The third phase of the EN CodeE Project provides a new insight into the organization and regulation of our genes and genome.
Encyclopedia e DNA Elements (ENCODE) The project is a worldwide effort to understand how the human genome works. With the completion of its final phase, the ENCODE Project has added millions of candidate DNA “keys”; from human and mouse genomes that appear to regulate when and where genes are activated, and a new registry that assigns a portion of these DNA keys. to biologically useful categories. The project also provides new visualization tools to help use ENCODE big data.
The final results of the project were published in nature, accompanied by 13 additional in-depth studies published in other major journals. EN CodeE is funded by the National Institute of Human Genome Research, part of the National Institutes of Health.
“A key priority of ENCODE 3 was to create tools to share data from thousands of ENCODE experiments with the wider research community to help expand our understanding of genome function,” said NHGRI Director Eric Green, MD. Ph.D. “ENQUE 3 research and visualization tools make this data accessible, thus advancing open science efforts”
To assess the possible functions of different regions of DNA, ENCODE researchers studied the biochemical processes that are commonly associated with genes that regulate genes. This biochemical approach is an efficient way to explore the entire genome rapidly and comprehensively. This method helps to find regions in DNA that are “functional candidate elements” – regions of DNA that are predicted to be functional elements based on these biochemical properties. Candidates can then be tested in further experiments to identify and characterize their functional roles in gene regulation.
“A major challenge at EN CodeE is that different genes and functional regions are active in different cell types,” said Elise Feingold, Ph.D., Scientific Advisor for Strategic Implementation at the NHGRI Genome Science Division and a lead ENCODE for institute. “This means that we need to test a large and diverse number of biological samples to work towards a catalog of functional candidate elements in the genome.”
Significant progress has been made in characterizing protein-encoding genes, which make up less than 2% of the human genome. Researchers know far less about the remaining 98% of the genome, including how much and which parts of it perform other functions. EN CodeE is helping to fill this significant knowledge gap.
The human body is made up of trillions of cells, with thousands of cell types. While all of these cells share a common set of DNA instructions, different cell types (e.g., heart, lungs, and brain) perform different functions using information encoded in DNA differently. Regions of DNA that act as keys to turn or turn off genes, or tune in to accurate levels of gene activity, help stimulate the formation of distinct cell types in the body and regulate their functioning in health and disease.
During the recently completed third phase of EN CodeE, researchers conducted nearly 6,000 experiments – 4,834 in humans and 1,158 in mice – to shed light on details of genes and their possible regulators in their respective genomes.
EN CodeE 3 researchers studied the development of mouse embryonic tissue to understand the timing of various genomic and biochemical changes that occur during mouse development. Mice, because of their genomic and biological similarities to humans, can help inform our understanding of biology and human disease.
These experiments in humans and mice were performed in several biological contexts. The researchers analyzed how chemical modifications of DNA, DNA-binding proteins, and RNA (a sister molecule with DNA) interact to regulate genes. The results from EN CodeE 3 also help explain how variations in DNA sequences outside protein coding regions can affect the expression of genes, even genes located too far away from a specific variant itself.
“The data generated in EN CodeE 3 dramatically enhances our understanding of the human genome, “said Brenton Graveley, PhD, professor and chair of the Department of Genetics and Genome Science at UCONN Health.” The project has added a resolution and clarity to extraordinary for previous data types, such as DNA-binding proteins and chromatin markers, and new types of data, such as long-range DNA interactions and protein-RNA interactions. “
As a new feature, ENCODE 3 researchers created a resource detailing different types of DNA regions and their respective candidate functions. A web-based tool called SCREEN allows users to visualize data that supports these interpretations.
The ENCODE project began in 2003 and is an extensive collaborative research effort involving groups across the US and internationally, involving over 500 scientists with diverse expertise. It has benefited from and built on decades of research into gene regulation conducted by independent researchers around the world. EN CodeE researchers have created a community resource, ensuring that project data is accessible to any researcher for their studies. These open science efforts have resulted in over 2,000 publications by non-ENKODE researchers using data generated by the ENCODE Project.
“This shows that the encyclopedia has been widely used, this is what we have always aimed for,” said Dr. Feingold. “Many of these publications deal with human disease, testifying to the value of the resource for linking basic biological knowledge to health research.”
Reference: Encyclopedic Project of DNA Elements (ENCODE)