Everything You Need to Know About the ENCODE Project

Everything You Need to Know About the ENCODE Project

The ENCODE (Encyclopedia of DNA Elements) Project began in 2003. Its objective is to identify all functional DNA elements within the human genome.

In this article we look at some of the project’s key findings and how information gathered from ENCODE could prove key in the search for a cure for cancer.

Who started the ENCODE Project?

ENCODE project

The ENCODE Project is led by a team of scientists known as the ENCODE Consortium and is financed by the National Human Genome Research Institute.

The consortium is an international collaboration between the world’s most revered medical institutions. The Consortium came together with the goal of building an integrated encyclopedia of functional human DNA elements. These include elements that act at RNA and protein levels as well as regulatory elements that control cells, effectively switching genes on and off.

Researchers involved in the ENCODE Project come from a number of institutions, including: Harvard and MIT’s Broad Institute, The University of Michigan, Baylor College of Medicine, The University of Alabama in Huntsville, Stanford University, The Jackson Laboratory, The University of California, Altius Institute for Biomedical Sciences, The University of Washington, The University of Chicago, Duke University, John Hopkins University, The University of Massachusetts, Yale University, The University of Connecticut, Cold Spring Harbor Laboratory, The Memorial Sloan Kettering Cancer Centre, and the Dana-Farber Cancer Institute.

What is the human genome and why is it so important?

The human genome is a detailed set of DNA instructions on how to build a human being. A copy of the genome is found in virtually every cell of the body. Genomes contain all of our genetic material in the form of DNA. DNA dictates our physiological makeup, from height and hair color to the way our bodies react to the external environment, such as our tolerance of sunlight.

Our unique genetic makeup can also impact our health, with certain gene sequences making us more or less susceptible to disease. Scientists hope that by mapping the almost 3 billion base pairs of DNA, they will come to a greater understanding of how our genes work.

Studies have historically concentrated on protein-coding regions. However, the ENCODE Project aims to identify other functions performed by our genes. These functions may include the mechanics of gene organization and regulation. Scientific understanding of the human genome is far from complete, particularly in the field of noncoding DNA.

What is the role of noncoding DNA?

“Coding DNA” codes for proteins, substances vital to cellular processes and survival. Historically, scientists only attributed significance to coding DNA, which accounts for just 1.5 percent of DNA found within the human genome. The remaining 98.5 percent of noncoding DNA was referred to as “junk DNA”.

Recent studies revisit the issue of junk DNA, indicating that noncoding DNA could be of greater consequence than first thought. Noncoding DNA may play a role in regulating cell function and behavior, perhaps even controlling protein coding genes. Scientists have discovered genetic markers in noncoding DNA associated with a number of serious diseases, including cancer.

How is the ENCODE Project attempting to reveal the true purpose of “junk DNA”?

The project combines findings amassed by 32 independent research groups, featuring contributions from over 400 eminent scientists. The ENCODE Project aims to increase understanding on little-known aspects of the genome. In particular, they are attempting to identify the functions of noncoding DNA.

In September 2012, the ENCODE Consortium published 20 separate papers. One of those papers indicated that rather than just 1.5 percent of DNA within the human genome being functional, as previously supposed, ENCODE studies reveal that 80 percent of the human genome contributes to key cellular processes.

As Peter Campbell of the Wellcome Sanger Institute points out, the ENCODE Project is the scientific community’s first attempt to characterize DNA in a systematic way. The revelations so far have been quite extraordinary.

As Bradley Bernstein of Harvard Medical School indicates, data gained through ENCODE has taken the scientific world by surprise. The ENCODE Project has identified many new regulatory elements. Scientists are now looking at their chromatin structures, transcription factors, and likely gene targets.

How is ENCODE contributing to cancer research?

Nowhere are the ENCODE Project’s findings more valuable than in the field of cancer research. As pointed out by John Stamatoyannopoulos of the University of Washington, cancer is ultimately a genomic disease. The ENCODE Project essentially paves the way for researchers to access layers of genetic information by running genetic sequences through a computer.

ENCODE data links cancer to disruption in one or more of 25 different transcription factors. Though several of these transcription factors had already been linked with the disease, the project revealed previously unidentified genetic causes.

ENCODE Project research reveals that DNA once written off by scientists as “junk” can have a huge impact in terms of diseases like cancer and genetic malignancies. ENCODE data has effectively sped up the process in terms of cancer research, taking us ever closer to finding a cure.