CDK

FACS profiles for cell cycle synchronization of HCT116 cells pulsed with EdU. Asynchronous (AS) HCT116 cells were treated with CDK4/6i (Palbociclib, 2 μM) for 20 hours to arrest in G0/G1 (middle panel), followed by a wash in fresh media for 8 hours to release into S phase (right panel).

In vitro inhibition of mouse corticotroph tumor cells by R-roscovitine. (A) Treatment of ACTH-secreting AtT20 cells with R-roscovitine (1-2 × 10-5 μM) led to decreased number of viable cells at 24 and 48 h, as depicted by Wst-1 proliferation assay (mean ± SE; **P < 0.01). (B) Western blot of protein extracts derived from AtT20 cells treated with vehicle or R-roscovitine. (C) R-roscovitine treatment (10 μM) for 48 h induced senescence as indicated by increased β-gal expression. (D) ACTH concentration by radioimmunoassays of culture medium from AtT20 cells treated with vehicle or R-roscovitine (mean ±SE; **P < 0.01 and ***P < 0.001). (E) Western blot of protein extracts derived from AtT20 cells treated with R-roscovitine. Vehicle is 0.2% DMSO.

For MTT assays, cells (2,000 ~ 5,000 cells/well) were subcultured into 96-well plates according to their growth properties. Cell proliferation was assayed at 72 hr after treatment of SNS-032 by adding 20 μl of 5 mg/ml 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) solution per 100 μl of growth medium. After incubating for 3-4 h at 37°C, the media were removed and 150 µl/well of MTT solvent (either absolute DMSO or isopropanol containing 4 μM HCl and 0.1% Nonidet-40) was added to dissolve the formazan. The absorbance of each well was measured by ELx808 (BioTek, Winooski, VT) or Wallac Victor2 (Perkin-Elmer Life Sciences, Boston, MA) Microplate Reader. Viable cells are presented as percent of control, vehicle-treated cells.

 

(a) Western blot for RALB-GTP, total RALB and GAPDH proteins in KG1 AML cells treated for 8 h with DMSO or dinaciclib (representative of three independent experiments).

(A) After mitotic arrest and treatment with the proteasome inhibitor MG132, HeLa cells were treated with the indicated kinase inhibitors The cells were harvested, and the lysates were separated by SDS-PAGE and immunoblotted for phosphorylated RV[S/T]F (p-RV[S/T]F, top). The blot was quantified using ImageJ software and normalized to the mitotic sample (bottom). MLN8054, Aurora A and Aurora B inhibitor; ZM447439 and hesperadin, Aurora B inhibitors; BI2536, PLK1 inhibitor; flavopiridol, CDK1 inhibitor. n = 3. **P < 0.01, paired Student’s t test.

Lysates of MDM treated with five-fold dilutions of the indicated compounds (starting concentration: AT7519, 0.5 mmol/l, roscovitine 4 mmol/l) were subjected to SDS-PAGE, transferred, and immunoblotted with antiphopho-SAMHD1, anti-SAMHD1 and anti-Hsp90 antibodies. MDM, monocyte-derived macrophage; SAMHD1, sterile a motif and HD domain-containing protein-1; SD, standard deviation.

(C) In vivo treatment of Tg:Pomc-Pttg;Pomc-eGFP embryos with small-molecule CDK inhibitors (50μM) or 0.2% DMSO as control from 18 to 40 hpf. One hundred to one hundred fifty embryos were treated with each compound. Representative images of live embryos are shown with gross morphology (Right) and pituitary Pomc-GFP–positive cells at higher magnification (Left) at 40 hpf. Embryos exposed to flavopiridol developed early developmental defect before pituitary POMC cell ontogeny occurs. (D) Relative expression of pituitary Pomc-eGFP fluorescence analyzed using Volocity 5.2 software (Improvision; mean ± SE of relative expression, n = 7). (E) R-roscovitine specifically suppresses expansion of pituitary POMC cells overexpressing zPttg from 18 to 48 hpf. Double transgenic Tg:Pomc-Pttg;Prl-RFP embryos were generated by breeding Tg:Pomc-Pttg fish with a previously generated PRL-RFP transgenic line, in which RFP was targeted to pituitary lactotrophs by a zebrafish Prolactin promoter (34). Representative fluorescent microscopy of pituitary POMC-eGFP (a and b) and PRL-RFP (c and d) expression in live Tg:Pomc-Pttg; Pomc-eGFP and Tg:Pomc-Pttg;Prl-RFP embryos treated with 0.2% DMSO (a and c) or 50 μM R-roscovitine (b and d). (F) Relative expression of pituitary POMC-eGFP or PRL-RFP fluorescence were analyzed (mean ± SE of relative expression; n = 10). Results represent one of three similar experiments;*P < 0.02 and **P < 0.000005. (Scale bar, 50 μm.)

 

JNJ-7706621 treatment of tamoxifen-resistant cell lines leads to arrest in the G2 cell cycle phase. M phase cells from the upper right quadrants were quantified relative to total G2/M phase cells. Statistical significant differences from vehicle-treated cells are denoted by asterisks; *P<0.05, **P<0.01.

(a) HEK-293 cells expressing V5-EXO1 were synchronized in different phases of the cell cycle. EXO1 was immunoprecipitated (IP) with anti-V5 antibody and Western blotted with anti-phospho-Ser (p-SP) or anti-phospho-Thr (p-TP) CDK substrate antibodies, as indicated. “+AZD” indicates cells pre-treated with the CDK inhibitor AZD5438 prior to analysis. (b) HEK-293 cells expressing V5-EXO1, synchronized in G2, were pre-treated with CDK inhibitors, AZD5438 or Roscovitine, prior to analysis of EXO1 phosphorylation by IP-Western.

Western blots of proteins associated with Chk1 activation and apoptosis.

J558 cells were treated with PHA793887 (0.02–5 umol/L) for 6 hours, after which Western blot analysis was performed to monitor XBP-1s expression. Tub, tubulin.

B, SK-OV-3, KB, and KB/VCR cells were pretreated with a CDK7-specific inhibitor and then assayed for RPB1.

(C) In vivo treatment of Tg:Pomc-Pttg;Pomc-eGFP embryos with small-molecule CDK inhibitors (50μM) or 0.2% DMSO as control from 18 to 40 hpf. One hundred to one hundred fifty embryos were treated with each compound. Representative images of live embryos are shown with gross morphology (Right) and pituitary Pomc-GFP–positive cells at higher magnification (Left) at 40 hpf. Embryos exposed to flavopiridol developed early developmental defect before pituitary POMC cell ontogeny occurs. (D) Relative expression of pituitary Pomc-eGFP fluorescence analyzed using Volocity 5.2 software (Improvision; mean ±SE of relative expression, n = 7). (E) R-roscovitine specifically suppresses expansion of pituitary POMC cells overexpressing zPttg from 18 to 48 hpf. Double transgenic Tg:Pomc-Pttg;Prl-RFP embryos were generated by breeding Tg:Pomc-Pttg fish with a previously generated PRL-RFP transgenic line, in which RFP was targeted to pituitary lactotrophs by a zebrafish Prolactin promoter (34). Representative fluorescent microscopy of pituitary POMC-eGFP (a and b) and PRL-RFP (c and d) expression in live Tg:Pomc-Pttg; Pomc-eGFP and Tg:Pomc-Pttg;Prl-RFP embryos treated with 0.2% DMSO (a and c) or 50 μM R-roscovitine (b and d). (F) Relative expression of pituitary POMC-eGFP or PRL-RFP fluorescence were analyzed (mean ±SE of relative expression; n = 10). Results represent one of three similar experiments;*P < 0.02 and **P < 0.000005. (Scale bar, 50 μm.)

Cell survival was determined using a WST-1 assay in the human lung cancer cells A549 A. and NCI-H358 B. following treatment with either an AKT1 specific inhibitor, A-674563 (black circle and line) or a pan-AKT inhibitor MK-2206 (gray square and line). *p < 0.05.

SJSA cells were treated with the alternate CDK4/6 inhibitors Ribociclib (LEE011) and Abemaciclib (LY2835219) for 30 h, alone or in combination with Nutlin at 20 µM for 6 h. Immunoblot analysis was performed as in (a). Like Palbociclib (PD0332991), the combination of Nutlin with alternate CDK4/6 inhibitors diminished p53 target gene expression when compared to Nutlin treatment alone.

Viability at 250 nM and CI vs. Fa for U2932 following 24 hours exposure to ABT-199, additional drugs with activity against CDK9, or the combinations. Mean of quadruplicates ± SEM.

Cell survival curves of A549 cells treated with increasing doses of A-674563, PHA-848125, and H89 2HCl for 72 hours. Cells were incubated with cell proliferation reagent WST-1 for 2 hours and absorbance was read at 450nm. Optical density was then normalized to a 1% DMSO control. The data is presented as the percentage of cell survival relative to the DMSO control ± SEM of three independent trials. Statistical significance was determined with multiple T-tests using the Holm-Sidak method without assuming a consistent SD and is represented by *p<0.05.

IB analysis of whole cell lysates derived from mouse CT26 or 4T1 tumor cell lines treated with or without the CDK4/6 inhibitor, ribociclib.

Predicted anticancer drugs inhibit the growth of neuroendocrine tumor cells. Multi-tyrosine kinase inhibitors sorafenib, sunitinib, regorafenib and cabozantinib effectively inhibit GOT1 cell growth with IC50 values in the micromolar range. Inhibitors of AKT (MK-2206), HDAC (vorinostat), HSP90 (alvespimycin) and CDK4/9 (P276-00) also inhibited GOT1 cell growth at micromolar concentrations, whereas inhibition of PARP1 (veliparib) had no effect. GOT1 cells were treated with anticancer drugs at various concentrations for 4 days. Cell viability was estimated using AlamarBlue®. Data points are the mean values of three individual experiments carried out in triplicate (n=9). Fitting of curves was done in GraphPad Prism software v6.04 using log (inhibitor) vs response nonlinear fit with variable slope. IC50 was interpolated at Y=50 and bars denote ±s.d.

One and three days after differentiation induction, protein level of Myh3 and Myogenin were analyzed by western blot.

HeLa cells were untreated or treated with either colcemid (10 μg/ml for 16 h), RO-3306 (9 μM for 16 h), or both colcemid and RO-3306, as indicated. Cells were then lysed, and proteins were detected by Western analysis.

Effect of Wogonin on the translocation and transcriptional activity of NFATc1. U2OS cells stably transfected with EGFP-NFATc1, RANKL (100 ng/ml) and different concentrations of Wogonin (5.0, 1.0, 0.1 and 0.0 mM) were added and incubated for 24 h. The IN Cell™ Analyzer 1000 was used to observe the translocation of NFATc1. (A) DMSO was used as a control. RANKL (100 ng/ml) significantly stimulated the translocation of NFATc1; Wogonin (5 mM) significantly decreased the translocation of NFATc1 induced by RANKL (magnification, x200). (B) Statistics showed that Wogonin could decrease the translocation of NFATc1 into the nucleus induced by RANKL in a concentration-dependent manner. RAW264.7 cells were transfected with pGL3-promoter-NFATc1-RE, and then RANKL (100 ng/ml) and different concentrations of Wogonin (5.0, 1.0, 0.1 and 0.0 mM) were added and incubated for 24 h. (C) RANKL significantly increased the transcriptional activity of NFATc1 and Wogonin decreased the transcriptional activity of NFATc1 induced by RANKL in a concentration-dependent manner. n=3; *P<0.05 and ***P<0.001 compared with the RANKL group. NAFTc1, nuclear factor of activated T cells c1; EGFP, enhanced green fluorescent protein; DMSO, dimethylsulfoxide, RANKL, receptor activator of nuclear factor κB ligand; RE, response element.

After 12 h PAB treatment, cells were treated with PAB in the absence and presence of RO-3306 or purvalanol A for 12 h and 36 h. (A) Expressions of p-histone h3 were detected by western blot.

Effect of Kenpaullone on GSK-3β and CDKs. (A and B) Naïve CD4+ T cells were stimulated with anti-CD3/CD28 (TCR), TGF-β (5 ng/ml) and IL-6 (20 ng/ml) in the presence of the indicated Kenpaullone (Kenp) concentrations for 30 min (A) or 24 h (A and B).

Inhibition of CDK9 leads to a decrease in RNApol II activity and repetitive element expression. HEK293T cells were treated with DMSO control and the indicated amounts of LDC000067, a CDK9 inhibitor, for a total of 3 h. (A) Immunoblots showing the levels of phosphorylated RNApol II largest subunit (pRPB1), total RPB1 and GAPDH, in response to different doses of CDK9 inhibitor. (B) Quantification of immunoblots from 2 independent experiments in which each condition was performed in duplicates, and in which pRPB1 and total RPB1 protein levels were normalized to GAPDH or as pRPB1/Total RPB1 ratio. (C, D) qRT-PCR analyses show a significant response to CDK9 inhibition of repetitive elements belonging to the LTR (C) and SINE (D) classes. Statistical analyses were performed to compare all groups using a One-way ANOVA followed by Bonforreoni’s multiple comparison test, *P < 0.05, **P < 0.01, #P < 0.0001.

a, Porcine blastocysts derived from the SU9516-treated group. Scale bar 100 μM. b, An image of a 7 day SU9516- treated parthenogenetically activated porcine embryo stained with Hoechst 33342. Scale bar 100 μM. c, Tetraploid karyotype from SU9516 treated blastocysts. Scale bar 50 μM. d, Porcine blastocysts derived from the cytochalasin B (CB)-treated group. Scale bar 100 μM. e, An image of a 7 day CB-treated parthenogenetically activated porcine embryo stained with Hoechst 33342. Scale bar 100 μM. f, diploid karyotype from CB treated blastocysts. Scale bar 50 μM

(c) Effect of AT7519 treatment on RNA pol II occupancy at the PRCC gene. MM1.S cells were treated with either DMSO vehicle (blue) or 2 μM AT7519 (brown) for 6 h, followed by RNA pol II ChIP-seq analysis. Twenty-fold magnifications of the rpm/bp scale of these gene tracks are shown in the right panel to show the difference in reads for elongating RNA pol II. TR, RNA pol II traveling ratio. (d) Genome-wide binding average RNA pol II (ChIP-seq) on active promoters and gene bodies following treatment of MM1.S cells with DMSO vehicle (blue) or 2 μM of AT7519 (brown) for 6 h. Magnification of the rpm/bp scale at gene bodies is shown in the inset. The inset includes RNA polymerase II traveling ratio distributions (TR, mean) derived from MM1.S cells treated with DMSO (blue) or 2 μM AT7519 (red). (e) Chemical structures of the pan-CDK inhibitor AT7519 and its biotinylated counterpart bio-AT7519. (f) In vitro kinase assays with recombinant cyclin T-CDK9 complex in the presence of increasing concentrations of AT7519 or bio-AT7519. The derived IC50 values for each compound are shown. (g) Effect of AT7519 and bio-AT7519 on MM1.S cell proliferation. Cells were treated with varying concentrations of drug for 72 h as indicated. The derived EC50 values for each compound are shown.

The protein levels of p-MCM2 and p-ERK in NOK, HN6 and Cal27 cells treated with 0, 10 and 20 μMXL413 were detected by western blotting.

FACS profiles for cell cycle synchronization of HCT116 cells pulsed with EdU. Asynchronous (AS) HCT116 cells were treated with CDK4/6i (Palbociclib, 2 μM) for 20 hours to arrest in G0/G1 (middle panel), followed by a wash in fresh media for 8 hours to release into S phase (right panel).

In vitro inhibition of mouse corticotroph tumor cells by R-roscovitine. (A) Treatment of ACTH-secreting AtT20 cells with R-roscovitine (1-2 × 10-5 μM) led to decreased number of viable cells at 24 and 48 h, as depicted by Wst-1 proliferation assay (mean ± SE; **P < 0.01). (B) Western blot of protein extracts derived from AtT20 cells treated with vehicle or R-roscovitine. (C) R-roscovitine treatment (10 μM) for 48 h induced senescence as indicated by increased β-gal expression. (D) ACTH concentration by radioimmunoassays of culture medium from AtT20 cells treated with vehicle or R-roscovitine (mean ±SE; **P < 0.01 and ***P < 0.001). (E) Western blot of protein extracts derived from AtT20 cells treated with R-roscovitine. Vehicle is 0.2% DMSO.

For MTT assays, cells (2,000 ~ 5,000 cells/well) were subcultured into 96-well plates according to their growth properties. Cell proliferation was assayed at 72 hr after treatment of SNS-032 by adding 20 μl of 5 mg/ml 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) solution per 100 μl of growth medium. After incubating for 3-4 h at 37°C, the media were removed and 150 µl/well of MTT solvent (either absolute DMSO or isopropanol containing 4 μM HCl and 0.1% Nonidet-40) was added to dissolve the formazan. The absorbance of each well was measured by ELx808 (BioTek, Winooski, VT) or Wallac Victor2 (Perkin-Elmer Life Sciences, Boston, MA) Microplate Reader. Viable cells are presented as percent of control, vehicle-treated cells.

 

(a) Western blot for RALB-GTP, total RALB and GAPDH proteins in KG1 AML cells treated for 8 h with DMSO or dinaciclib (representative of three independent experiments).

(A) After mitotic arrest and treatment with the proteasome inhibitor MG132, HeLa cells were treated with the indicated kinase inhibitors The cells were harvested, and the lysates were separated by SDS-PAGE and immunoblotted for phosphorylated RV[S/T]F (p-RV[S/T]F, top). The blot was quantified using ImageJ software and normalized to the mitotic sample (bottom). MLN8054, Aurora A and Aurora B inhibitor; ZM447439 and hesperadin, Aurora B inhibitors; BI2536, PLK1 inhibitor; flavopiridol, CDK1 inhibitor. n = 3. **P < 0.01, paired Student’s t test.

Lysates of MDM treated with five-fold dilutions of the indicated compounds (starting concentration: AT7519, 0.5 mmol/l, roscovitine 4 mmol/l) were subjected to SDS-PAGE, transferred, and immunoblotted with antiphopho-SAMHD1, anti-SAMHD1 and anti-Hsp90 antibodies. MDM, monocyte-derived macrophage; SAMHD1, sterile a motif and HD domain-containing protein-1; SD, standard deviation.

(C) In vivo treatment of Tg:Pomc-Pttg;Pomc-eGFP embryos with small-molecule CDK inhibitors (50μM) or 0.2% DMSO as control from 18 to 40 hpf. One hundred to one hundred fifty embryos were treated with each compound. Representative images of live embryos are shown with gross morphology (Right) and pituitary Pomc-GFP–positive cells at higher magnification (Left) at 40 hpf. Embryos exposed to flavopiridol developed early developmental defect before pituitary POMC cell ontogeny occurs. (D) Relative expression of pituitary Pomc-eGFP fluorescence analyzed using Volocity 5.2 software (Improvision; mean ± SE of relative expression, n = 7). (E) R-roscovitine specifically suppresses expansion of pituitary POMC cells overexpressing zPttg from 18 to 48 hpf. Double transgenic Tg:Pomc-Pttg;Prl-RFP embryos were generated by breeding Tg:Pomc-Pttg fish with a previously generated PRL-RFP transgenic line, in which RFP was targeted to pituitary lactotrophs by a zebrafish Prolactin promoter (34). Representative fluorescent microscopy of pituitary POMC-eGFP (a and b) and PRL-RFP (c and d) expression in live Tg:Pomc-Pttg; Pomc-eGFP and Tg:Pomc-Pttg;Prl-RFP embryos treated with 0.2% DMSO (a and c) or 50 μM R-roscovitine (b and d). (F) Relative expression of pituitary POMC-eGFP or PRL-RFP fluorescence were analyzed (mean ± SE of relative expression; n = 10). Results represent one of three similar experiments;*P < 0.02 and **P < 0.000005. (Scale bar, 50 μm.)

 

JNJ-7706621 treatment of tamoxifen-resistant cell lines leads to arrest in the G2 cell cycle phase. M phase cells from the upper right quadrants were quantified relative to total G2/M phase cells. Statistical significant differences from vehicle-treated cells are denoted by asterisks; *P<0.05, **P<0.01.

(a) HEK-293 cells expressing V5-EXO1 were synchronized in different phases of the cell cycle. EXO1 was immunoprecipitated (IP) with anti-V5 antibody and Western blotted with anti-phospho-Ser (p-SP) or anti-phospho-Thr (p-TP) CDK substrate antibodies, as indicated. “+AZD” indicates cells pre-treated with the CDK inhibitor AZD5438 prior to analysis. (b) HEK-293 cells expressing V5-EXO1, synchronized in G2, were pre-treated with CDK inhibitors, AZD5438 or Roscovitine, prior to analysis of EXO1 phosphorylation by IP-Western.

Western blots of proteins associated with Chk1 activation and apoptosis.

J558 cells were treated with PHA793887 (0.02–5 umol/L) for 6 hours, after which Western blot analysis was performed to monitor XBP-1s expression. Tub, tubulin.

B, SK-OV-3, KB, and KB/VCR cells were pretreated with a CDK7-specific inhibitor and then assayed for RPB1.

(C) In vivo treatment of Tg:Pomc-Pttg;Pomc-eGFP embryos with small-molecule CDK inhibitors (50μM) or 0.2% DMSO as control from 18 to 40 hpf. One hundred to one hundred fifty embryos were treated with each compound. Representative images of live embryos are shown with gross morphology (Right) and pituitary Pomc-GFP–positive cells at higher magnification (Left) at 40 hpf. Embryos exposed to flavopiridol developed early developmental defect before pituitary POMC cell ontogeny occurs. (D) Relative expression of pituitary Pomc-eGFP fluorescence analyzed using Volocity 5.2 software (Improvision; mean ±SE of relative expression, n = 7). (E) R-roscovitine specifically suppresses expansion of pituitary POMC cells overexpressing zPttg from 18 to 48 hpf. Double transgenic Tg:Pomc-Pttg;Prl-RFP embryos were generated by breeding Tg:Pomc-Pttg fish with a previously generated PRL-RFP transgenic line, in which RFP was targeted to pituitary lactotrophs by a zebrafish Prolactin promoter (34). Representative fluorescent microscopy of pituitary POMC-eGFP (a and b) and PRL-RFP (c and d) expression in live Tg:Pomc-Pttg; Pomc-eGFP and Tg:Pomc-Pttg;Prl-RFP embryos treated with 0.2% DMSO (a and c) or 50 μM R-roscovitine (b and d). (F) Relative expression of pituitary POMC-eGFP or PRL-RFP fluorescence were analyzed (mean ±SE of relative expression; n = 10). Results represent one of three similar experiments;*P < 0.02 and **P < 0.000005. (Scale bar, 50 μm.)

Cell survival was determined using a WST-1 assay in the human lung cancer cells A549 A. and NCI-H358 B. following treatment with either an AKT1 specific inhibitor, A-674563 (black circle and line) or a pan-AKT inhibitor MK-2206 (gray square and line). *p < 0.05.

SJSA cells were treated with the alternate CDK4/6 inhibitors Ribociclib (LEE011) and Abemaciclib (LY2835219) for 30 h, alone or in combination with Nutlin at 20 µM for 6 h. Immunoblot analysis was performed as in (a). Like Palbociclib (PD0332991), the combination of Nutlin with alternate CDK4/6 inhibitors diminished p53 target gene expression when compared to Nutlin treatment alone.

Viability at 250 nM and CI vs. Fa for U2932 following 24 hours exposure to ABT-199, additional drugs with activity against CDK9, or the combinations. Mean of quadruplicates ± SEM.

Cell survival curves of A549 cells treated with increasing doses of A-674563, PHA-848125, and H89 2HCl for 72 hours. Cells were incubated with cell proliferation reagent WST-1 for 2 hours and absorbance was read at 450nm. Optical density was then normalized to a 1% DMSO control. The data is presented as the percentage of cell survival relative to the DMSO control ± SEM of three independent trials. Statistical significance was determined with multiple T-tests using the Holm-Sidak method without assuming a consistent SD and is represented by *p<0.05.

IB analysis of whole cell lysates derived from mouse CT26 or 4T1 tumor cell lines treated with or without the CDK4/6 inhibitor, ribociclib.

Predicted anticancer drugs inhibit the growth of neuroendocrine tumor cells. Multi-tyrosine kinase inhibitors sorafenib, sunitinib, regorafenib and cabozantinib effectively inhibit GOT1 cell growth with IC50 values in the micromolar range. Inhibitors of AKT (MK-2206), HDAC (vorinostat), HSP90 (alvespimycin) and CDK4/9 (P276-00) also inhibited GOT1 cell growth at micromolar concentrations, whereas inhibition of PARP1 (veliparib) had no effect. GOT1 cells were treated with anticancer drugs at various concentrations for 4 days. Cell viability was estimated using AlamarBlue®. Data points are the mean values of three individual experiments carried out in triplicate (n=9). Fitting of curves was done in GraphPad Prism software v6.04 using log (inhibitor) vs response nonlinear fit with variable slope. IC50 was interpolated at Y=50 and bars denote ±s.d.

One and three days after differentiation induction, protein level of Myh3 and Myogenin were analyzed by western blot.

HeLa cells were untreated or treated with either colcemid (10 μg/ml for 16 h), RO-3306 (9 μM for 16 h), or both colcemid and RO-3306, as indicated. Cells were then lysed, and proteins were detected by Western analysis.

Effect of Wogonin on the translocation and transcriptional activity of NFATc1. U2OS cells stably transfected with EGFP-NFATc1, RANKL (100 ng/ml) and different concentrations of Wogonin (5.0, 1.0, 0.1 and 0.0 mM) were added and incubated for 24 h. The IN Cell™ Analyzer 1000 was used to observe the translocation of NFATc1. (A) DMSO was used as a control. RANKL (100 ng/ml) significantly stimulated the translocation of NFATc1; Wogonin (5 mM) significantly decreased the translocation of NFATc1 induced by RANKL (magnification, x200). (B) Statistics showed that Wogonin could decrease the translocation of NFATc1 into the nucleus induced by RANKL in a concentration-dependent manner. RAW264.7 cells were transfected with pGL3-promoter-NFATc1-RE, and then RANKL (100 ng/ml) and different concentrations of Wogonin (5.0, 1.0, 0.1 and 0.0 mM) were added and incubated for 24 h. (C) RANKL significantly increased the transcriptional activity of NFATc1 and Wogonin decreased the transcriptional activity of NFATc1 induced by RANKL in a concentration-dependent manner. n=3; *P<0.05 and ***P<0.001 compared with the RANKL group. NAFTc1, nuclear factor of activated T cells c1; EGFP, enhanced green fluorescent protein; DMSO, dimethylsulfoxide, RANKL, receptor activator of nuclear factor κB ligand; RE, response element.

After 12 h PAB treatment, cells were treated with PAB in the absence and presence of RO-3306 or purvalanol A for 12 h and 36 h. (A) Expressions of p-histone h3 were detected by western blot.

Effect of Kenpaullone on GSK-3β and CDKs. (A and B) Naïve CD4+ T cells were stimulated with anti-CD3/CD28 (TCR), TGF-β (5 ng/ml) and IL-6 (20 ng/ml) in the presence of the indicated Kenpaullone (Kenp) concentrations for 30 min (A) or 24 h (A and B).

Inhibition of CDK9 leads to a decrease in RNApol II activity and repetitive element expression. HEK293T cells were treated with DMSO control and the indicated amounts of LDC000067, a CDK9 inhibitor, for a total of 3 h. (A) Immunoblots showing the levels of phosphorylated RNApol II largest subunit (pRPB1), total RPB1 and GAPDH, in response to different doses of CDK9 inhibitor. (B) Quantification of immunoblots from 2 independent experiments in which each condition was performed in duplicates, and in which pRPB1 and total RPB1 protein levels were normalized to GAPDH or as pRPB1/Total RPB1 ratio. (C, D) qRT-PCR analyses show a significant response to CDK9 inhibition of repetitive elements belonging to the LTR (C) and SINE (D) classes. Statistical analyses were performed to compare all groups using a One-way ANOVA followed by Bonforreoni’s multiple comparison test, *P < 0.05, **P < 0.01, #P < 0.0001.

a, Porcine blastocysts derived from the SU9516-treated group. Scale bar 100 μM. b, An image of a 7 day SU9516- treated parthenogenetically activated porcine embryo stained with Hoechst 33342. Scale bar 100 μM. c, Tetraploid karyotype from SU9516 treated blastocysts. Scale bar 50 μM. d, Porcine blastocysts derived from the cytochalasin B (CB)-treated group. Scale bar 100 μM. e, An image of a 7 day CB-treated parthenogenetically activated porcine embryo stained with Hoechst 33342. Scale bar 100 μM. f, diploid karyotype from CB treated blastocysts. Scale bar 50 μM

(c) Effect of AT7519 treatment on RNA pol II occupancy at the PRCC gene. MM1.S cells were treated with either DMSO vehicle (blue) or 2 μM AT7519 (brown) for 6 h, followed by RNA pol II ChIP-seq analysis. Twenty-fold magnifications of the rpm/bp scale of these gene tracks are shown in the right panel to show the difference in reads for elongating RNA pol II. TR, RNA pol II traveling ratio. (d) Genome-wide binding average RNA pol II (ChIP-seq) on active promoters and gene bodies following treatment of MM1.S cells with DMSO vehicle (blue) or 2 μM of AT7519 (brown) for 6 h. Magnification of the rpm/bp scale at gene bodies is shown in the inset. The inset includes RNA polymerase II traveling ratio distributions (TR, mean) derived from MM1.S cells treated with DMSO (blue) or 2 μM AT7519 (red). (e) Chemical structures of the pan-CDK inhibitor AT7519 and its biotinylated counterpart bio-AT7519. (f) In vitro kinase assays with recombinant cyclin T-CDK9 complex in the presence of increasing concentrations of AT7519 or bio-AT7519. The derived IC50 values for each compound are shown. (g) Effect of AT7519 and bio-AT7519 on MM1.S cell proliferation. Cells were treated with varying concentrations of drug for 72 h as indicated. The derived EC50 values for each compound are shown.

The protein levels of p-MCM2 and p-ERK in NOK, HN6 and Cal27 cells treated with 0, 10 and 20 μMXL413 were detected by western blotting.