New announcement in Nature journal

05/09/2012

www.nature.com/nature
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VOL.489 NO.7414 DATED 06 SEPTEMBER 2012

EMBARGO:      
1800 London time (BST) / 1300 US Eastern Time Wednesday 05 September
0200 Japanese time / 0300 Australian Eastern Time Thursday 06 September
Wire services’ stories must always carry the embargo time at the head of each item, and may not be sent out more than 24 hours before that time.
Solely for the purpose of soliciting informed comment on Nature papers, you may show relevant parts of this document, and the papers to which it refers, to independent specialists – but you must ensure in advance that they understand and accept Nature’s embargo conditions.

Genomics: Describing biology’s dark matter (six papers pp 57-113; N&V)

Far from being junk, the vast majority of our DNA participates in at least one biochemical event in at least one cell type, according to the Encyclopedia of DNA Elements (ENCODE) project. Their mapping of regions of transcription, transcription factor association, chromatin structure and histone modification is published in six papers in Nature this week, along with twenty-four associated papers in two other journals – Genome Research and Genome Biology.

In the overview paper in Nature, the consortium guides readers through the project itself, the data and their integrated analyses. They show that 80% of the human genome has at least one biochemical activity assigned to it. In addition, most of the genome lies close to a regulatory event: with 95% of the genome within 8 kilobases (kb) of a DNA–protein interaction, and 99% within 1.7 kb of at least one of the biochemical events measured by ENCODE.
As well as expanding our understanding of how gene expression is regulated on a genome-wide scale, the newly identified functional elements should help the interpretation of results of genome-wide association studies (GWAS). Single nucleotide polymorphisms (SNPs) associated with disease in these studies are enriched within non-coding functional elements, most residing in or near ENCODE-defined regions that are outside of protein-coding genes.


To maximize the exploration of the wealth of information contained within the thirty papers across three publishing houses, the consortium has developed a new concept, the ‘Threads’ — each one is dedicated to a theme that runs through the papers, linking information on a given topic. Nature Publishing Group has developed an innovative online publishing platform and iPad app to showcase the complex relationships among the Threads and the papers. The research will be freely available to all.

In a related News and Views article, six academics discuss what the research means for the community.

CONTACT
Ewan Birney (European Bioinformatics Institute, Hinxton, UK)
Tel: +44 1223 494420; E-mail: birney@ebi.ac.uk

John A. Stamatoyannopoulos (University of Washington, Seattle, WA, USA)
Tel: +1 206 267 1098; E-mail: stam@uw.edu

Mark B. Gerstein Yale University, New Haven, CT, USA
Tel: + 1 203 432 8189; E-mail: mark.gerstein@yale.edu

Thomas R. Gingeras (Cold Spring Harbor Laboratory, New York, NY, USA)
Tel: +1 516 422 4105; E-mail: gingeras@cshl.edu

Job Dekker (University of Massachusetts Medical School, Worcester, MA, USA)
Tel: + 1 508 856 4371; E-mail: job.dekker@umassmed.edu

***Please note: A press conference will take place under embargo at the Science Museum’s Who Am I gallery in the Wellcome Wing on Wednesday 05 September at 12.00 London time.***

Ewan Birney, Roderic Guigo and Tim Hubbard will speak about the research followed by questions from reporters. There will also be an aerial silk dance spectacle performed to illustrate some of the gene stories in the research.

There will not be a dial in facility for this briefing. For more information please contact Ruth Francis: r.francis@nature.com

***The Science Museum will open a new free display that radically changes our understanding of genetics and sense of human identity. Switch to a different you? takes a closer look at ground-breaking research that reveals the hidden ‘switches’ that turn our genes on and off. The display case, featuring a number of objects and case studies relating to identical twins and potential new treatments, will be on display in the Who Am I? gallery from 6 Sept – 5 Dec 2012. Members of the public are invited to witness an aerial silk spectacle – the Dance of DNA – specially created for the launch at 1.30pm on 06 September.***


***A press conference call will take place under strict embargo at 15.00 London / 10:00 AM EST, Wednesday September 5th, 2012 with Eric Green, Rick Myers, Ewan Birney, John Stamatoyannopoulos and Mike Snyder***
Conference ID: ENCODE
Participant dial in: +1 785 424 1052


News and Comment: Lessons for big-data projects (pp 45-51)
  
In a Comment piece in this week’s Nature, lead analysis coordinator Ewan Birney reflects on his personal experience at the centre of this monumental effort, and on the lessons that ENCODE holds for other big-data projects. “I am proud of what we have delivered, but there are things we could have done better,” he admits. To be successful, Birney advises, “consortia need clear management, codes of conduct and participants who are committed to working for the common good”.


Importantly, collaborators need to change their mindset, says Birney -- typically, scientists work with a handful of collaborators to try to do what's best for science, their own careers and laboratories. This doesn't work in consortium science. Instead, participants have to try to make the best data set they can for other people to use. "Maybe the creators will use the data, maybe they won't. What's important is the use of the community resource, not individual success. This requires a shift in perspective to a common goal of data output rather than publications."
An associated News Feature investigates how much more information the human genome may hold, and how scientists are approaching the amount of data with which they are faced. An infographic in the issue summarizes ENCODE in numbers.
CONTACT
Ewan Birney (European Bioinformatics Institute, Hinxton, UK)
Tel: +44 1223 494420; E-mail: birney@ebi.ac.uk

For further information please contact the Nature press office: press@nature.com


PRESS CONTACTS…

From North America and Canada
Neda Afsarmanesh, Nature New York
Tel: +1 212 726 9231; E-mail: n.afsarmanesh@us.nature.com

From Japan, Korea, China, Singapore and Taiwan
Eiji Matsuda, Nature Tokyo
Tel: +81 3 3267 8751; E-mail: e.matsuda@natureasia.com

From the UK
Rebecca Walton, Nature London
Tel: +44 20 7843 4502; E-mail: r.walton@nature.com

Notes to Editors

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