2020 Wednesday, July 29th
The third phase of the ENCODE project provides new insights into the organization and regulation of our genes and genome.
The Encyclopedia of DNA Elements (ENCODE) is a global effort to understand how the human genome works. In the final phase, the ENCODE project has added millions of DNA “switches” from the human and mouse genomes, which appear to regulate when and where the genes are activated, and a new registry that includes some of these DNA switches. into useful biological categories. The project also proposes new visualization tools for the use of large ENCODE datasets.
The last results of the project were published in 2006 naturealong with 13 additional in-depth studies published in other major journals. ENCODE is funded by the National Institute for Human Genome Research, part of the National Institutes of Health.
“A key priority for ENCODE 3 has been to develop tools to share data from thousands of ENCODE experiments with the wider research community to facilitate understanding of our genome function,” said Eric Green, MD, Ph.D. “3 coding search and visualization tools make this data available, thus promoting open science efforts.”
To assess the potential functions of different areas of DNA, ENCODE researchers have studied biochemical processes that are typically associated with switches that regulate genes. This biochemical method is an effective way to study the entire genome quickly and in detail. This method helps to identify regions of DNA that are “candidate functional elements” – regions of DNA that are predicted to be functional elements based on these biochemical properties. Candidates can be tested in further experiments to identify and describe their functional roles in gene regulation.
“The main challenge for ENCODE is that different genes and functional regions are active in different cell types,” said Elise Feingold, Ph.D., Strategic Implementation Advisor and Head of ENCODE, NHGRI’s Genome Sciences Division. institute. “That means we have to test many and varied biological samples to create a catalog of functional elements for genome candidates.”
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 much and which parts of it perform other functions. ENCODE helps fill this large knowledge gap.
The human body is made up of trillions of cells with thousands of species of cells. 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 DNA-encoded information differently. Regions of DNA that act as switches to turn genes on or off, or to match the exact level of gene activity, help the body to form different cell types and control their function in health and disease situations.
In the recently completed third phase of ENCODE, the researchers performed nearly 6,000 experiments – 4,834 in humans and 1,158 in mice – to illuminate gene fragments and their potential regulators in their respective genomes.
Researchers at ENCODE 3 studied the development of embryonic tissue in mice to understand the timing of various genomic and biochemical changes that occur during mouse development. Because of their genomic and biological similarity to humans, mice can help us understand our understanding of human biology and disease.
These experiments in humans and mice have been performed in several biological contexts. The researchers analyzed how chemical modifications of DNA, proteins that bind to DNA, and RNA (sister molecule to DNA) interact to regulate genes. The results of ENCODE 3 also help to explain how variations in DNA sequences beyond protein coding regions can affect the expression of genes, even those that are far from the specific variant itself.
“The data generated by ENCODE 3 greatly enhances our understanding of the human genome, ”said Brenton Graveley, Ph.D., Professor and President of the Department of Genetics and Genome Sciences at UCONN Health. previous data types such as DNA-binding proteins and chromatin tags, and new data types such as long-range DNA interactions and protein-RNA interactions’.
As a new feature, ENCODE 3 researchers have developed a resource that details the different areas of DNA and their respective candidate functions. An online tool called SCREEN allows users to visualize data that supports these interpretations.
The ENCODE project was launched in 2003. And there is extensive research involving teams across the United States and internationally, encompassing the efforts of more than 500 researchers with diverse competencies. It has been useful and has been based on decades of gene regulation research conducted by independent researchers around the world. ENCODE researchers have developed a community resource, ensuring that project data is available to each researcher for their studies. These open science efforts have led to the creation of more than 2,000 publications from non-ENCODE researchers using the data generated by the ENCODE project.
“It 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 diseases. This demonstrates the value of resources in linking basic biological knowledge to health research.”
NHGRI is one of the 27 institutes and centers of the National Institutes of Health. The NHGRI part-time research program supports grants for research, training and career development in all locations. Additional information about NHGRI can be found at https://www.genome.gov.
About National Institutes of Health (NIH):
The National Medical Research Agency (NIH) is made up of 27 institutes and centers and is part of the U.S. Department of Health and Human Services. The NIH is a leading federal agency that conducts and supports basic, clinical, and applied medical research and investigates the causes, treatment, and cure of both common and rare diseases. For more information about NIH and its programs, visit www.nih.gov.
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