Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Massive DNA encyclopedia scraps the junk

06.09.2012
Fast forward for biomedical research

Today, an international team of researchers reveal that much of what has been called ‘junk DNA’ in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes.

Without these switches, genes would not work – and mutations in these regions might lead to human disease. Discovered by hundreds of scientists working on the ENCODE Project, the new information is so comprehensive and complex that it has given rise to a new publishing model in which electronic documents and datasets are interconnected.

Just as the Human Genome Project revolutionised biomedical research, ENCODE will drive new understanding and open new avenues for biomedical science. Led by the National Genome Research Institute (NHGRI) in the US and the EMBL-European Bioinformatics Institute (EMBL-EBI) in the UK, ENCODE now presents a detailed map of genome function that identifies 4 million gene ‘switches’. This essential reference will help researchers pinpoint very specific areas of research for human disease. The findings are published in 30 connected, open-access papers appearing in three science journals: Nature, Genome Biology and Genome Research.

“Our genome is simply alive with switches: millions of places that determine whether a gene is switched on or off,” says Ewan Birney of EMBL-EBI, lead analysis coordinator for ENCODE. “The Human Genome Project showed that only 2% of the genome contains genes, the instructions to make proteins. With ENCODE, we can see that around 80% of the genome is actively doing something. We found that a much bigger part of the genome – a surprising amount, in fact – is involved in controlling when and where proteins are produced, than in simply manufacturing the building blocks.”

“ENCODE data can be used by any disease researcher, whatever pathology they may be interested in,” said Ian Dunham of EMBL-EBI, who played a key role in coordinating the analysis. “In many cases you may have a good idea of which genes are involved in your disease, but you might not know which switches are involved. Sometimes these switches are very surprising, because their location might seem more logically connected to a completely different disease. 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.”

“ENCODE gives us the knowledge we need to look beyond the linear structure of the genome to how the whole network is connected,” commented Dr Michael Snyder, professor and chair at Stanford University and a principal investigator on ENCODE. “We are beginning to understand the information generated in genome-wide association studies – not just where certain genes are located, but which sequences control them. Because of the complex, three-dimensional shape of our genome, those controls are sometimes far from the gene they regulate and looping around to make contact. Were it not for ENCODE, we might never have looked in those regions. This is a major step toward understanding the wiring diagram of a human being. ENCODE helps us look deeply into the regulatory circuit that tells us how all of the parts come together to make a complex being.”

Until recently, generating and storing large volumes of data has been a challenge in biomedical research. Now, with the falling cost and rising productivity of genome sequencing, the focus has shifted to analysis – making sense of the data produced in genome-wide association studies. ENCODE partners have been working systematically through the human genome, using the same computational and wet-lab methods and reagents in laboratories distributed throughout the world.

To give some sense of the scale of the project: ENCODE combined the efforts of 442 scientists in 32 labs in the UK, US, Spain, Singapore and Japan. They generated and analysed over 15 terabytes (15 trillion bytes) of raw data – all of which is now publicly available. The study used around 300 years’ worth of computer time studying 147 tissue types to determine what turns specific genes on and off, and how that ‘switch’ differs between cell types.

The articles published today represent hundreds of pages of research. But the digital publishing group at Nature recognises that ‘pages’ are a thing of the past. All of the published ENCODE content, in all three journals, is connected digitally through topical ‘threads’, so that readers can follow their area of interest between papers and all the way down to the original data.

“Getting the best people with the best expertise together is what this is all about,” said Ewan Birney. “ENCODE has really shown that leading life scientists are very good at collaborating closely on a large scale to produce excellent foundational resources that the whole community can use.”

“Until now, everyone’s been generating and publishing this data piecemeal and unintentionally trapping it in niche communities and static publications. How could anyone outside that community exploit that knowledge if they don’t know it’s there?” commented Roderic Guigo of the Centre de Regulació Genómica (CRG) in Barcelona, Spain. “We have now an interactive encyclopaedia that everyone can refer to, and that will make a huge difference.”

Published online in Nature, Genome Biology and Genome Research on 6 September 2012.

Policy regarding use

EMBL press and picture releases including photographs, graphics and videos are copyrighted by EMBL. They may be freely reprinted and distributed for non-commercial use via print, broadcast and electronic media, provided that proper attribution to authors, photographers and designers is made.

Contacts:
contactpress@ebi.ac.uk
Mary Todd-Bergman
EMBL-EBI Outreach Programme Project Leader
Hinxton, UK
Tel: +44 1223 494665
mary@ebi.ac.uk
www.ebi.ac.uk
Sonia Furtado Neves
EMBL Press Officer
Meyerhofstr. 1, 69117 Heidelberg, Germany
Tel.: +49 (0)6221 387 8263
Fax: +49 (0)6221 387 8525
sonia.furtado@embl.de
www.embl.org
Keep up-to-date with EMBL Research News at: www.embl.org/news
Contact Français:
Isabelle Kling,
Chef de projet EMBL
Meyerhofstr. 1, 69117 Heidelberg, Germany
Tel.: +49 (0)6221 387 8355
isabelle.kling@embl.de

Sonia Furtado Neves | EMBL Research News
Further information:
http://www.embl.org

More articles from Life Sciences:

nachricht Closing in on advanced prostate cancer
13.12.2017 | Institute for Research in Biomedicine (IRB Barcelona)

nachricht Visualizing single molecules in whole cells with a new spin
13.12.2017 | Wyss Institute for Biologically Inspired Engineering at Harvard

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Long-lived storage of a photonic qubit for worldwide teleportation

MPQ scientists achieve long storage times for photonic quantum bits which break the lower bound for direct teleportation in a global quantum network.

Concerning the development of quantum memories for the realization of global quantum networks, scientists of the Quantum Dynamics Division led by Professor...

Im Focus: Electromagnetic water cloak eliminates drag and wake

Detailed calculations show water cloaks are feasible with today's technology

Researchers have developed a water cloaking concept based on electromagnetic forces that could eliminate an object's wake, greatly reducing its drag while...

Im Focus: Scientists channel graphene to understand filtration and ion transport into cells

Tiny pores at a cell's entryway act as miniature bouncers, letting in some electrically charged atoms--ions--but blocking others. Operating as exquisitely sensitive filters, these "ion channels" play a critical role in biological functions such as muscle contraction and the firing of brain cells.

To rapidly transport the right ions through the cell membrane, the tiny channels rely on a complex interplay between the ions and surrounding molecules,...

Im Focus: Towards data storage at the single molecule level

The miniaturization of the current technology of storage media is hindered by fundamental limits of quantum mechanics. A new approach consists in using so-called spin-crossover molecules as the smallest possible storage unit. Similar to normal hard drives, these special molecules can save information via their magnetic state. A research team from Kiel University has now managed to successfully place a new class of spin-crossover molecules onto a surface and to improve the molecule’s storage capacity. The storage density of conventional hard drives could therefore theoretically be increased by more than one hundred fold. The study has been published in the scientific journal Nano Letters.

Over the past few years, the building blocks of storage media have gotten ever smaller. But further miniaturization of the current technology is hindered by...

Im Focus: Successful Mechanical Testing of Nanowires

With innovative experiments, researchers at the Helmholtz-Zentrums Geesthacht and the Technical University Hamburg unravel why tiny metallic structures are extremely strong

Light-weight and simultaneously strong – porous metallic nanomaterials promise interesting applications as, for instance, for future aeroplanes with enhanced...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

See, understand and experience the work of the future

11.12.2017 | Event News

Innovative strategies to tackle parasitic worms

08.12.2017 | Event News

AKL’18: The opportunities and challenges of digitalization in the laser industry

07.12.2017 | Event News

 
Latest News

A whole-body approach to understanding chemosensory cells

13.12.2017 | Health and Medicine

Water without windows: Capturing water vapor inside an electron microscope

13.12.2017 | Physics and Astronomy

Cellular Self-Digestion Process Triggers Autoimmune Disease

13.12.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>