Isochores: Three-Dimensional Information Layer in DNA Challenges Junk DNA Paradigm

Over the past forty years, many different types of DNA structures in the genome of living organisms have been classified as “junk DNA”, i.e., non-functional genetic units that are thought to be traces of a long and protracted evolution. Gradually, however, it is becoming apparent that these genetic regions perform important functions (pseudogenes, introns, etc.). A similar case that recently has become known are DNA sequences with a frequently repeating structural known as the isochores. The finding that isochores are genetic elements that store the information for the correct spatial arrangement of DNA in the cell nucleus


Opinion
Without doubt, the genetic material of all living beings (DNA) is one of the most fascinating biomolecules. Not long after characterizing its three-dimensional helix structure (1953), James Watson said: "I believe few discoveries have been of such perfect beauty." As it seems, the moments of surprise associated with the study of DNA have not been exhausted even today-after almost 70 years of intensive research. After the genetic code was deciphered and the packaging of DNA was characterized in the 1960s and 1970s, some influential experts came to the conclusion that only protein-coding DNA sequences comprising approximately 2% of the whole genome were functional. Based on the theory of evolution, the remaining 98% were dubbed "junk DNA", i.e. genetic waste that had become inoperable in the course of many millions of years of evolutionary change [1].
However, this notion has increasingly been questioned over the past 20 years, as a large number of findings suggest that at least 80% of the human genome is functional (ENCODE Consortium 2012). The main fallacy of the junk DNA hypothesis was the hasty assumption that genetic sections that are not used for the synthesis of proteins do not serve any function at all. Indeed, it has repeatedly been found that gene sequences previously thought to be functionless perform important regulatory functions. The term "pseudogene", which is often used in this context, has therefore often proven to be incorrect [2]. Similarly, introns, which were previously thought to be evolutionary remnants, have also been shown to be functional upon closer examination [3].
Another type of genetic regions, which were also classified as "junk DNA" for a long time, are the isochores. These are long, repetitive DNA segments containing a frequently recurring structural motif, which have been considered to be relics of viruses [4]. However, recently the Italian molecular biologist Giorgio Bernardi reported in a review article that the isochores apparently perform very important functions for the entire cell [5]. Bernardi found "…that these structures, essentially based on the distribution and topology of short sequences, mold primary chromatin domains (and define nucleosome binding)." Put simply, this means that the isochores, depending on their structural makeup, significantly influence the 3D-structure of the packaging of the DNA in the cell nucleus. Bernardi speaks in this context of a "genomic code"-i.e. coded information about how the Abstract Over the past forty years, many different types of DNA structures in the genome of living organisms have been classified as "junk DNA", i.e., non-functional genetic units that are thought to be traces of a long and protracted evolution. Gradually, however, it is becoming apparent that these genetic regions perform important functions (pseudogenes, introns, etc.). A similar case that recently has become known are DNA sequences with a frequently repeating structural known as the isochores. The finding that isochores are genetic elements that store the information for the correct spatial arrangement of DNA in the cell nucleus challenges the evolutionary junk DNA paradigm.

American Journal of Biomedical Science & Research Am J Biomed Sci & Res
Copy@ Boris Schmidtgall

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DNA in the cell nucleus should be arranged three-dimensionally: "Furthermore, being pervasive in the genome, the genomic code solves old outstanding problems, such as 'non-coding DNA', 'junk DNA' or 'selfish DNA'". Accordingly, the effect of the isochores is by no means locally limited, but affects the entire structure of the hereditary molecules in the cell nucleus.

Conclusion
Bernardi concludes at several points in his review article that with the discovery of the "genomic code" the evolutionary concept of "junk DNA" becomes very questionable. However, he still tries to trace the origin of genetic information back to evolution: "By the end of the 1980s, our knowledge of the isochore organization of the human genome had not only rejected what had been called the 'bean-bag' view of the genome, that is, a collection of genes randomly scattered over vast expanses of 'junk DNA'; but it had also indicated that the genome is an integrated structural, functional, and evolutionary system." The quoted sentence seems quite conclusive in itself except the word 'evolutionary'. In this sentence, this word is completely superfluous. The term 'evolutionary' here does not arise in a meaningful way from what has been said before, but merely represents an ideological confession of the author. In view of the findings described, however, it is inappropriate to describe the system as 'evolutionary'. For how can a system at the same time exhibit essential characteristics of a created object (integrated, structured, functional) and yet emerge from undirected natural processes? This dichotomy occurs particularly often in connection with discoveries in the field of molecular biology and is never resolved. This may be due to the fact that hardly any other field provides such clear indications of design as molecular biology or genetics. Therefore, in this context the evolutionary world view can only be maintained through rhetorical concealment.
It remains to be hoped that in the future scientists will be honest and courageous enough not to follow the ideological dictates of the educational and media institutions. Instead of repeated avowals to naturalism we need to focus on the scientific findings and the conclusions that necessarily follow from them.