The third phase of the ENCODE project provides new insights into the organization and regulation of our genes and genomes.
Encyclopedia of DNA The Elements (ENCODE) project is an worldwide effort to understand how the human genome functions. With the completion of its latest phase, the ENCODE project has added millions of candidate DNA “switches” from the human and mouse genomes that turn on the genes when and where they occur, and a new registry assigning a portion of these DNA switches Regulate For useful biological categories. The project also provides new visualization tools to aid in the use of ENCODE’s large dataset.
The latest project results were published in NatureWith 13 additional in-depth studies published in other leading journals. ENCODE is funded by the National Institute of Human Genome Research, part of the National Institutes of Health.
“A key priority of NCODE3 is to share data from thousands of NCODE experiments with the wider research community to help expand our understanding of genome function,” said NHGRI Director Eric Green, MD, PhD. “ENCODE 3 search and visualization tools make these data accessible, furthering efforts in open science.”
To assess the potential functions of various DNA regions, ENCODE researchers studied biochemical processes typically associated with the switches that regulate genes. This biochemical approach is an effective way to rapidly and comprehensively detect the entire genome. This method helps to detect regions in DNA that are “candidate functional elements” – DNA regions that are predicted to be functional elements based on these biochemical properties. Candidates can be tested in further experiments to identify and characterize their functional roles in gene regulation.
“A key challenge in NCODE is that different genes and functional regions are active in different cell types,” said Ellis Fingold, a scientific consultant for strategic implementation in the Division of Genome Sciences at NHGRI, and ENCODE for PhD. Institute. “This means that we need to test large numbers of biological samples to work towards a list of candidate functional elements in the genome.”
Significant progress has been made in characterizing protein-coding genes, which comprise less than 2% of the human genome. Researchers know little about the remaining 98% of the genome, including how many and what parts of it perform other functions. ENCODE is helping to fill this important knowledge gap.
The human body is made up of trillions of cells, with thousands of types of cells. While all these cells share a common set of DNA instructions, diverse cell types (eg, heart, lungs, and brain) function differently using different information in DNA. DNA regions that act as switches to switch genes on or off or to change exact levels of gene activity help build different cell types in the body and regulate their functioning in health and disease Huh.
During the recently completed third phase of ENCODE, researchers performed approximately 6,000 experiments — 4,834 in humans and 1,158 in mice — that published details of the genes and their potential regulators in their respective genomes.
ENCODE 3 researchers studied the development of embryonic mouse tissues to understand the timing of various genomic and biochemical changes that occur during mouse development. Mice, due to their genomic and biological similarity to humans, can help inform our understanding of human biology and disease.
These experiments were performed in many biological contexts in humans and mice. The researchers analyzed the chemical modification of DNA, the proteins that bind DNA, and Royal army (A sister molecule to DNA) interact to regulate genes. The ENCODE 3 results also help explain how variations in DNA sequences outside protein-coding regions can affect the expression of genes, even with genes uniquely located at a distance.
“The data generated in ENCODE 3 dramatically enhances our understanding of the human genome, ”said Brenton Gravelle, PhD, professor and president of the Department of Genetics and Genome Sciences at UCONN Health. “The project has added tremendous resolution and clarity to previous data types, such as DNA-binding protein and chromatin marks, and new data types, such as long-range DNA interactions and protein-RNA interactions.”
As a new feature, ENCODE 3 researchers created a resource detailing the various 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 a broad collaborative research effort involving groups in the US and internationally, involving over 500 scientists. It has benefited from and produced decades of research on gene regulation conducted by independent researchers around the world. ENCODE researchers have created a community resource, which ensures that project data is accessible to any researcher for their study. These open science efforts have resulted in more than 2,000 publications by non-NCODE researchers that use data generated by the ENCODE project.
“It shows that the encyclopedia is widely used, which is what we aimed for forever,” Dr. Fingold said. “Many of these publications relate to human disease, which relates to the value of a resource related to basic biological knowledge for health research.”
Reference: Encyclopedia of DNA Elements (ENCODE) Project