Sp CDK7/ Sp Mcs6 ( NP_596349.1 ), Cn Cyclin H (CNAG_04405 and XP_012051791.1 ), Hs CycH ( NP_001230.1 ), Sc CycH/ Sc Ccl1 ( NP_015350.1 ), Sp CycH/ Sp Mcs2 ( NP_595776.1 ), Cn Mat1 (CNAG_05877 and XP_012050601.1 ), Hs Mat1 ( NP_002422.1 ), Sc Mat1/ Sc Tfb3 ( NP_010748.3 ), and Sp Mat1/ Sp Pmh1 ( NP_596334.1 ). Numbers represent sequence distances.

Article Snippet: ChromoTek mNeonGreen-Trap Agarose beads (cat. no. nta) and V5-Trap agarose beads (cat. no. v5ta) were used to pull down mNeonGreen-tagged CDK7 from the cleared lysates, with KN99 serving as a control for untagged CDK7.

Techniques: Sequencing

Journal: mBio

Article Title: Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans

doi: 10.1128/mbio.02898-25

Figure Lengend Snippet: Cn CDK7 forms a CAK complex with Mat1 and cyclin H that localizes to the nucleus. ( A ) Schematic depicting the addition of the mNeonGreen (mNG), V5 epitope (V5), and 6× His (His) tags on CDK7, CycH, and Mat1, respectively, in the CDK7 triple-tagged strain as described in the Supplemental Method. ( B ) Immunoprecipitation (IP) and Western blotting with antibodies to each tag demonstrates formation of a CAK complex: in the left panel, Cn CDK7 was immunoprecipitated from the CDK7 triple-tagged strain with anti-mNG trap and subjected to SDS-PAGE and Western blotting with anti-mNG, anti-6× His, and anti-V5, detecting CDK7, CycH, and Mat1, respectively (lane 2). In the right panel, CycH was immunoprecipitated from the CDK7 triple-tagged strain with V5-Trap, followed by Western blotting with the various antitag antibodies (lane 2). In both panels, the non-tagged parent KN99 WT strain (WT) was taken through the same procedure as a negative control (lane 1). The total lysates used for each IP were probed with anti-PSTAIR to demonstrate the presence of Cdc2 in all IP samples. Epifluorescence microscopy validated the fluorescence of Cn CDK7 in the CDK7 triple-tagged strain ( C ) and the nuclear localization of the Cn CAK complex ( D ). DIC, Differential interference contrast.

Article Snippet: ChromoTek mNeonGreen-Trap Agarose beads (cat. no. nta) and V5-Trap agarose beads (cat. no. v5ta) were used to pull down mNeonGreen-tagged CDK7 from the cleared lysates, with KN99 serving as a control for untagged CDK7.

Techniques: Immunoprecipitation, Western Blot, SDS Page, Negative Control, Epifluorescence Microscopy, Fluorescence

Journal: mBio

Article Title: Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans

doi: 10.1128/mbio.02898-25

Figure Lengend Snippet: Chemical structures of the human CDK7 inhibitors tested in this study. Inhibitors are arranged based on their molecular scaffold (in blue): pyrimidine (THZ1, SY-1365, and CDK7-IN-3), pyrrolidinopyrazole from p21-activated kinase (PAK4) (CDK7-IN-1, YKL-5-124, and IV-361) and pyrazolopyrimidine (samuraciclib). Red regions indicate the covalent warhead. THZ1 served as a molecular starting point for the creation of all compounds (indicated by the arrows), except Samuraciclib.

Article Snippet: ChromoTek mNeonGreen-Trap Agarose beads (cat. no. nta) and V5-Trap agarose beads (cat. no. v5ta) were used to pull down mNeonGreen-tagged CDK7 from the cleared lysates, with KN99 serving as a control for untagged CDK7.

Techniques:

Journal: mBio

Article Title: Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans

doi: 10.1128/mbio.02898-25

Figure Lengend Snippet: Cn CDK7 is inhibited by human CDK7 inhibitors. Kinase assays were performed over a 300 min time course in the absence (DMSO) and presence of the indicated concentrations of each CDK7 inhibitor, using pulled-down CAK, CDK7 peptide substrate, and Kinase-Glo reagent. The latter allowed ATP consumption (due to the phosphorylation of the peptide substrate by CDK7) to be measured as a relative luminescence unit. The full dose–response time curves are shown in . Only CDK7 enzyme activity at 300 min is plotted and is expressed as “relative activity (%)” after normalization as described in Materials and Methods. The CDK1/CDK2/CDK4/CDK5 inhibitor, Purvalanol A, is included as a negative control. The results represent the mean relative activity ± SEM ( n = 2–3 independent experiments). Statistical analysis was performed using ordinary one-way analysis of variance with Dunnett’s multiple comparison test, comparing each concentration to the DMSO control. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. ns, not significant.

Article Snippet: ChromoTek mNeonGreen-Trap Agarose beads (cat. no. nta) and V5-Trap agarose beads (cat. no. v5ta) were used to pull down mNeonGreen-tagged CDK7 from the cleared lysates, with KN99 serving as a control for untagged CDK7.

Techniques: Phospho-proteomics, Activity Assay, Negative Control, Comparison, Concentration Assay, Control

Journal: mBio

Article Title: Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans

doi: 10.1128/mbio.02898-25

Figure Lengend Snippet: Phosphoproteomic analysis of SY-1356-treated Cn strain H99. ( A ) K-means clustering using the STRING database was performed on the 122 proteins that had reduced phosphorylation following CDK7 inhibition with SY-1365 (see the Supplemental Method and for details). This resulted in four functional clusters (PPI enrichment P value <5 × 10⁻⁴). Proteins in pink are discussed in the main text. ( B ) Representative Western blot of n = 3 independent experiments (see scatter dot plot), validating reduced phosphorylation of the MAPK, Hog1 (Hog1p) following treatment with SY-1365, as compared to total Hog1 (Hog1t). In the scatter dot plot, the reduction in Hog1p levels after 1 h treatment with SY-1365 is statistically significant ( *P = 0.013, unpaired t -test; bars represent mean intensity ± SD).

Article Snippet: ChromoTek mNeonGreen-Trap Agarose beads (cat. no. nta) and V5-Trap agarose beads (cat. no. v5ta) were used to pull down mNeonGreen-tagged CDK7 from the cleared lysates, with KN99 serving as a control for untagged CDK7.

Techniques: Phospho-proteomics, Inhibition, Functional Assay, Western Blot

Journal: mBio

Article Title: Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans

doi: 10.1128/mbio.02898-25

Figure Lengend Snippet: Cn CDK7 phosphorylates Ser5 and Ser2 in the CTD of the Rpb1 subunit of RNAPII in vivo ( A ) Representative Western blot of three independent experiments (see adjacent scatter dot plot) showing that SY-1365 inhibits phosphorylation of Rpb1 on Ser5 (Rpb1-Ser5p). In the adjacent scatter dot plot, the reduction in Rpb1-Ser5p after 1 h treatment with SY-1365 when normalized to DMSO treatment is statistically significant (* P = 0.013, unpaired t -test; bars indicate mean intensity ± SD). ( B ) Representative Western blot of three independent experiments (see adjacent scatter dot plot) showing that SY-1365 inhibits phosphorylation of Rpb1 on Ser2 (Rpb1-Ser2p). In the adjacent scatter dot plot, the reduction in Rpb1-Ser2p after 1 h treatment with SY-1365 when normalized to DMSO treatment is statistically significant (* P = 0.0145, unpaired t -test; bars indicate mean intensity ± SD). In panels A and B , the levels of Rpb1-Ser5p and Rpb1-Ser2p in the SY-1365- and DMSO-treated samples were normalized to histone H3, which was used as a loading control.

Article Snippet: ChromoTek mNeonGreen-Trap Agarose beads (cat. no. nta) and V5-Trap agarose beads (cat. no. v5ta) were used to pull down mNeonGreen-tagged CDK7 from the cleared lysates, with KN99 serving as a control for untagged CDK7.

Techniques: In Vivo, Western Blot, Phospho-proteomics, Control

Journal: mBio

Article Title: Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans

doi: 10.1128/mbio.02898-25

Figure Lengend Snippet: RNA-seq data analysis of SY-1365-treated Cn identifies CDK7 functions including splicing regulation. RNA-seq was performed on untreated and SY-1365-treated Cn ( n = 3) as described in Materials and Methods. ( A ) A principal component analysis plot shows that replicates correlate well, with each treatment group having a distinct cluster profile. Gene set enrichment analysis (GSEA) was performed using the clusterProfiler R package to identify Gene Ontology categories ( B ) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways ( C ) that were significantly enriched following SY-1365 treatment. Diamond plots display the enriched pathways, where size represents the percentage of enriched genes and color indicates the statistical significance of enrichment. ( D ) Table presenting alternative splicing events (ASEs) determined upon SY-1365 treatment. Inhibition of Cn CDK7 leads to more intron retention events over intron exclusion. Normalized coverage plots of representative ASE with ( E ) intron retention and ( F ) intron exclusion upon SY-1365 treatment.

Article Snippet: ChromoTek mNeonGreen-Trap Agarose beads (cat. no. nta) and V5-Trap agarose beads (cat. no. v5ta) were used to pull down mNeonGreen-tagged CDK7 from the cleared lysates, with KN99 serving as a control for untagged CDK7.

Techniques: RNA Sequencing, Alternative Splicing, Inhibition

Journal: mBio

Article Title: Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans

doi: 10.1128/mbio.02898-25

Figure Lengend Snippet: Model depicting the role of Cn CDK7 in regulating the cell cycle, transcriptional processes, and translation. Cell cycle regulation: in the nucleus, Cn CDK7 in the CAK complex activates Cdk1 to promote cell cycle progression through G 2 /M. Activated Cdk1 also phosphorylates Cdc24 to promote actin polymerization. Cn CDK7 either directly phosphorylates components of the Hog1 signaling pathway or acts through an intermediary protein affected by Cn CDK7-dependent phosphorylation. Transcription: also in the nucleus, TFIIH-associated CAK phosphorylates Ser5 on the CTD of the Rpb1 subunit of RNAPII (see ), allowing RNAPII release from the promoter to initiate transcription. Ser5 phosphorylated-RNAPII pauses ~30 bp post-initiation and interacts with the capping enzymes, Ceg1p (RNA guanylyltransferase) and Cet1p (RNA triphosphatase), to form a capping complex. This complex allows the co-transcriptional formation of the 7-methylguanosine (7 mG) cap (red circle) on the 5′ end of newly synthesized (nascent) mRNA, ensuring mRNA stability, nuclear export, and translation. Cbc1 (mammalian Cbp80 homolog) and Cbc2 (mammalian Cbp20 homolog) then form a heterodimeric cap binding complex (CBC) that binds to the 7mG cap to stimulate formation of the pre-initiation complex (PIC) via the transcription regulator, Mot1. Post-release of the RNAPII transcriptional pause, Cn CDK7 is essential for Ser2 phosphorylation of Rpb1 to allow transcription elongation (see ). This occurs via Cn CDK7-mediated activation of CDK9. The CBC also links capping to splicing by promoting the recruitment of U1 snRNP to the 5′ splice site to initiate spliceosome assembly. The spliceosome, comprising U1–U6 snRNPs, Sf3b1, Msl5 (binds to the branch point sequences of the intron), and Cwf19 (facilitates spliceosome disassembly and mRNA release), mediates intron removal. As in humans, Cn CDK7 may also enhance spliceosome maturation by activating Cn CDK11 to phosphorylate Sf3b1 . Translation: in the cytoplasm, Pab1 binds the 3′ poly(A) tail of mature mRNAs, protecting them from degradation. Two major deadenylation complexes then act sequentially to regulate mRNA stability and turnover: the Pan2/Pan3 complex trims the poly(A) tail, while the Ccr4-NOT complex trims it further, leading to mRNA decay. The CBC at the 5′ end is replaced by eIF4E, which, along with eIF4A and eIF4G, initiates recruitment of additional eIFs to assemble ribosomal subunits on the mRNA, ultimately leading to the formation of a functional ribosome and the initiation of translation. Proteins with solid lines were identified in the CDK7 phosphoproteome (see ), while proteins, interactions, and functions delineated by broken lines are based on studies in higher eukaryotes and the presence of the homologous protein in Cn .

Article Snippet: ChromoTek mNeonGreen-Trap Agarose beads (cat. no. nta) and V5-Trap agarose beads (cat. no. v5ta) were used to pull down mNeonGreen-tagged CDK7 from the cleared lysates, with KN99 serving as a control for untagged CDK7.

Techniques: Phospho-proteomics, Synthesized, Binding Assay, Activation Assay, Functional Assay

Journal: Frontiers in Cell and Developmental Biology

Article Title: New insights into keloid pathogenesis: biomarker potential for CDK7 and DDB2

doi: 10.3389/fcell.2025.1718189

Figure Lengend Snippet: Identification and GSEA of hub genes. (A) Venn diagram with two colors representing distinct data sources. (B) PPI network of hub genes, with crimson nodes indicating hub genes. (C) Bubble plot of GO pathway enrichment analysis for the 41 DEGs. (D) Chord diagram of KEGG pathway enrichment analysis for the 41 DEGs. (E) Box plot of CDK7 expression levels. (F) Box plot of DDB2 expression levels. (G) GSEA for hub gene CDK7. (H) GSEA for hub gene DDB2.

Article Snippet: Antibodies were sourced as follows: CDK7 (67889-1-Ig, 1:1000, Proteintech Group), DDB2 (10431-1-AP, 1:1000, Proteintech Group), and β-Actin (TDYO51, 1:5000, TDY BIOTECH).

Techniques: Expressing

Journal: Frontiers in Cell and Developmental Biology

Article Title: New insights into keloid pathogenesis: biomarker potential for CDK7 and DDB2

doi: 10.3389/fcell.2025.1718189

Figure Lengend Snippet: Interactive network analysis. (A) DDB2–miRNA and CDK7–miRNA networks. (B) DDB2–transcription factor and CDK7–transcription factor networks. (C) CDK7–drug interaction network.

Article Snippet: Antibodies were sourced as follows: CDK7 (67889-1-Ig, 1:1000, Proteintech Group), DDB2 (10431-1-AP, 1:1000, Proteintech Group), and β-Actin (TDYO51, 1:5000, TDY BIOTECH).

Techniques:

Journal: Frontiers in Cell and Developmental Biology

Article Title: New insights into keloid pathogenesis: biomarker potential for CDK7 and DDB2

doi: 10.3389/fcell.2025.1718189

Figure Lengend Snippet: The result of the basic experiment of CDK7 and DDB2. (A,B) The plots showed the results of qRT-PCR. (C–E) The result of the expression levels of CDK7 and DDB2 proteins in normal skin and keloid. (F,G) The result of the total expression levels of CDK7 and DDB2 proteins in normal skin and keloid. (H,I) Observation of intracellular localization and expression patterns of CDK7 and DDB2 proteins in normal skin and keloid.The results are presented as mean ± SD. **, ***, **** respectively represent P values of t-test < 0.01, < 0.001, < 0.0001.

Article Snippet: Antibodies were sourced as follows: CDK7 (67889-1-Ig, 1:1000, Proteintech Group), DDB2 (10431-1-AP, 1:1000, Proteintech Group), and β-Actin (TDYO51, 1:5000, TDY BIOTECH).

Techniques: Quantitative RT-PCR, Expressing