[1] CNSs in plants[2] and animals[1] are highly associated with transcription factor binding sites and other cis-acting regulatory elements.
Introns are stretches of sequence found mostly in eukaryotic organisms which interrupt the coding regions of genes, with basepair lengths varying across three orders of magnitude.
Intron sequences may be conserved, often because they contain expression regulating elements that put functional constraints on their evolution.
If these regions perform an important regulatory function, the increase in 3'-UTR length over evolutionary time suggests that conserved UTRs contribute to organism complexity.
Regulatory motifs in UTRs often conserved in genes belonging to the same metabolic family could potentially be used to develop highly specific medicines that target RNA transcripts.
A simpler alternative is that, because eukaryotic genomes may have no means to prevent the proliferation of transposable elements, they are free to accumulate as long as they are not inserted into or near a gene in such a way that they would disrupt essential functions.
[6] A recent study showed that transposons contribute at least 16% of the eutherian-specific CNSs, marking them as a "major creative force" in the evolution of gene regulation in mammals.
In LTR retrotransposons, after the RNA template is degraded, a DNA strand complementary to the reverse-transcribed cDNA returns the element to a double-stranded state.
The primary evidence for this process is the presence of fully functioning orthologues to these inactivated sequences in other related genomes.
With two functional copies of a gene, there is no selective pressure to maintain expressibility of both, leaving one free to accumulate mutations as a nonfunctioning pseudogene.
This is the typical case, whereby neutral selection allows pseudogenes to accumulate mutations, serving as "reservoirs" of new genetic material, with potential to be reincorporated into the genome.
[9] The simplest explanation for this is that these noncoding regions may serve some biological function, and this has been found to be the case for several conserved pseudogenes.
[4] The presence of CNSs could be due in some cases to a lack of divergence time,[15] though the more common thinking is that they perform functions which place varying degrees of constraint on their evolution.
[19] The regulatory functions commonly associated with conserved non-coding regions are thought to play a role in the evolution of eukaryotic complexity.
[21] Because changes in gene regulation are thought to account for most of the differences between humans and chimpanzees, researchers have looked to CNSs to try to show this.