Abstract
Comprehensive characterization of all encoded elements is a fundamental pre-requisite for understanding biological function. DNA sequence as regulatory elements is well-established; however, DNA structure is relatively unexplored in this context. Using G-quadruplex or G4 DNA (structural motifs commonly found within eukaryote telomores) as a model we researched the role of DNA structure in transcription in both prokaryotes and eurkaryotes.
We first studied 18 representative prokaryotic species. Analyses of over 61,000ORFs indicated enrichment of G4 motifs in putative regulatory regions. Based on this and several other lines of evidence we predicted that G4 DNA may present regulatory signals and hypothesized regulatory role of G4 DNA during super coiling stress. Our hypothesis gains support from analysis for 55 DNA-binding proteins in Escherichia coli, which reveals significant (p<0.001) association of G4 motifs with target sites of global regulators FIS, Lrp, and the sigma factor RpoD (σ70), which are believed to be induced by supercoiled DNA (1).
Next we analyzed human, chimpanzee, mouse, and rat genomes (>90,000 promoters). This indicates significant G4 DNA enrichment within proximal promoters and more than 700 promoters were found to conserve at least one G4 motif 'orthologously' across mouse, rat, and human. Genes harboring conserved motifs within putative regulatory regions show significantly enriched expression (z score > 4.0)in more than 75 human tissues. Based on this, we hypothesized wide spread role ofG4 DNA in eukaryotic gene regulation. Whole genome expression using microarrays in human cell lines along with real time PCR results support our hypothesis.
We further investigated the molecular mechanism of transcriptional activation mediated by G4 DNA. Expression of the proto-oncogene c-myc was taken as a case study and our results including chromatin immunoprecipitation show the tandem role of G4 motif and a transcription factor in regulation of c-myc. Takentogether, this argues for a more wide spread role of G4 DNA than previously appreciated, where G4 DNA could be a candidate regulatory signal.
We first studied 18 representative prokaryotic species. Analyses of over 61,000ORFs indicated enrichment of G4 motifs in putative regulatory regions. Based on this and several other lines of evidence we predicted that G4 DNA may present regulatory signals and hypothesized regulatory role of G4 DNA during super coiling stress. Our hypothesis gains support from analysis for 55 DNA-binding proteins in Escherichia coli, which reveals significant (p<0.001) association of G4 motifs with target sites of global regulators FIS, Lrp, and the sigma factor RpoD (σ70), which are believed to be induced by supercoiled DNA (1).
Next we analyzed human, chimpanzee, mouse, and rat genomes (>90,000 promoters). This indicates significant G4 DNA enrichment within proximal promoters and more than 700 promoters were found to conserve at least one G4 motif 'orthologously' across mouse, rat, and human. Genes harboring conserved motifs within putative regulatory regions show significantly enriched expression (z score > 4.0)in more than 75 human tissues. Based on this, we hypothesized wide spread role ofG4 DNA in eukaryotic gene regulation. Whole genome expression using microarrays in human cell lines along with real time PCR results support our hypothesis.
We further investigated the molecular mechanism of transcriptional activation mediated by G4 DNA. Expression of the proto-oncogene c-myc was taken as a case study and our results including chromatin immunoprecipitation show the tandem role of G4 motif and a transcription factor in regulation of c-myc. Takentogether, this argues for a more wide spread role of G4 DNA than previously appreciated, where G4 DNA could be a candidate regulatory signal.
| Original language | English |
|---|---|
| Journal | Journal of Biomolecular Structure and Dynamics |
| Publication status | Published - 2007 |
| Externally published | Yes |