Table of Contents

Japanese Table of Contents

Volume 489 Number 7414 pp5-170

6 September 2012

About the cover

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).

This Week


  • Accountable and transparent

    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.

  • Moonlight drive

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

World View

  • We must be open about our mistakes

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

Seven Days


News in Focus


  • ENCODE: The human encyclopaedia

    No Alt text available for this image

    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


Books and Arts

  • Architecture: Life in stone

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

    • Review of The Pinecone: The Story of Sarah Losh, Forgotten Romantic Heroine — Antiquarian, Architect and Visionary
      Jenny Uglow
  • Technology: Baroque geekery

    Tim Boon assesses a take on the evolving technology behind recordings of J. S. Bach.

    • Review of Reinventing Bach
      Paul Elie
  • Q&A: Maths demystifier

    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.






Career Briefs

  • Investment increases

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

  • Teachers lack resources

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

naturejobs job listings and advertising features


  • If only ...

    A taste of your own medicine.

    • Tony Ballantyne

News & Views



  • An integrated encyclopedia of DNA elements in the human genome OPEN

    • The ENCODE Project Consortium

    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.

    See also
  • The accessible chromatin landscape of the human genome OPEN

    • Robert E. Thurman
    • Eric Rynes
    • Richard Humbert
    • Jeff Vierstra
    • Matthew T. Maurano
    • Eric Haugen
    • Nathan C. Sheffield
    • Andrew B. Stergachis
    • Hao Wang
    • Benjamin Vernot
    • Kavita Garg
    • Sam John
    • Richard Sandstrom
    • Daniel Bates
    • Lisa Boatman
    • Theresa K. Canfield
    • Morgan Diegel
    • Douglas Dunn
    • Abigail K. Ebersol
    • Tristan Frum
    • Erika Giste
    • Audra K. Johnson
    • Ericka M. Johnson
    • Tanya Kutyavin
    • Bryan Lajoie
    • Bum-Kyu Lee
    • Kristen Lee
    • Darin London
    • Dimitra Lotakis
    • Shane Neph
    • Fidencio Neri
    • Eric D. Nguyen
    • Hongzhu Qu
    • Alex P. Reynolds
    • Vaughn Roach
    • Alexias Safi
    • Minerva E. Sanchez
    • Amartya Sanyal
    • Anthony Shafer
    • Jeremy M. Simon
    • Lingyun Song
    • Shinny Vong
    • Molly Weaver
    • Yongqi Yan
    • Zhancheng Zhang
    • Zhuzhu Zhang
    • Boris Lenhard
    • Muneesh Tewari
    • Michael O. Dorschner
    • R. Scott Hansen
    • Patrick A. Navas
    • George Stamatoyannopoulos
    • Vishwanath R. Iyer
    • Jason D. Lieb
    • Shamil R. Sunyaev
    • Joshua M. Akey
    • Peter J. Sabo
    • Rajinder Kaul
    • Terrence S. Furey
    • Job Dekker
    • Gregory E. Crawford
    • John A. Stamatoyannopoulos

    An extensive map of human DNaseI 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.

    See also
  • An expansive human regulatory lexicon encoded in transcription factor footprints OPEN

    • Shane Neph
    • Jeff Vierstra
    • Andrew B. Stergachis
    • Alex P. Reynolds
    • Eric Haugen
    • Benjamin Vernot
    • Robert E. Thurman
    • Sam John
    • Richard Sandstrom
    • Audra K. Johnson
    • Matthew T. Maurano
    • Richard Humbert
    • Eric Rynes
    • Hao Wang
    • Shinny Vong
    • Kristen Lee
    • Daniel Bates
    • Morgan Diegel
    • Vaughn Roach
    • Douglas Dunn
    • Jun Neri
    • Anthony Schafer
    • R. Scott Hansen
    • Tanya Kutyavin
    • Erika Giste
    • Molly Weaver
    • Theresa Canfield
    • Peter Sabo
    • Miaohua Zhang
    • Gayathri Balasundaram
    • Rachel Byron
    • Michael J. MacCoss
    • Joshua M. Akey
    • M. A. Bender
    • Mark Groudine
    • Rajinder Kaul
    • John A. Stamatoyannopoulos

    DNase I footprinting in 41 cell and tissue types reveals millions of short sequence elements encoding an expansive repertoire of conserved recognition sequences for DNA-binding proteins.

    See also
  • Architecture of the human regulatory network derived from ENCODE data OPEN

    • Mark B. Gerstein
    • Anshul Kundaje
    • Manoj Hariharan
    • Stephen G. Landt
    • Koon-Kiu Yan
    • Chao Cheng
    • Xinmeng Jasmine Mu
    • Ekta Khurana
    • Joel Rozowsky
    • Roger Alexander
    • Renqiang Min
    • Pedro Alves
    • Alexej Abyzov
    • Nick Addleman
    • Nitin Bhardwaj
    • Alan P. Boyle
    • Philip Cayting
    • Alexandra Charos
    • David Z. Chen
    • Yong Cheng
    • Declan Clarke
    • Catharine Eastman
    • Ghia Euskirchen
    • Seth Frietze
    • Yao Fu
    • Jason Gertz
    • Fabian Grubert
    • Arif Harmanci
    • Preti Jain
    • Maya Kasowski
    • Phil Lacroute
    • Jing Leng
    • Jin Lian
    • Hannah Monahan
    • Henriette O’Geen
    • Zhengqing Ouyang
    • E. Christopher Partridge
    • Dorrelyn Patacsil
    • Florencia Pauli
    • Debasish Raha
    • Lucia Ramirez
    • Timothy E. Reddy
    • Brian Reed
    • Minyi Shi
    • Teri Slifer
    • Jing Wang
    • Linfeng Wu
    • Xinqiong Yang
    • Kevin Y. Yip
    • Gili Zilberman-Schapira
    • Serafim Batzoglou
    • Arend Sidow
    • Peggy J. Farnham
    • Richard M. Myers
    • Sherman M. Weissman
    • Michael Snyder

    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.

    See also
  • Landscape of transcription in human cells OPEN

    • Sarah Djebali
    • Carrie A. Davis
    • Angelika Merkel
    • Alex Dobin
    • Timo Lassmann
    • Ali Mortazavi
    • Andrea Tanzer
    • Julien Lagarde
    • Wei Lin
    • Felix Schlesinger
    • Chenghai Xue
    • Georgi K. Marinov
    • Jainab Khatun
    • Brian A. Williams
    • Chris Zaleski
    • Joel Rozowsky
    • Maik Röder
    • Felix Kokocinski
    • Rehab F. Abdelhamid
    • Tyler Alioto
    • Igor Antoshechkin
    • Michael T. Baer
    • Nadav S. Bar
    • Philippe Batut
    • Kimberly Bell
    • Ian Bell
    • Sudipto Chakrabortty
    • Xian Chen
    • Jacqueline Chrast
    • Joao Curado
    • Thomas Derrien
    • Jorg Drenkow
    • Erica Dumais
    • Jacqueline Dumais
    • Radha Duttagupta
    • Emilie Falconnet
    • Meagan Fastuca
    • Kata Fejes-Toth
    • Pedro Ferreira
    • Sylvain Foissac
    • Melissa J. Fullwood
    • Hui Gao
    • David Gonzalez
    • Assaf Gordon
    • Harsha Gunawardena
    • Cedric Howald
    • Sonali Jha
    • Rory Johnson
    • Philipp Kapranov
    • Brandon King
    • Colin Kingswood
    • Oscar J. Luo
    • Eddie Park
    • Kimberly Persaud
    • Jonathan B. Preall
    • Paolo Ribeca
    • Brian Risk
    • Daniel Robyr
    • Michael Sammeth
    • Lorian Schaffer
    • Lei-Hoon See
    • Atif Shahab
    • Jorgen Skancke
    • Ana Maria Suzuki
    • Hazuki Takahashi
    • Hagen Tilgner
    • Diane Trout
    • Nathalie Walters
    • Huaien Wang
    • John Wrobel
    • Yanbao Yu
    • Xiaoan Ruan
    • Yoshihide Hayashizaki
    • Jennifer Harrow
    • Mark Gerstein
    • Tim Hubbard
    • Alexandre Reymond
    • Stylianos E. Antonarakis
    • Gregory Hannon
    • Morgan C. Giddings
    • Yijun Ruan
    • Barbara Wold
    • Piero Carninci
    • Roderic Guigó
    • Thomas R. Gingeras

    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.

    See also


  • The long-range interaction landscape of gene promoters OPEN

    • Amartya Sanyal
    • Bryan R. Lajoie
    • Gaurav Jain
    • Job Dekker

    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.

    See also




  • No meridional plasma flow in the heliosheath transition region

    • Robert B. Decker
    • Stamatios M. Krimigis
    • Edmond C. Roelof
    • Matthew E. Hill

    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 Voyager1 unexpectedly finds that the deflected, meridional, flow is consistent with zero within the transition region.

  • Highly stretchable and tough hydrogels

    • Jeong-Yun Sun
    • Xuanhe Zhao
    • Widusha R. K. Illeperuma
    • Ovijit Chaudhuri
    • Kyu Hwan Oh
    • David J. Mooney
    • Joost J. Vlassak
    • Zhigang Suo

    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.

    See also
  • Activation of old carbon by erosion of coastal and subsea permafrost in Arctic Siberia

    • J. E. Vonk
    • L. Sánchez-García
    • B. E. van Dongen
    • V. Alling
    • D. Kosmach
    • A. Charkin
    • I. P. Semiletov
    • O. V. Dudarev
    • N. Shakhova
    • P. Roos
    • T. I. Eglinton
    • A. Andersson
    • Ö. Gustafsson

    Extensive release of carbon from coastal permafrost is found to dominate the sedimentary carbon budget of the world’s largest continental shelf, with about two-thirds of this old carbon escaping to the atmosphere as carbon dioxide.

  • Recent Antarctic Peninsula warming relative to Holocene climate and ice-shelf history

    • Robert Mulvaney
    • Nerilie J. Abram
    • Richard C. A. Hindmarsh
    • Carol Arrowsmith
    • Louise Fleet
    • Jack Triest
    • Louise C. Sime
    • Olivier Alemany
    • Susan Foord

    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.

    See also
  • Dopamine neurons modulate pheromone responses in Drosophila courtship learning

    • Krystyna Keleman
    • Eleftheria Vrontou
    • Sebastian Krüttner
    • Jai Y. Yu
    • Amina Kurtovic-Kozaric
    • Barry J. Dickson

    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.

    See also
  • Heterodimeric JAK–STAT activation as a mechanism of persistence to JAK2 inhibitor therapy

    • Priya Koppikar
    • Neha Bhagwat
    • Outi Kilpivaara
    • Taghi Manshouri
    • Mazhar Adli
    • Todd Hricik
    • Fan Liu
    • Lindsay M. Saunders
    • Ann Mullally
    • Omar Abdel-Wahab
    • Laura Leung
    • Abby Weinstein
    • Sachie Marubayashi
    • Aviva Goel
    • Mithat Gönen
    • Zeev Estrov
    • Benjamin L. Ebert
    • Gabriela Chiosis
    • Stephen D. Nimer
    • Bradley E. Bernstein
    • Srdan Verstovsek
    • Ross L. Levine

    Chronic exposure to JAK2 inhibitors leads to reactivation of downstream signalling through the formation of heterodimers between JAK2 and other JAK kinases in myeloproliferative neoplasms, which can be overcome with Hsp90 inhibitors.

  • Endogenous antigen tunes the responsiveness of naive B cells but not T cells

    • Julie Zikherman
    • Ramya Parameswaran
    • Arthur Weiss

    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.