Journal: PLoS ONE

Article Title: Transcriptional and Epigenetic Regulation of KIF14 Overexpression in Ovarian Cancer

doi: 10.1371/journal.pone.0091540

Figure Lengend Snippet: Promoter deletion constructs fused to Luciferase were tested for activity in HeLa, SKOV3 and OvCa429 cells. pRSV-Luc, positive control, 0, empty vector control. Numbers are base pairs relative to the transcriptional start site (0). Bioinformatic analysis (Genomatix) of the most active region within the KIF14 promoter (−2366 to −2245) identified putative binding sites for transcription factors YY1, HSF1 and Sp1. Specific transcription factor recognition sites are underlined, and space within sequence denotes location of deletion constructs. N = 3, * Significance at P <0.05, unpaired t-test. P = 0.01 (HeLa); P = 0.01 (SKOV3); P = 0.03 (OvCa429).

Article Snippet: 1 μL of synthesized cDNA was added to 1X TaqMan PCR master mix (ABI), and 1X TaqMan Gene Expression Assay primer-probe mix for KIF14 (Hs00978216_m1), Sp1 (Hs00916521_m1), YY1 (Hs00231533_m1), and HSF1 (Hs01027608_g1).

Techniques: Construct, Luciferase, Activity Assay, Positive Control, Plasmid Preparation, Control, Binding Assay, Sequencing

Journal: PLoS ONE

Article Title: Transcriptional and Epigenetic Regulation of KIF14 Overexpression in Ovarian Cancer

doi: 10.1371/journal.pone.0091540

Figure Lengend Snippet: siRNA knockdown of endogenous Sp1 (orange), HSF1 (green), and YY1 (red) transcription factors, and measurement of their mRNA expression along with corresponding KIF14 mRNA levels (blue) via real-time PCR in A SKOV3 and B OvCa429 cells. Y-axes: normalized mRNA expression relative to MOCK. GL2, control siRNA; N = 3, * Significance at P <0.05, unpaired t-test. Three different siRNA molecules (A, B, C) were used to knock down each gene. P values for panel A (SKOV3 cells): P = 0.02 for Sp1 expression (orange) with Sp1 siRNAs A, B, and C; P = 0.03 (siRNA-A), P = 0.047 (siRNA–B), P = 0.04 (siRNA–C) for KIF14 expression (blue). P = 0.001 for HSF1 expression (green) with HSF1 siRNAs A, B, and C; P = 0.23 (siRNA-A), P = 0.12 (siRNA-B), P = 0.4 (siRNA-C) for KIF14 expression (blue). P = 0.01 for YY1 expression (red) with YY1 siRNAs A, B and C; P = 0.006 for KIF14 expression (blue) with YY1 siRNAs A, B, and C. P values for panel B (OvCa429 cells): P = 0.03 for Sp1 expression (orange) with Sp1 siRNAs A, B, and C; P = 0.05 (siRNA-A), P = 0.04 (siRNA-B), P = 0.045 (siRNA-C) for KIF14 expression (blue). P = 0.003 for HSF1 expression (green) with HSF1 siRNAs A, B, and C; P = 0.31 (siRNA-A), P = 0.45 (siRNA-B), P = 0.39 (siRNA-C) for KIF14 expression (blue). P = 0.02 (siRNA-A), P = 0.01 (siRNA-B), P = 0.01 for YY1 expression (red); P = 0.02 (siRNA-A), P = 0.001 (siRNA-B), P = 0.006 (siRNA-C) for KIF14 expression (blue).

Article Snippet: 1 μL of synthesized cDNA was added to 1X TaqMan PCR master mix (ABI), and 1X TaqMan Gene Expression Assay primer-probe mix for KIF14 (Hs00978216_m1), Sp1 (Hs00916521_m1), YY1 (Hs00231533_m1), and HSF1 (Hs01027608_g1).

Techniques: Knockdown, Expressing, Real-time Polymerase Chain Reaction, Control

Journal: PLoS ONE

Article Title: Transcriptional and Epigenetic Regulation of KIF14 Overexpression in Ovarian Cancer

doi: 10.1371/journal.pone.0091540

Figure Lengend Snippet: A siRNA knockdown of endogenous Sp1 (orange), HSF1 (green), and YY1 (red) transcription factors, and measurement of their protein expression along with corresponding KIF14 protein levels (blue) via immunoblot in SKOV3 cells. x-axis: normalized protein expression relative to MOCK. B Representative immunoblot of KIF14 and transcription factor expression. Numbers represent normalized expression values for the experiment shown. Similar results were seen with OvCa429 cells. GL2, control siRNA; N = 3; *, P <0.05 for transcription factor expression; #, P <0.05 for KIF14 expression, unpaired t-test. P values for panel A (SKOV3 cells): P = 0.009 (siRNA-A), P = 0.003 (siRNA-B), P = 0.006 (siRNA-C) for Sp1 expression (orange); P = 0.005 (siRNA-A), P = 0.007 (siRNA-B), P = 0.004 (siRNA-C) for KIF14 expression (blue). P = 0.01 for HSF1 expression (green) with HSF1 siRNAs A, B, and C; P = 0.54 (siRNA-A), P = 0.65 (siRNA-B), P = 0.41 (siRNA-C) for KIF14 expression (blue). P = 0.001 for YY1 expression (red) with YY1 siRNAs A, B and C; P = 0.01 (siRNA-A), P = 0.02 (siRNA-B), P = 0.005 (siRNA-C) for KIF14 expression (blue).

Article Snippet: 1 μL of synthesized cDNA was added to 1X TaqMan PCR master mix (ABI), and 1X TaqMan Gene Expression Assay primer-probe mix for KIF14 (Hs00978216_m1), Sp1 (Hs00916521_m1), YY1 (Hs00231533_m1), and HSF1 (Hs01027608_g1).

Techniques: Knockdown, Expressing, Western Blot, Control

Journal: PLoS ONE

Article Title: Transcriptional and Epigenetic Regulation of KIF14 Overexpression in Ovarian Cancer

doi: 10.1371/journal.pone.0091540

Figure Lengend Snippet: ChIP assays of endogenous YY1, Sp1 and HSF1 followed by real time PCR with the KIF14 promoter region (−2300 to −2133) in cell lines SKOV3, OvCa429, and HeLa compared to IgG (negative control). Values represent average quantity of promoter region product relative to IgG control. Error bars represent standard deviation of triplicate assays.

Article Snippet: 1 μL of synthesized cDNA was added to 1X TaqMan PCR master mix (ABI), and 1X TaqMan Gene Expression Assay primer-probe mix for KIF14 (Hs00978216_m1), Sp1 (Hs00916521_m1), YY1 (Hs00231533_m1), and HSF1 (Hs01027608_g1).

Techniques: Real-time Polymerase Chain Reaction, Negative Control, Control, Standard Deviation

Journal: PLoS ONE

Article Title: Transcriptional and Epigenetic Regulation of KIF14 Overexpression in Ovarian Cancer

doi: 10.1371/journal.pone.0091540

Figure Lengend Snippet: Quantitative mRNA expression analysis of primary OvCa tumors with KIF14 HIGH (red) and KIF14 LOW (green) mRNA expression (but no KIF14 genomic gain) for Sp1 (circle), YY1 (triangle), and HSF1 (diamond) normalized to normal ovary expression (set as 1, black dashed line). Mean, black line. Individual tumors represented by symbols. * Significance at P <0.05, paired t-test. P = 0.03 (Sp1), P = 0.01 (YY1), P = 0.32 (HSF1).

Article Snippet: 1 μL of synthesized cDNA was added to 1X TaqMan PCR master mix (ABI), and 1X TaqMan Gene Expression Assay primer-probe mix for KIF14 (Hs00978216_m1), Sp1 (Hs00916521_m1), YY1 (Hs00231533_m1), and HSF1 (Hs01027608_g1).

Techniques: Expressing

Journal: PLoS ONE

Article Title: Transcriptional and Epigenetic Regulation of KIF14 Overexpression in Ovarian Cancer

doi: 10.1371/journal.pone.0091540

Figure Lengend Snippet: Pearson correlation between KIF14 gain/no gain tumors and Sp1 , HSF1 and YY1 mRNA.

Article Snippet: 1 μL of synthesized cDNA was added to 1X TaqMan PCR master mix (ABI), and 1X TaqMan Gene Expression Assay primer-probe mix for KIF14 (Hs00978216_m1), Sp1 (Hs00916521_m1), YY1 (Hs00231533_m1), and HSF1 (Hs01027608_g1).

Techniques:

Journal: Cancer Research and Treatment : Official Journal of Korean Cancer Association

Article Title: DNA Methyltransferase Gene Polymorphisms for Prediction of Radiation-Induced Skin Fibrosis after Treatment of Breast Cancer: A Multifactorial Genetic Approach

doi: 10.4143/crt.2016.256

Figure Lengend Snippet: Association analysis between polymorphisms of DNA methyltransferase genes and risk of grade ≥ 2 radiation-induced fibrosis (LENT-SOMA scale) in breast cancer patients

Article Snippet: Determination of SNPs was conducted on genomic DNA by real-time polymerase chain reaction (PCR) using the following TaqMan Pre-Designed SNP Genotyping assays (Applied Biosystems, Milan, Italy): C_27838930_10 ( DNMT1 rs2228611); C_8722920_10 ( DNMT3A rs1550117); C_7863728_10 ( DNMT3A rs7581217); C_16013055_10 ( DNMT3B rs2424908); and C_16269889_10 ( XRCC1 rs2682585).

Techniques: Significance Assay

Journal: Cancer Research and Treatment : Official Journal of Korean Cancer Association

Article Title: DNA Methyltransferase Gene Polymorphisms for Prediction of Radiation-Induced Skin Fibrosis after Treatment of Breast Cancer: A Multifactorial Genetic Approach

doi: 10.4143/crt.2016.256

Figure Lengend Snippet: Association analysis between polymorphisms of DNA methyltransferase genes and risk of grade ≥ 2 radiation-induced fibrosis (LENT-SOMA scale) in breast cancer patients

Article Snippet: Determination of SNPs was conducted on genomic DNA by real-time polymerase chain reaction (PCR) using the following TaqMan Pre-Designed SNP Genotyping assays (Applied Biosystems, Milan, Italy): C_27838930_10 ( DNMT1 rs2228611); C_8722920_10 ( DNMT3A rs1550117); C_7863728_10 ( DNMT3A rs7581217); C_16013055_10 ( DNMT3B rs2424908); and C_16269889_10 ( XRCC1 rs2682585).

Techniques: Significance Assay

Journal: Molecular Systems Biology

Article Title: A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X

doi: 10.1038/s44320-024-00013-0

Figure Lengend Snippet: Reagents and tools.

Article Snippet: For the RNA-seq, RNA was extracted from 25 μl intact lysate (non-digested) using the Direct-zol kit (Zymo Research) and stranded total RNA libraries were prepared using the TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina), following manufacturer’s instructions.

Techniques: Sequencing, Software, Flow Cytometry, Staining, Real-time Polymerase Chain Reaction