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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.

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Distribution of the number of G-quadruplex motifs in the core promoter region of differentially expressed and unchanged genes. Data with more than 16 G-quadruplex motifs in the promoter are not shown (less than 1% of total)
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Figure 3: Distribution of the number of G-quadruplex motifs in the core promoter region of differentially expressed and unchanged genes. Data with more than 16 G-quadruplex motifs in the promoter are not shown (less than 1% of total)

Mentions: Next we analyzed whether we could detect any difference in the distribution of G-quadruplex motifs in our up- and down-regulated set of genes. Surprisingly, the normalized distribution of down-regulated mRNAs shows a higher occurrence of one or two G-quadruplex motifs in their core promoter region (± 2 kb of TSS) compared to unchanged or up-regulated mRNAs. In contrast to this, genes with four or more G-quadruplexes are over-represented in the set of up-regulated mRNAs (Figure 3). To further validate the microarray results, we randomly chose 8 genes for quantitative real time PCR: Four genes showed changes in expression under treatment with both molecules (CTPS2, DPY30, DIO2, EGFR) and 2 genes each showed changes with either one of the molecules (PhenDC3: CANX and AK1; 360A: PFKM and SH3GL1). To further check whether the changes in gene expression show a dependency with respect to compound concentrations the cells were treated with 4 different concentrations (10, 20, 50 and 100 μM) of the G-quadruplex specific molecules PhenDC3 and 360A for 48 hours. We also used minimum (10 μM) and maximum (100 μM) concentrations of the control bisquinolinium 8979A. In addition, expression of TGOLN2 was also analyzed as a control because it did not appear to induce significant changes in expression in the microarray experiments. As a result of the real-time PCR data we were able to ascertain that all genes exhibited changes in their mRNA levels with a trend consistent to the microarray results (see Table 2). Except CANX, all genes showed a concentration-dependent increase or decrease in expression.


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)

Distribution of the number of G-quadruplex motifs in the core promoter region of differentially expressed and unchanged genes. Data with more than 16 G-quadruplex motifs in the promoter are not shown (less than 1% of total)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Distribution of the number of G-quadruplex motifs in the core promoter region of differentially expressed and unchanged genes. Data with more than 16 G-quadruplex motifs in the promoter are not shown (less than 1% of total)
Mentions: Next we analyzed whether we could detect any difference in the distribution of G-quadruplex motifs in our up- and down-regulated set of genes. Surprisingly, the normalized distribution of down-regulated mRNAs shows a higher occurrence of one or two G-quadruplex motifs in their core promoter region (± 2 kb of TSS) compared to unchanged or up-regulated mRNAs. In contrast to this, genes with four or more G-quadruplexes are over-represented in the set of up-regulated mRNAs (Figure 3). To further validate the microarray results, we randomly chose 8 genes for quantitative real time PCR: Four genes showed changes in expression under treatment with both molecules (CTPS2, DPY30, DIO2, EGFR) and 2 genes each showed changes with either one of the molecules (PhenDC3: CANX and AK1; 360A: PFKM and SH3GL1). To further check whether the changes in gene expression show a dependency with respect to compound concentrations the cells were treated with 4 different concentrations (10, 20, 50 and 100 μM) of the G-quadruplex specific molecules PhenDC3 and 360A for 48 hours. We also used minimum (10 μM) and maximum (100 μM) concentrations of the control bisquinolinium 8979A. In addition, expression of TGOLN2 was also analyzed as a control because it did not appear to induce significant changes in expression in the microarray experiments. As a result of the real-time PCR data we were able to ascertain that all genes exhibited changes in their mRNA levels with a trend consistent to the microarray results (see Table 2). Except CANX, all genes showed a concentration-dependent increase or decrease in expression.

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