Deciphered the function of the junk DNA

Deciphered the function of the junk DNA

Researchers determine the function of the supposed DNA waste

Eleven years after the Human Genome Project decoded the human genome, an international team of researchers took another important step towards understanding the blueprint of life. Hundreds of scientists from the ENCODE project, led by the National Genome Research Institute in the United States and the EMBL-European Bioinformatics Institute in the United Kingdom, have now presented a detailed map of the functions of the human genome and identified four million gene switches.

Since the decoding of human genes as part of the "Human Genome Project" more than a decade ago, molecular biologists worldwide have asked themselves why only two percent of genes consist of genes that serve as a guide for the formation of proteins. Theoretically, in the course of evolution, these also known as junk DNA, supposedly useless components of the genome could have been eliminated. But the junk DNA is by no means superfluous, according to the researchers of the ENCODE project, it fulfills a crucial regulatory function for the activity of the genes. The scientists have published their results in over 30 articles in the three renowned specialist magazines "Nature", "Genome Biology" and "Genome Research".

Four million gene switches identified For nine years, researchers around the world have been working on the ENCODE project to investigate genome areas that lie outside the gene sequences that are used to guide the construction of the proteins. In doing so, they discovered a surprisingly far-reaching function of junk DNA. Four million identified gene switches determine the activity of the genes. "Mutations in these regions can lead to human disease," reports the European Bioinformatics Institute in a recent press release. The number of gene switches identified was astonishingly high, emphasized the head of the institute, Rolf Apweiler. The junk DNA is actually a “control panel” with millions of control elements that determine the activity of the genes. “80 percent of the genome is involved in this regulation in some form,” write the researchers of the ENCODE project.

Identified gene switches in the junk DNA regulate gene activity A total of 442 scientists from the USA, Great Britain, Spain, Singapore and Japan have been involved in the investigation of human genetics within the framework of the ENCODE project over the past nine years. They sequenced over 1,600 genomes from 147 tissue types. They collected the huge amount of 15 terabytes of raw data, which was then analyzed. Initially, the researchers focused on the areas of the genome that are directly responsible for the construction instructions for the proteins. However, this was only two percent of the genome. The following investigations focused in particular on the analysis of so-called junk DNA. Here the scientists identified four million gene switches that contribute to the production of millions of different proteins by regulating gene activity. Each gene can be switched on and off, but can also be read in at least two to three different ways, explained the head of the European Bioinformatics Institute. These gene versions are called transcripts.

The high complexity of gene switches makes it difficult to understand diseases Dr. Michael Snyder, professor and chair of Stanford University and chief investigator at ENCODE, explained that the project provides the insights "that we need to look behind the linear structure of the genome and to recognize the entire network." ENCODE enables a deep Insight into the “control loop that tells us how all the parts come together to form a complex being,” Snyder continues. However, the result is fascinating and frustrating at the same time, added Rolf Apweiler. The complexity of the function of the four million gene switches is simply so high that a simple cause-effect relationship in relation to certain diseases is difficult to determine. Ultimately, the aim of the work is to help develop drugs that are cheaper, more effective, and safer than today, but that the development of diseases is much more complex than previously thought. Apweiler therefore wondered “whether our brain cells will ever be enough” to understand how an illness develops and how to intervene in this process.

Deciphering the schematic of life Nevertheless, the scientists are convinced of the importance of their research results. The free publication of the data is a milestone in genome research. The ENCODE project made a significant contribution “to understanding the circuit diagram of humans,” explained Michael Snyder. In addition to the fundamental understanding of biology, the study can also promote the study of genetic influences on the development of diseases using the data. "We are beginning to understand the information generated in genome-wide association studies," said Snyder. Various studies that compare the genome of people with complex diseases such as diabetes, heart disease such as heart attack or obesity with the genome of healthy people have already been published. But these have located most of the differences outside the gene sequences that are responsible for the formation of the proteins.

Encyclopedia on the function of the genome Given the results of the ENCODE project, these genome-wide association studies appear in a completely different light, explained Rolf Apweiler. The focus is now on the millions of gene switches that apparently have a significant impact on the development of diseases. While the regulatory elements were previously thought to be close to the gene sequences that determine the formation of proteins, the researchers pointed out in the course of the ENCODE project after that the comparatively distant sections also play a role. According to the researchers, such a comprehensive analysis of the genome was made possible by significant advances in sequencing technology, which not only made genetic analysis faster, but also significantly cheaper. "Deciphering the first human genome cost about 500 million euros, nowadays you can decipher a person's genome for 1,000 to 1,500 euros," emphasized the head of the European Bioinformatics Institute. Thanks to the new possibilities, "we now have an interactive encyclopedia that everyone can refer to, which will make a big difference" in future research, says Spanish researcher Roderic Guigo from the Center de Regulació Genomica (CRG) who is also involved in the project in Barcelona. (fp)

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