Noncoding DNA and Genome Evolution


Noncoding DNA and Genome Evolution

 

Noncoding DNA, why does it exist? There are many possibilities but it is thought that noncoding DNA has a function that has not yet been discovered hence why the cell is maintain it – it is essential for proper cell function.

Another possibility is that noncoding sequences might be used for genome organisation for example chromatin is attached to sites within the nucleus, so noncoding DNA might be used by these attachment sites.

The final possibility is that noncoding DNA is tolerated since there is no selective pressure to get rid of it.  And thus this noncoding DNA is passed on along with the coding DNA, making the noncoding DNA just ‘Junk’.

Little can be said about evolution of the noncoding DNA.  Gene duplications and rearrangements result in sections of DNA that are non-functional and thus no longer under the same selective pressure as functional genes  and therefore are able to accumulate mutations and diverge from the original sequence.

 

Transposable Elements and Genome Evolution

Transposable elements are able to initiate recombination events – this causes genome rearrangements. This has little to do with the transposable activity of the transposable elements, but rather because different copies of the same element have sequence similarity and can therefore cause recombination between parts of the same, or parts of different, chromosomes within which they are localised. In many cases this will cause the deletion of important genes and will therefore be a disadvantage to the organism but there are cases where this can be advantageous.

Genome evolution can also be affected by the movement of transposons. The movement of transposons into an upstream regulatory sequence can affect the transcription of that gene by affecting this efficiency of attachment of specific DNA-binding proteins. In this way, transposons can either reduce or increase transcription. Transposons are able to carry promoters and enhancers and can thereby increase efficiency of the genes which it is adjacent to.

Origins of introns

It is generally accepted that Group I, II and III self-splicing introns evolved from RNA; however the origins of GU-AG introns, that are found in large number in eukaryotes, is more greatly debated.

There are two main theories surrounding the origin of GU-AG introns:

  • Introns Early – This theory states that introns existed a long time ago and are gradually getting lost from eukaryotic genomes. There are several models for this hypothesis, each of which are detailed below.
    • ‘Exon Theory of Genes’ – this model suggests that introns were formed when the first DNA genomes were constructed. The first DNA genomes contained many short genes, each coding for a small polypeptide or single protein domain.  These small polypeptides formed associations with each other in order to carry out specific functions. It was more beneficial during synthesis for these polypeptides to be transcribed together as a single precursor mRNA, the sequences separating these genes encoding polypeptides became introns as they were spliced out before translation.

Due to the fact that bacterial genomes do not possess GU-AG introns, if the introns Early theory is correct, one must assume that at some point in evolutionary history these introns were lost from bacterial genomes. It is difficult to envisage how such a thing could happen without disrupting the genes. Therefor this proves a big stumbling block for this theory.

  • Introns Late – states that introns evolved recently and are gradually accumulating in eukaryotic genomes.
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