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Volume 489 Issue 7414, 6 September 2012

The ENCODE (Encyclopedia of DNA Elements) project aims to describe all functional elements encoded in the human genome. Nine years on from ENCODE's launch, its main efforts culminate this week in the coordinated publication of 30 papers, 6 of them in this issue of Nature. It has been a major undertaking and some of the lessons learned in setting it up could prove of value to others contemplating international collaboration. In a Comment piece, Ewan Birney, lead ENCODE analysis coordinator, explains how they did it. Cover by Carl DeTorres; Voyager image, NASA).

Editorial

  • The US government has changed how biomedical scientists disclose their financial interests. The revised rules are welcome, but Internet access to the identified conflicts should be a requirement.

    Editorial

    Advertisement

  • Publication of ENCODE data drives innovation in data mining.

    Editorial
  • The data from the ageing Voyager probes are illuminating the edge of the Solar System.

    Editorial
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World View

  • Greater transparency about the scientific process and a closer focus on correcting defective data are the way forward, says Jim Woodgett.

    • Jim Woodgett
    World View
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Research Highlights

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Seven Days

  • The week in science: arXiv finds fresh funding; hantavirus outbreak surprises experts; and Australia says it will join Europe’s emissions trading system.

    Seven Days
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News

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Correction

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News Feature

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Comment

  • The US Environmental Protection Agency needs to speed up its risk analyses and address uncertainty, say George M. Gray and Joshua T. Cohen.

    • George M. Gray
    • Joshua T. Cohen
    Comment
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Books & Arts

  • Georgina Ferry enjoys a biography of a little-known Victorian woman who built monuments to nature.

    • Georgina Ferry
    Books & Arts
  • Tim Boon assesses a take on the evolving technology behind recordings of J. S. Bach.

    • Tim Boon
    Books & Arts
  • Mathematician Glen Whitney left a job in finance to set up the Museum of Mathematics (MoMath), which is due to open in Manhattan, New York, on 15 December. He wants to spread the word that mathematics is a beautiful discipline and all around us, from the geometry of soap bubbles to the algorithms that control traffic lights.

    • Jascha Hoffman
    Books & Arts
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Correspondence

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Obituary

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News & Views

  • Hydrogels have many potential applications, but their mechanical strength is low. By simultaneously crosslinking two kinds of polymers in different ways, a highly fracture-resistant hydrogel has been made. See Letter p.133

    • Kenneth R. Shull
    News & Views
  • The theory that predicts how the lightest elements formed after the Big Bang has hitherto failed to explain the amount of cosmic lithium. The detection of interstellar lithium beyond the Milky Way gives this theory a boost. See Article p.121

    • Garik Israelian
    News & Views
  • Male fruitflies quickly learn that courting already-mated females is useless. It turns out that a small subset of neurons in the male brain signals this negative experience and controls pheromone sensitivity. See Letter p.145

    • Aki Ejima
    News & Views
  • A temperature record derived from measurements of an ice core drilled on James Ross Island, Antarctica, prompts a rethink of what has triggered the recent warming trends on the Antarctic Peninsula. See Letter p.141

    • Eric J. Steig
    News & Views
  • Membranes have been made that are hygro-responsive — their wetting properties change when immersed in water. This striking property allows the membrane to separate emulsions into their oil and water constituents.

    • Robert W. Field
    News & Views
  • Black holes are best known for pulling matter in. But a distant supermassive black hole, observed as it was when the Universe was less than a billion years old, has been seen pushing gas out of its host galaxy.

    • Daniel Mortlock
    News & Views
  • The mechanistic details of the attachment of a small protein, ubiquitin, to other proteins are unclear. Crystal structures of the complexes formed by the E2–ubiquitin and RING E3 enzymes offer new insights. See Article p.115

    • Christopher D. Lima
    • Brenda A. Schulman
    News & Views
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Introduction

    • Magdalena Skipper
    • Ritu Dhand
    • Philip Campbell
    Introduction
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News Feature

  • First they sequenced it. Now they have surveyed its hinterlands. But no one knows how much more information the human genome holds, or when to stop looking for it.

    • Brendan Maher

    Collection:

    News Feature
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Comment

  • To be successful, consortia need clear management, codes of conduct and participants who are committed to working for the common good, says ENCODE lead analysis coordinator Ewan Birney.

    • Ewan Birney

    Collection:

    Comment
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News & Views Forum

  • The Encyclopedia of DNA Elements (ENCODE) project dishes up a hearty banquet of data that illuminate the roles of the functional elements of the human genome. Here, six scientists describe the project and discuss how the data are influencing research directions across many fields. See Articles p.57, p.75, p.83, p.91, p.101 & Letter p.109

    • Joseph R. Ecker
    • Wendy A. Bickmore
    • Eran Segal

    Collection:

    News & Views Forum
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News & Views

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Article

  • This overview of the ENCODE project outlines the data accumulated so far, revealing that 80% of the human genome now has at least one biochemical function assigned to it; the newly identified functional elements should aid the interpretation of results of genome-wide association studies, as many correspond to sites of association with human disease.

    • Ian Dunham
    • Anshul Kundaje
    • Ewan Birney

    Collection:

    Article Open Access
  • An extensive map of human DNase I hypersensitive sites, markers of regulatory DNA, in 125 diverse cell and tissue types is described; integration of this information with other ENCODE-generated data sets identifies new relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns.

    • Robert E. Thurman
    • Eric Rynes
    • John A. Stamatoyannopoulos

    Collection:

    Article Open Access
  • A description is given of the ENCODE consortium’s efforts to examine the principles of human transcriptional regulatory networks; the results are integrated with other genomic information to form a hierarchical meta-network where different levels have distinct properties.

    • Mark B. Gerstein
    • Anshul Kundaje
    • Michael Snyder

    Collection:

    Article Open Access
  • A description is given of the ENCODE effort to provide a complete catalogue of primary and processed RNAs found either in specific subcellular compartments or throughout the cell, revealing that three-quarters of the human genome can be transcribed, and providing a wealth of information on the range and levels of expression, localization, processing fates and modifications of known and previously unannotated RNAs.

    • Sarah Djebali
    • Carrie A. Davis
    • Thomas R. Gingeras

    Collection:

    Article Open Access
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Letter

  • Chromosome conformation capture carbon copy (5C) is used to look at the relationships between functional elements and distal target genes in 1% of the human genome in three dimensions; the study describes numerous long-range interactions between promoters and distal sites that include elements resembling enhancers, promoters and CTCF-bound sites, their genomic distribution and complex interactions.

    • Amartya Sanyal
    • Bryan R. Lajoie
    • Job Dekker

    Collection:

    Letter Open Access
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Article

  • This study presents the crystal structure of a RING-type E3 ligase bound to ubiquitin-loaded E2; the structure reveals how ubiquitin binding to E2 leads to changes in the catalytic site, priming it for catalysis by the E3 enzyme.

    • Anna Plechanovová
    • Ellis G. Jaffray
    • Ronald T. Hay
    Article
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Letter

  • The radially outward flow of plasma from the Sun is expected to be deflected when it meets the flow of interstellar plasma through which the Solar System moves, but the spacecraft Voyager 1 unexpectedly finds that the deflected, meridional, flow is consistent with zero within the transition region.

    • Robert B. Decker
    • Stamatios M. Krimigis
    • Matthew E. Hill
    Letter
  • Hydrogels with improved mechanical properties, made by combining polymer networks with ionic and covalent crosslinks, should expand the scope of applications, and may serve as model systems to explore mechanisms of deformation and energy dissipation.

    • Jeong-Yun Sun
    • Xuanhe Zhao
    • Zhigang Suo
    Letter
  • An ice-core record from the northeastern Antarctic Peninsula shows that the present warming period in the region is unusual in the context of natural climate variability over the past two thousand years, and that continued warming could cause ice-shelf instability farther south along the peninsula.

    • Robert Mulvaney
    • Nerilie J. Abram
    • Susan Foord
    Letter
  • Young male fruitflies learn to avoid futile courtship of non-virgin females because the latter are scented with the male pheromone cis-vaccenyl acetate; this behaviour results from an increase in the males’ innate sensitivity for the pheromone and is controlled by a small set of dopaminergic neurons.

    • Krystyna Keleman
    • Eleftheria Vrontou
    • Barry J. Dickson
    Letter
  • Mature B cells encounter antigens during development that induce anergy or functional unresponsiveness; this large reservoir of dormant autoreactive B cells may serve as a pool of extended antibody specificity for purposes of protective immunity, as well as the source of pathogenic autoantibodies that characterize rheumatic diseases such as systemic lupus erythematosus.

    • Julie Zikherman
    • Ramya Parameswaran
    • Arthur Weiss
    Letter
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Feature

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Career Brief

  • Growth in research spending among European businesses could prompt recruitment in developing nations.

    Career Brief
  • Restrictions among non-tenure-track faculty members impair students' educational experience.

    Career Brief
  • Novice entrepreneurs build business skills best when they trust their mentors.

    Career Brief
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Futures

  • A taste of your own medicine.

    • Tony Ballantyne
    Futures
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