Discussion

As mentioned previously, G4 complex seems to play some role in regulation of onco-genes. The G4 motif sequences were found near some notable regions such as the MYC genes among others in many instances using the patient's real qG4-ChIP-seq data. We found some interesting genes near the motif sequence such as MYC and GRM6 which plays a key role in the progression of cancer [20, 30]. In addition, regulatory elements were also found nearby such as the H3K27ac hESC enhancer. One interesting discovery we found is that there were other genes related to illnesses besides cancer that also seem to be present nearby such as the KCNT1 gene which is involved in patients with epilepsy. In addition, the protein complexes forming with statistically significant values in g:Profiler also suggest that the quadruplex plays some role in binding functionality of enhancers and/or repressors nearby onco-related genes as shown in Figures 7 and 8 in the Results section. The results highly suggest that the G4 quadruplex plays a regulatory role and thus we propose three possible mechanisms.

Mutated G4 Quadruplex May Sterically Hinder Repressor Protein Binding

While many regions of the human genome may naturally contain G4 motif sequence even in healthy humans, we suspect that slight mutations to the sequence may form too stable of a complex that may hinder inhibition of certain genes highly correlated with cancer. For example, we observed cross-referenced ChIP-Seq showed regions mapping to the MYC gene among some other onco-related genes. The MYC gene is normally suppressed by the p53 protein [31]. However, in the presence of a stable and tightly bound G4 complex especially near the gene, the structure may act as a hindrance for a normal repressor protein to bind that would normally inhibit the gene expression.

G4 Quadruplex May Act as a Recognition Sequence for Enhancer Proteins

In some cases by contrast, we suspect that G4 quadruplex can act as a 3D binding structure for activators to bind to, which in turn will bring other transcription factors to initiate further gene expression. For example, some transcription factors such as SP1 or MAZ have shown binding affinity near certain structures of G4 quadruplex [32]. A similar effect is demonstrated in G4 RNA complexes that show high affinity for proteins contributing to Lou Gherigs as stated in the Introduction. Perhaps, mutations of the G4 quadruplex may promote itself for higher binding affinity of certain regulatory proteins.

G4 Quadruplex Forming Randomly May Act as a Prevention Mechanism for DNA Transcription

This is perhaps the most clear and straightforward mechanism for gene regulation. As RNA polymerases transcribe the DNA, they may be blocked by stable G4 complexes along the way, leading to impaired transcription elongation. Hence in this case, the problem is not caused during the initiation event but rather later down the road as the enzyme struggles to continue transcription.