Limits...
Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines.

Halder R, Riou JF, Teulade-Fichou MP, Frickey T, Hartig JS - BMC Res Notes (2012)

Bottom Line: Here we utilize two G-quadruplex-specific bisquinolinium derivatives PhenDC3 and 360A and investigate their effects on the expression of the HeLa S3 transcriptome.Our results show wide-spread changes in the transcriptome with specificity for genes with G-quadruplex motifs near their transcription start sites (TSS).Specific effects on quadruplex-containing genes have been observed utilizing whole-transcriptome analysis upon treatment of cultured cells with quadruplex-selective bisquinolinium compounds.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, Konstanz, Germany.

ABSTRACT

Background: Guanosine rich sequences capable of forming G-quadruplex (G4) motifs are enriched near the gene transcription start site (TSS) in the human genome. When probed at the single gene level, G-quadruplex motifs residing in promoter regions show substantial effects on gene transcription. Moreover, further changes in transcription levels are noticed when G4-motifs are targeted with G-quadruplex-specific small molecules.

Results: Global studies concerning general changes of the transcriptome via targeting promoter-based G-quadruplex motifs are very limited and have so far only been carried out with compounds displaying weak selectivity for quadruplex sequences. Here we utilize two G-quadruplex-specific bisquinolinium derivatives PhenDC3 and 360A and investigate their effects on the expression of the HeLa S3 transcriptome. Our results show wide-spread changes in the transcriptome with specificity for genes with G-quadruplex motifs near their transcription start sites (TSS). Using real-time PCR we further confirmed the specificity of PhenDC3 and 360A as potent molecules to target G-quadruplex-regulated genes.

Conclusions: Specific effects on quadruplex-containing genes have been observed utilizing whole-transcriptome analysis upon treatment of cultured cells with quadruplex-selective bisquinolinium compounds.

Show MeSH
Expression data plots for different categories: A) PhenDC3 up-regulated, B) PhenDC3 down-regulated, C) 360A up-regulated, D) 360A down-regulated, E) up-regulated with both compounds, F) down-regulated with both compounds.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3375199&req=5

Figure 2: Expression data plots for different categories: A) PhenDC3 up-regulated, B) PhenDC3 down-regulated, C) 360A up-regulated, D) 360A down-regulated, E) up-regulated with both compounds, F) down-regulated with both compounds.

Mentions: Whole genome expression of genes was determined using Illumina HumanHT-12v4 expression BeadChips after 48 hours of treatment with 10 μM of the G-quadruplex-specific molecules PhenDC3 or 360A in HeLa S3 cells. To account for non-specific effects mediated by the bisquinolinium compounds, 8979A (Figure 1C) was used as a control as it has a similar structure and charges but displays a very limited binding affinity to G-quadruplex motifs [43]. All molecule treatments were performed in triplicate. For analysis, the intensity values of each sample were subjected to 'quantile normalization'. The expression data was analyzed using the CLANS software [48]. First, the two control sets (untreated and 8979A-treated) samples were compared to confirm the non-specificity of the control molecule. Our analysis identified only 85 and 117 illumina identifiers down- and up-regulated, respectively, under the control condition. Next, we compared the expression of PhenDC3- or 360A-treated samples with the control samples (untreated and 8979A treated) to exclude those genes which might have been affected in their expression by treatment with the control molecule. We therefore considered the untreated and the 8979A-treated sample each as a control. Only genes showing a correlation coefficient of ≥ 0.9 to our conditions of interest (Figure 2) and an anova P-value ≤ 0.05 were taken into account and constitute our set of differentially expressed genes. The detailed gene list is given in Additional file 2: Table S4.


Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines.

Halder R, Riou JF, Teulade-Fichou MP, Frickey T, Hartig JS - BMC Res Notes (2012)

Expression data plots for different categories: A) PhenDC3 up-regulated, B) PhenDC3 down-regulated, C) 360A up-regulated, D) 360A down-regulated, E) up-regulated with both compounds, F) down-regulated with both compounds.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3375199&req=5

Figure 2: Expression data plots for different categories: A) PhenDC3 up-regulated, B) PhenDC3 down-regulated, C) 360A up-regulated, D) 360A down-regulated, E) up-regulated with both compounds, F) down-regulated with both compounds.
Mentions: Whole genome expression of genes was determined using Illumina HumanHT-12v4 expression BeadChips after 48 hours of treatment with 10 μM of the G-quadruplex-specific molecules PhenDC3 or 360A in HeLa S3 cells. To account for non-specific effects mediated by the bisquinolinium compounds, 8979A (Figure 1C) was used as a control as it has a similar structure and charges but displays a very limited binding affinity to G-quadruplex motifs [43]. All molecule treatments were performed in triplicate. For analysis, the intensity values of each sample were subjected to 'quantile normalization'. The expression data was analyzed using the CLANS software [48]. First, the two control sets (untreated and 8979A-treated) samples were compared to confirm the non-specificity of the control molecule. Our analysis identified only 85 and 117 illumina identifiers down- and up-regulated, respectively, under the control condition. Next, we compared the expression of PhenDC3- or 360A-treated samples with the control samples (untreated and 8979A treated) to exclude those genes which might have been affected in their expression by treatment with the control molecule. We therefore considered the untreated and the 8979A-treated sample each as a control. Only genes showing a correlation coefficient of ≥ 0.9 to our conditions of interest (Figure 2) and an anova P-value ≤ 0.05 were taken into account and constitute our set of differentially expressed genes. The detailed gene list is given in Additional file 2: Table S4.

Bottom Line: Here we utilize two G-quadruplex-specific bisquinolinium derivatives PhenDC3 and 360A and investigate their effects on the expression of the HeLa S3 transcriptome.Our results show wide-spread changes in the transcriptome with specificity for genes with G-quadruplex motifs near their transcription start sites (TSS).Specific effects on quadruplex-containing genes have been observed utilizing whole-transcriptome analysis upon treatment of cultured cells with quadruplex-selective bisquinolinium compounds.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, Konstanz, Germany.

ABSTRACT

Background: Guanosine rich sequences capable of forming G-quadruplex (G4) motifs are enriched near the gene transcription start site (TSS) in the human genome. When probed at the single gene level, G-quadruplex motifs residing in promoter regions show substantial effects on gene transcription. Moreover, further changes in transcription levels are noticed when G4-motifs are targeted with G-quadruplex-specific small molecules.

Results: Global studies concerning general changes of the transcriptome via targeting promoter-based G-quadruplex motifs are very limited and have so far only been carried out with compounds displaying weak selectivity for quadruplex sequences. Here we utilize two G-quadruplex-specific bisquinolinium derivatives PhenDC3 and 360A and investigate their effects on the expression of the HeLa S3 transcriptome. Our results show wide-spread changes in the transcriptome with specificity for genes with G-quadruplex motifs near their transcription start sites (TSS). Using real-time PCR we further confirmed the specificity of PhenDC3 and 360A as potent molecules to target G-quadruplex-regulated genes.

Conclusions: Specific effects on quadruplex-containing genes have been observed utilizing whole-transcriptome analysis upon treatment of cultured cells with quadruplex-selective bisquinolinium compounds.

Show MeSH