The third phase of the ENCODE project offers new insights into the organization and regulation of our genes and genome.
Encyclopedia of Russia DNA The Elements Project (ENCODE) is a worldwide effort to understand how the human genome works. Following the final phase, the ENCODE project has added millions of candidate DNA “switches”; from the human and mouse genomes, which appear to regulate when and where genes are turned on, and a new registry that assigns part of these DNA switches. to useful biological categories. The project also offers new visualization tools to help use large ENCODE datasets.
The latest project results were published in Nature, accompanied by 13 additional in-depth studies published in other major journals. ENCODE is funded by the National Institute of Human Genome Research, a member of the National Institutes of Health.
“ENCODE 3’s top priority was to develop tools to share data from thousands of ENCODE experiments with the wider research community to help expand our understanding of genome function,” said Eric Green, Ph.D., Ph.D., Ph.D. “ENCODE 3 search and visualization tools make this data available, thus advancing efforts in open science.”
To assess the potential functions of different regions of DNA, ENCODE researchers studied biochemical processes that are typically associated with gene-regulating switches. This biochemical approach is an effective way to quickly and comprehensively study the entire genome. This method helps to find areas in DNA that are “candidates for functional elements” – DNA regions that are thought to be functional elements based on these biochemical properties. Candidates can then be tested in subsequent experiments to identify and characterize their functional role in gene regulation.
“A key challenge at ENCODE is that different genes and functional regions operate in different cell types,” said Eliza Feingold, Ph.D., Strategic Implementation Advisor in the Department of Genome Sciences at NGRI and ENCODE’s guide to the institute. “This means that we need to test a large and diverse number of biological samples to work on a catalog of candidate functional elements in the genome.”
Significant progress has been made in characterizing genes encoding proteins that make up less than 2% of the human genome. Researchers know much less about the remaining 98% of the genome, including how many and which parts of it perform other functions. ENCODE helps to fill this significant knowledge gap.
The human body is made up of trillions of cells, with thousands of cell types. Although all of these cells share a common set of DNA instructions, different cell types (such as the heart, lungs, and brain) perform different functions using the information encoded in DNA in different ways. Areas of DNA that act as switches to turn genes on or off or to set accurate levels of gene activity help control the formation of different types of cells in the body and regulate their functioning in health and disease.
During the recently completed third phase of ENCODE, researchers conducted nearly 6,000 experiments – 4,834 in humans and 1,158 in mice – to elucidate the details of genes and their potential regulators in their respective genomes.
ENCODE 3 researchers studied the development of mouse embryonic tissues to understand the time scales of various genomic and biochemical changes that occur during mouse development. Mice, through their genomic and biological similarities to humans, can help inform our understanding of human biology and disease.
These experiments on humans and mice were performed in several biological contexts. The researchers analyzed how the chemical modifications of DNA, DNA-binding proteins, and RNA (sister of the DNA molecule) interact to regulate genes. The results of ENCODE 3 also help to explain how variations in DNA sequences outside the proteins encoding the protein can affect gene expression, even genes located far from a particular variant.
“The data generated in ENCODE 3 dramatically enhances our understanding of the human genome, “said Brentton Graley, Ph.D., Professor and Department of Genetics and Genome Sciences at UCONN Health.” such as DNA-binding proteins and chromatin labels, and new types of data, such as long-range DNA interactions and protein-RNA interactions. “
As a new feature, ENCODE 3 researchers have created a resource detailing different types of DNA regions and their respective candidate functions. A web tool called SCREEN allows users to visualize data that supports these interpretations.
The ENCODE project began in 2003 and is a large collaborative research project involving groups in the United States and abroad, involving more than 500 scientists with diverse knowledge. This has benefited and is being built by decades of gene regulation research conducted by independent researchers around the world. ENCODE researchers have created a community resource, ensuring that project data is available to any researcher for their research. These efforts in open science have resulted in more than 2,000 publications by non-ENCODE researchers using data generated by the ENCODE project.
“This shows that the encyclopedia is widely used, which is what we have always strived for,” said Dr. Feingold. “Many of these publications are related to human disease, which demonstrates the value of a resource for linking basic biological knowledge with research.”
Reference: Project “Encyclopedia of DNA Elements” (ENCODE)