What are the dark sides of coding

Fig. 1: The dark sides of the genome are becoming increasingly illuminated. (From Pennisi 2010, reprinted with kind permission)

The textbook knowledge was initially simple and clear: the DNA in the genome (entire genetic material) contains the instructions for the structure of proteins. The instructions are divided into genes and are brought from the cell nucleus to the location of protein synthesis, the ribosomes, by chemically related nucleic acids, the RNA. Between the individual genes there are large areas in the genome to which no function or meaning could be assigned (“junk DNA”, “genetic waste”).

Research over the past decade has shed increasing light on the extensive areas of the genome that initially appeared to be useless. The science journalist Elizabeth Pennisi (2010) has briefly summarized important publications from this period for the journal Science.

As far as we know today, the human genome contains around 21,000 genes that code for proteins. They take up about 1.5% of the genome. It was previously doubted that the rest - at least more than 98% - was useless waste, since the ballast to this extent should have been disposed of over time, especially according to evolutionary ideas.

Pennisi cites the following findings, which show the genome in a new light:

1. Humans not only have many protein-coding genes that are also found in the mouse genome, but large parts of the non-coding DNA are also similar in both organisms. Without a function of these areas, the finding is difficult to explain, since mutations are not corrected by selection if they are not functioning and thus accumulate. As a result, the corresponding DNA sequences in different organisms are becoming increasingly dissimilar. Studies on mouse embryos show that non-coding regions of the genome play a role in gene regulation. Some of the genes whose activity they control are located far away from them in the genome.

2. Other extensive studies in which genetic risk factors for diseases were investigated also provided evidence of the functionality of non-coding genomic regions: approx. 40% of DNA sequences in which healthy and diseased individuals differ by a single DNA base are located in areas between genes.

3. In other studies it has been shown that far more DNA is transcribed into RNA than just for the messenger RNA (mRNA) or the RNA of the ribosomes (rRNA). About 80% of the DNA of a cell seems to be transcribed into RNA without the majority of these transcribed areas being known what their function is.

4. During research on plants and roundworms, mechanisms were discovered how to switch off genes with small RNA fragments. The research and development of the method known as RNA interference (RNAi) was awarded a Nobel Prize in 2006. Many studies have confirmed that very short RNA fragments of 21 to 30 bases interact with the chromosomes and can thus control and regulate the activity of genes. If any of these short RNA sequences are missing in yeast cells, cell division is disturbed and they are also involved in developmental processes and carcinogenesis.

5. But not only these small RNA snippets caused a sensation, also the so-called large intervening noncoding RNA (lincRNA), which is located between the genes, unfolds a regulatory function on genes. It could be, at least some researchers say in this direction, that this part of the genome turns out to be just as important in terms of its importance as the protein-coding genes.

Despite the now well-known diverse tasks, the alleged "junk DNA" was and is still being used as an argument against the idea of ​​optimal design. Genetic “waste” can only have arisen through a previous natural evolution, but cannot be interpreted as the result of an intelligent creation. In view of the current state of research on the “dark matter” of the genome, however, the notion of genetic waste should be shelved for the time being - and perhaps forever. The argument based on the “junk DNA” that there are design errors and that this speaks against a creation has meanwhile become very questionable due to the progress of research.

In conclusion, Pennisi states that ten years ago research focused almost exclusively on protein-coding genes from the genome. Today we are also interested in many other areas of the genome. Your summary can arouse amazement at the fascinating diversity and density of control and regulation mechanisms in cells.

The genome itself does not provide that
hoped for decisive insights into
the basic causes of life.

At the same time, however, the author's retrospective documents that by looking at the research object - or to take up her image: its lighting - also shadows are produced: individual aspects are emphasized, others neglected or even faded out.

Current research into the genome shows that despite all the fascinating findings, many hopes have not been fulfilled. The perspective has to be broadened, because the genome itself does not provide the key insights into the fundamental causes of life that were hoped for, but increasingly appears as part of a comprehensive and more complex system. If previously dark areas are captured by the light cone of new questions, this causes on the one hand disillusionment with regard to the crucial answers hoped for from the genome; At the same time, however, new horizons for exciting research are opened up in a new light.