Encode

The ENCODE Project: ENCyclopedia Of DNA Elements.

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ENCODE Overview

The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The project started with two components – a pilot phase and a technology development phase.

The pilot phase tested and compared existing methods to rigorously analyze a defined portion of the human genome sequence (See: ENCODE Pilot Project). The conclusions from this pilot project were published in June 2007 in Nature and Genome Research [genome.org]. The findings highlighted the success of the project to identify and characterize functional elements in the human genome. The technology development phase also has been a success with the promotion of several new technologies to generate high throughput data on functional elements.

With the success of the initial phases of the ENCODE Project, NHGRI funded new awards in September 2007 to scale the ENCODE Project to a production phase on the entire genome along with additional pilot-scale studies. Like the pilot project, the ENCODE production effort is organized as an open consortium and includes investigators with diverse backgrounds and expertise in the production and analysis of data (See: ENCODE Participants and Projects). This production phase also includes a Data Coordination Center [genome.ucsc.edu] to track, store and display ENCODE data along with a Data Analysis Center to assist in integrated analyses of the data. All data generated by ENCODE participants will be rapidly released into public databases (See: Accessing ENCODE Data) and available through the project’s Data Coordination Center.

Source: genome.gov

 

Detailed map of genome function.

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Scientists have published the most detailed analysis to date of the human genome.

They’ve discovered a far larger chunk of our genetic code is biologically active than previously thought.

The researchers hope the findings will lead to a deeper understanding of numerous diseases, which could lead to better treatments.

More than 400 scientists in 32 laboratories in the UK, US, Spain, Singapore and Japan were involved.

Their findings are published in 30 connected open-access papers appearing in three journals, Nature, Genome Biology and Genome Research.

The Encyclopedia of DNA Elements (Encode) was launched in 2003 with the goal of identifying all the functional elements within the human genome.

A pilot project looking at 1% of the genome was published in 2007.

Now the Encode project has analysed all three billion pairs of genetic code that make up our DNA.

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This will give researchers a whole new world to explore and ultimately, it’s hoped, will lead to new treatments.”

Dr Ewan Birney Encode

They have found 80% of our genome is performing a specific function.

Up to now, most attention has been focused on protein-coding genes, which make up just 2% of the genome.

Genes are small sections of DNA that contain instructions for which chemicals – proteins – they should produce.

The Encode team analysed the vast area of the genome sometimes called “junk DNA” because it seemed to have little function and was poorly understood.

Dr Ewan Birney, of the European Bioinformatics Institute in Cambridge, who led the analysis, told me: “The term junk DNA must now be junked.

“It’s clear from this research that a far bigger part of the genome is biologically active than was previously thought.”

Switches

The scientists also identified four million gene “switches”. These are sections of DNA that control when genes are switched on or off in cells.

They said the switches were often a long way along the genome from the gene they controlled.

Dr Birney said: “This will help in our understanding of human biology. Many of the switches we have identified are linked to changes in risk for conditions from heart disease to diabetes or mental illness. This will give researchers a whole new world to explore and ultimately, it’s hoped, will lead to new treatments.”

Scientists acknowledge that it is likely to be many years before patients see tangible benefits from the project.

But another of the Encode team, Dr Ian Dunham said the data could ultimately be of help in every area of disease research.

“Encode gives us a set of very valuable leads to follow to discover key mechanisms at play in health and disease. Those can be exploited to create entirely new medicines, or to repurpose existing treatments.”

Wellcome Trust Sanger Institute director Prof Mike Stratton said the results were “remarkable” and would “stand as a foundation stone for human biology for many years”.

He added: “The Encode project will change the way many researchers conduct their science and give those who seek to understand disease a much better grasp of where genetic variation can affect our genome for ill.”

Source: BBC