Revealing the intrinsic functioning of human and mouse genomes

New insights into the organization and regulation of our genes and genome.


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The Encyclopedia of DNA Elements (ENCODE) Consortium is a universal coordinated effort of research groups funded by the National Human Genome Research Institute (NHGRI). The objective of ENCODE is to make a comprehensive parts list of functional elements in the human genome, including elements that work at the protein and RNA levels, and regulatory elements that control the cells and conditions where a gene is active.

The project will detail how the human genome functions. Recently, the project completed its latest phase- scientists have added millions of candidate DNA “switches” from the human and mouse genomes. These genomes appear to control when and where genes are turned on, and a new registry that assigns a portion of these DNA switches to useful biological categories. 

It also provides the latest visualization tools to help in the use of ENCODE’s large datasets.

NHGRI Director Eric Green, M.D., Ph.D. said, “A major priority of ENCODE 3 was to develop means to share data from the thousands of ENCODE experiments with the broader research community to help expand our understanding of genome function. ENCODE 3 search and visualization tools make these data accessible, thereby advancing efforts in open science.”

To evaluate the potential functions of various DNA locales, ENCODE specialists considered biochemical procedures that are normally connected with the switches that regulate genes. This biochemical methodology is an effective method to investigate the whole genome wholly and quickly. 

This strategy assists with finding regions in the DNA that are “candidate functional elements” – DNA regions that are anticipated to be practical components dependent on these biochemical properties. Candidates would then be able to be tested in further experiments to distinguish and portray their useful roles in gene regulation.

Elise Feingold, Ph.D., scientific advisor for strategic implementation in the Division of Genome Sciences at NHGRI and a lead on ENCODE for the institute, said, “A key challenge in ENCODE is that different genes and functional regions are active in different cell types. This means that we need to test a large and diverse number of biological samples to work towards a catalog of candidate functional elements in the genome.”

During the recently completed third phase of ENCODE, scientists performed almost 6000 experiments in several biological contexts- 4,834 in humans and 1,158 in mice- to enlight details of the genes and their potential regulators in their respective genomes.

Scientists studied developing embryonic mouse tissues to comprehend the timeline of various genomic and biochemical changes that occur during mouse development. 

Scientists analyzed how chemical modifications of DNA, proteins that bind to DNA, and RNA (a sister molecule to DNA) interact to regulate genes. Results from ENCODE 3 also help explain how variations in DNA sequences outside of protein-coding regions can influence the expression of genes, even genes located far away from a specific variant itself.

Brenton Graveley, Ph.D., professor and chair of the Department of Genetics and Genome Sciences at UCONN Health, said, “The data generated in ENCODE 3 dramatically increase our understanding of the human genome. The project has added tremendous resolution and clarity for previous data types, such as DNA-binding proteins and chromatin marks, and new data types, such as long-range DNA interactions and protein-RNA interactions.”

As a new feature, ENCODE 3 scientists created a resource detailing different kinds of DNA regions and their corresponding candidate functions. A web-based tool called SCREEN(link is external) allows users to visualize the data supporting these interpretations.

The project’s latest results were published in Nature, accompanied by 13 additional in-depth studies published in other major journals.


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