ABOUT GENOME

The genome is all the genetic information of a living organism. Genetic information is stored in DNA. Genetic information is transferred to RNA through a transcription process, which in turn produces proteins and exhibits the traits of the living organism. There are two theories about the biological function of DNA.

The mainstream of biology has supported the theory that DNA is a storage device for genetic information. However, the rapid increase in non-protein-coding DNA (ncDNA) and non-protein-coding RNA (ncRNA) in higher organisms cannot be explained.

On the other hand, the theory regarding DNA as a regulator of cell functions does not provide a biological model that can explain life phenomena.

Cells of all living organisms fall into one of two groups: prokaryotic cells without a nucleus or eukaryotic cells with a nucleus. The cells of all higher organisms, including humans, are eukaryotic, and prokaryotes include bacteria and archaea. For a while, the DNA of these two types of cells has been considered the same in terms of a collection of genes, except for the difference in the number of genes.

“Anything found to be true of E. coli must also be true of elephants” is a well-known phrase of Jacques Lucien Monod (1910 – 1976), a French biochemist who won the Nobel Prize in Physiology or Medicine in 1965. E. coli is a prokaryote, and an elephant is a eukaryote. This statement is based on the idea that eukaryotic cells are not far from the prokaryotic cells but merely have more complexity.

However, many life events occurring in eukaryotic cells present several contradictions to this view. Cancers that originate in the genome, for example, occur only in eukaryotes. We need a deeper look at the functional differences in genomes between prokaryotes and eukaryotes.

The DNA of prokaryotic cells is in the cytoplasm, and the DNA of eukaryotic cells is in the nucleus. The nuclear membrane blocks the movement of most substances in and out of the nucleus. The presence of a nucleus has the following significances.

In prokaryotes, DNA is mainly composed of protein-coding genes as a key component of the genome, and the proportion of ncDNAs is very small.

On the other hand, in eukaryotes, the higher the organism, the lower the proportion of protein-coding DNAs, and the higher the proportion of ncDNAs. In humans, the proportion of protein-coding genes is very small, about 1.7% and the rest is ncDNA, and our knowledge about this region is still very little.

In addition, the proportion of mRNAs that encode proteins is also very small among the total RNAs produced through transcription from DNA, and non-coding RNA accounts for most of the total RNAs.

An accurate understanding of the commonalities and differences in mRNA function between prokaryotic and eukaryotic cells will provide clues to the cause of cancer.

Individual cells must be driven in the direction that the tissues, organs, organ systems, and ultimately the entire human body pursue. The biochemical properties of the protein alone cannot perform the biological functions of cells, and there must be an operating system.

According to Albert-László Barabási [1], a renowned physicist in network theory research, the networks in complex systems like the cell are difficult to control, and most nodes must be controlled simultaneously to drive such systems.

For example, even in automobiles, having much low complexity compared to the proteome, coordinated information must be provided through the steering wheel, accelerator, brake, clutch, and transmission at the right time to drive the car in the desired direction reliably.

What makes human cells have the proper structure and function as one of the most complex systems is the presence of the proteome as tools, such as automobiles in the example above.

Therefore, the operational information entering the proteome should be transmitted simultaneously through multiple channels, with a high degree of order and scheme. In this way, a cell can have the structure and functions required by tissues, organs, organ systems, and the human body.

A binary code composed of ‘0’ and ‘1’ is recorded in a one-dimensional structure in the storage device of a computer. However, the code is not considered a one-dimensional structure as it appears. In the code, the operating system, various apps, and data are arranged in a multi-dimensional structure.

DNA has a quaternary code consisting of four bases, ‘A,’ ‘C,’ ‘G’ and ‘T,’ arranged in a one-dimensional structure that contains huge non-protein-coding regions in addition to the protein-coding regions.

Is DNA simply a one-dimensional structure that stores genes? Or is it a multi-dimensional program structure formed of genes as commands?

1. Liu Y-Y, Slotine J-J, Barabási A-L. Controllability of complex networks. Nature. 2011 May 12;473(7346):167–73.