2023/07/17

CpG islands are collapsing in all kind of organisms - Evolution never happened

CpG islands are collapsing in all kind of organisms - Evolution never happened


CpG islands are quite short regions of DNA rich in CpG sites, often located near the promoters of genes. Methylation of the CpG sites influences the activity of nearby genes and is critical to the regulation of gene expression. CpG islands often function as transcription enhancers regulating the intensity of transcription. Both methylated and unmethylated CpG islands may function as promoters. These well organized genomic regions are necessary for successful gene expression. Methylated CpG islands are also used as markers for binding of transcription factors functioning as transcription start sites. They play an important role in cellular differentiation especially in multicellular eukaryotes. Different cells having the same DNA are epigenetically programmed and CpG island methylation has a crucial role in this differentiation procedure.

DNA transcription start site
and intensity is regulated by
methylation levels of
CpG islands (promoter, enhancer).
Methylated cytosines are prone to turn to thymines in deamination caused by oxidative stress. There are several clever DNA repair mechanisms in the cell but for some reason, this kind of genetic error is left alone without a repair. Gradually, this leads to GC content of genomes to turn to AT content. These 'mutational hotspots' are the most significant reason for genetic entropy especially because they often hit CpG islands. When CpG island's C's turn to T's, the regulatory area doesn't work in an efficient way and eventually it stops working. This will result in 'loss of function' genes, so called LoF-variants. It means that the DNA sequences for the required gene are present but it lacks the regulatory area. CpG island collapse may affect both transcription start sites (promoter) and transcription enhancers. 

The cell is able to modify and rearrange DNA in several ways. However, there is no scientific evidence of the cell's ability to modify CpG islands. Mutations that change CpG island structures are irreversible and are leading to inevitable genetic entropy. However, in some cases the cell is able to use an alternative solution in order for the transcription to function normally. Alternative promoters and enhancers have been discovered.

There are numerous examples of collapsed CpG islands resulting in 'loss of function enhancers' or 'loss of function promoters'. Here's a few of them:

Role of Enhancers in Development and Diseases
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8715447/

Enhancers in disease: molecular basis and emerging treatment strategies
https://www.sciencedirect.com/science/article/pii/S1471491421001970

How some birds lost the ability to fly
https://www.snexplores.org/article/how-some-birds-lost-ability-fly

Progressive Loss of Function in a Limb Enhancer during Snake Evolution
https://pubmed.ncbi.nlm.nih.gov/27768887/

Critical roles of super-enhancers in the pathogenesis of autoimmune diseases
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7398324/

Summary and conclusions:
  • Methylated cytosines are prone to turn to thymines resulting in gradual loss of genetic integrity.
  • Genome's GC content inevitably turns to AT content in all kind of organisms.
  • CpG islands, rich in CpG sites, are necessary genomic regions for DNA transcription. The cell uses them both for transcription start sites (promoters) and transcription intensity regulators (enhancers).
  • C>T mutations when targeting CpG islands result in non functional promoters and enhancers. This can be observed as loss of function genes, LoF-variants.
  • Broken CpG islands are not repaired by the cell's DNA repair mechanisms. Damages are irreversible.
  • Mutations lead to corruption of information, not evolution.
  • Well organized CpG islands point to design and creation. Collapsing CpG islands point to genetic entropy. Evolution has no chance.