The Important Role of Non-Coding “JUNK” DNA

Historically, the majority of the genome, which is not directly related to the triplet code, has been called “junk”. This is absolutely wrong. In 2004 it was confirmed [Shabalina, Spiridonov, 2004]. This work “The mammalian transcriptome and the function of noncoding DNA sequences. Genome Biology” clearly proves the important function of the so-called Junk DNA.

Approximately 99% of the protein-coding genes in the mouse have a homologue in the human genome

The detailed list of protein-coding genes was made after the completion of projects on sequencing the mouse and Human genomes. In general, the protein composition of the mouse is similar to the Human, and approximately 99% of the protein-coding genes in the mouse have a homologue in the human genome. The total amount of protein-coding genes in the mammalian genome is estimated to be approximately 30,000. Such an estimate is surprisingly close to the number of protein-coding genes in the genome of nematodes.

Cross-species comparison helps to understand the non-coding part of DNA

The function of non-coding DNA remains poorly understood, and perhaps, interspecies comparison is the only way to demonstrate that well conserved DNA sequences that have been developing slowly as a result of competitive selection, are functionally important. In general, non-coding regions are less conserved than protein-coding parts of genes. Comparative analysis of non-coding regions in genomes of higher eukaryotes shows mosaic structure alternation of highly conserved and distinct segments. Conserved elements, the so-called phylogenetic footprints, make up a significant proportion of noncoding DNA. Comparative analysis of the Human and mouse genomes showed that approximately 5% of the genomic sequence consists of highly conserved segments of 50-100 base pairs; this proportion is much higher, than can be explained only by the presence of only protein coding sequences. The average number of intergenic regions in the mouse and Human (15-19%) does not differ from the number of nucleotides in introns and intergenic regions of nematodes (18%).

The fraction of protein-coding DNA in the genome is reduced with increasing complexity of the organism

Some short intergenic regions of mammals represent mandatory sites for known transcription factors and regulatory proteins, while others have no known biological function. The fraction of protein-coding DNA in the genome is reduced with increasing complexity of the organism. In bacteria, about 90% of the genome encodes proteins. This number decreases to 68% in the yeast, 23-24% in some nematodes, and 1.5-2% in mammals.

The classical wrong DNA model does not explain why mammals and lower biological systems (insects, worms) vary so greatly in the volume of “non-coding” DNA

Various mechanisms for increasing the diversity of proteins include: the use of multiple segments at the beginning of transcription, alternative binding of pre-mRNAs and their processing, polyadenylation, as well as post-translational protein modification. However, these methods of increasing the diversity of proteins also failed to explain why mammals and lower biological systems (insects, worms) vary so greatly in the volume of “non-coding” DNA, having the same sets of genes and proteins as well as similar mechanisms for their diversification. There is no answer to the question: if it is not the genes or proteins, what determines the complexity of highly organized organisms? We can certainly say that the complexity of organisms correlates less with the number of protein-coding genes, than with the length and diversity of non-coding DNA sequences.

In general, the complexity of organisms correlates with the increase of the following parameters:

with a transcribed, but non-translated part of the genome;
with the length and number of introns in the protein-coding genes;
with the number and complexity of cis-control elements (CRE)and with the increased number of involved complex and multiple promoters for single genes;
with the number of genes for protein-encoding and for non-coding RNA genes;
with the complexity and length of noncoding regions of 3′ – ends of mRNA;
with the ratio and the absolute number of transcription factors within the entire genome.

In other words, the structural and physiological complexity of the organism is highly dependent on the complexity of regulation of gene expression and on the size and diversity of the transcriptome. The reason for this is that single-stranded RNAs have unique properties, which ensure regulatory functions. These are their ability to recognize DNA sequences via complementary interactions; their conformational elasticity, and the ability to be translated into proteins. Thus, the complexity of organisms is related to the RNA pool, which acts differently in evolutionary different taxa? But what does it mean, “acts differently”? This is another pretense of an explanation of how the genome operates and creates an organism from itself. And this is the version offered in the cited paper. However, as the authors point out, the paradox of the growing share of the non-coding part of the genome with increasing complexity of biosystems still challenges both genetics and biology, although, since the discovery of non-coding DNA, 40 years have passed. As we can see, even the recent studies come to nothing with the strange fact: the higher the biosystem in evolutionary terms, the more “junk” it has in its genome, up to 98% in humans.

Wave genetics explains these issues. Another Understanding of the Model of Genetic Code Theoretical Analysis