ENCODE: an encyclopedia which reveals that “DNA on its own is nothing”

Publié le : 14 September 2012

In order to obtain a clearer understanding of the functioning of the human genome, a scientific project called ENCODE (Encyclopedia of DNA Elements) has led to the publication of 30 articles in several scientific journals: Nature, Genome Biology and Genome Research. This project has thrown light "on an unknown yet important part of our genome: the part that does not manufacture genes and which was called ‘junk DNA’." The objective of this project, still under way and involving 440 researchers from different countries, is to "identify all the ‘functional elements’ of the human genome" that will provide "a database for the scientific community."

Reminder: "DNA is a molecule present in the centre of all our cells (in the nucleus). Its sequencing revealed that we have around 20,000 genes […]. These genes are pieces of DNA that contain the ‘code’ for making proteins. This part of the genome – called coding DNA – represents only 1 to 2% of the total DNA." It is for this reason that in the 1970s the rest of the DNA, the non-coding DNA, was called ‘junk DNA’. But biologists, who had adopted a reductionist approach ("whereby the living organism is expressed by genes"), thereafter abandoned this word ‘junk’, "and accepted the evidence that many important things happen in these 98% of the genome."

Jean-Jacques Kupiec, researcher at the French National Institute of Health and Medical Research (INSERM) in the Centre Cavaillès of the Ecole Normale Supérieure in Paris, interviewed by Sylvestre Huet for the daily Libération, explains that the sequencing of the human genome in 2000 "indeed provided precious [information]" but "did not live up to the initial hopes of giving us a deep understanding of the living organism, not did it provide therapeutic solutions for most of our genetic diseases." He adds that: "DNA on its own is nothing, or rather it never exists in isolation […]. The DNA of a cell always works in interaction with other proteins."

ENCODE provides the answers that we were seeking. The project has made it possible to "draw up a detailed map of the functions of the genome by identifying over 4 million genetic ‘interrupters’ [and to discover] that, contrary to the initial idea of ‘junk’ DNA, […] 80.4% of the genome has an active function in the regulation of the production of proteins. This majority DNA does not code directly for proteins but is responsible for the overall complexity of the genome, activating or inhibiting the production of a protein in a given place." This map will "also enable us to understand numerous diseases that are the results of genetic mutations in areas not coding for genes."

Jean-Jacques Kupiec adds that "ENCODE emerges as a logical follow-up: after sequencing the genomes, we can now begin to understand how the cell interprets the genome, because the sequence alone does not provide answers to all our questions about the living organism. […] This amounts to saying that the level for explaining the living organism is not the genes but the cell, regarded as a whole. We thus introduce a holistic view whereby the whole commands the part." According to him, biology has always been split between the reductionist and holistic approach. This contradiction can now be overtaken by a third theory, neither reductionist nor holistic. This theory "confers a decisive role on random phenomena […] notably in the expression of genes […]. It is opposed to the deterministic view based on the notion of a genetic programme."

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