Table of Contents

Volume 509 Number 7502 pp533-656

29 May 2014

About the cover

More than a decade after publication of the draft human genome sequence, there is no direct equivalent for the human proteome. But in this issue of Nature two groups present mass spectrometry-based analysis of human tissues, body fluids and cells mapping the large majority of the human proteome. Akhilesh Pandey and colleagues identified 17,294 protein-coding genes and provide evidence of tissue- and cell-restricted proteins through expression profiling. They highlight the importance of proteogenomic analysis by identifying translated proteins from annotated pseudogenes, non-coding RNAs and untranslated regions. The data set is available on Bernhard Kuster and colleagues have assembled protein evidence for 18,097 genes in ProteomicsDB (available on and highlight the utility of the data, for example the identification of hundreds of translated lincRNAs, drug-sensitivity markers and discovering the quantitative relationship between mRNA and protein levels in tissues. Elsewhere in this issue, Vivien Marx reports on a third major proteomics project, the antibody-based Human Protein Atlas programme ( Cover: Nik Spencer/Nature

This Week



World View


Seven Days

  • Seven days: 23–29 May 2014

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News in Focus


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Books and Arts

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  • Variations

    The importance of a good education.

    • William Meikle


Technology Feature

  • Proteomics: An atlas of expression

    The first draft of the complete human proteome has been more than a decade in the making. In the process, the effort has also delivered lessons about technology and biology.

    • Vivien Marx



  • A draft map of the human proteome

    • Min-Sik Kim
    • Sneha M. Pinto
    • Derese Getnet
    • Raja Sekhar Nirujogi
    • Srikanth S. Manda
    • Raghothama Chaerkady
    • Anil K. Madugundu
    • Dhanashree S. Kelkar
    • Ruth Isserlin
    • Shobhit Jain
    • Joji K. Thomas
    • Babylakshmi Muthusamy
    • Pamela Leal-Rojas
    • Praveen Kumar
    • Nandini A. Sahasrabuddhe
    • Lavanya Balakrishnan
    • Jayshree Advani
    • Bijesh George
    • Santosh Renuse
    • Lakshmi Dhevi N. Selvan
    • Arun H. Patil
    • Vishalakshi Nanjappa
    • Aneesha Radhakrishnan
    • Samarjeet Prasad
    • Tejaswini Subbannayya
    • Rajesh Raju
    • Manish Kumar
    • Sreelakshmi K. Sreenivasamurthy
    • Arivusudar Marimuthu
    • Gajanan J. Sathe
    • Sandip Chavan
    • Keshava K. Datta
    • Yashwanth Subbannayya
    • Apeksha Sahu
    • Soujanya D. Yelamanchi
    • Savita Jayaram
    • Pavithra Rajagopalan
    • Jyoti Sharma
    • Krishna R. Murthy
    • Nazia Syed
    • Renu Goel
    • Aafaque A. Khan
    • Sartaj Ahmad
    • Gourav Dey
    • Keshav Mudgal
    • Aditi Chatterjee
    • Tai-Chung Huang
    • Jun Zhong
    • Xinyan Wu
    • Patrick G. Shaw
    • Donald Freed
    • Muhammad S. Zahari
    • Kanchan K. Mukherjee
    • Subramanian Shankar
    • Anita Mahadevan
    • Henry Lam
    • Christopher J. Mitchell
    • Susarla Krishna Shankar
    • Parthasarathy Satishchandra
    • John T. Schroeder
    • Ravi Sirdeshmukh
    • Anirban Maitra
    • Steven D. Leach
    • Charles G. Drake
    • Marc K. Halushka
    • T. S. Keshava Prasad
    • Ralph H. Hruban
    • Candace L. Kerr
    • Gary D. Bader
    • Christine A. Iacobuzio-Donahue
    • Harsha Gowda
    • Akhilesh Pandey

    A draft map of the human proteome is presented here, accounting for over 80% of the annotated protein-coding genes in humans; some novel protein-coding regions, including translated pseudogenes, non-coding RNAs and upstream open reading frames, are identified.

  • Mass-spectrometry-based draft of the human proteome

    • Mathias Wilhelm
    • Judith Schlegl
    • Hannes Hahne
    • Amin Moghaddas Gholami
    • Marcus Lieberenz
    • Mikhail M. Savitski
    • Emanuel Ziegler
    • Lars Butzmann
    • Siegfried Gessulat
    • Harald Marx
    • Toby Mathieson
    • Simone Lemeer
    • Karsten Schnatbaum
    • Ulf Reimer
    • Holger Wenschuh
    • Martin Mollenhauer
    • Julia Slotta-Huspenina
    • Joos-Hendrik Boese
    • Marcus Bantscheff
    • Anja Gerstmair
    • Franz Faerber
    • Bernhard Kuster

    A mass-spectrometry-based draft of the human proteome and a public database for analysis of proteome data are presented; assembled information is used to estimate the size of the protein-coding genome, to identify organ-specific proteins, proteins predicting drug resistance or sensitivity, and many translated long intergenic non-coding RNAs, and to reveal conserved control of protein abundance.

  • Structural basis of the non-coding RNA RsmZ acting as a protein sponge

    • Olivier Duss
    • Erich Michel
    • Maxim Yulikov
    • Mario Schubert
    • Gunnar Jeschke
    • Frédéric H.-T. Allain

    A novel combined NMR and EPR spectroscopy approach reveals the structure and assembly mechanism of a 70-kDa bacterial ribonucleoprotein complex acting as a protein sponge in translational regulation.


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    • William D. Cochran
    • Michael Endl
    • Howard Isaacson
    • Diana Juncher
    • Geoffrey W. Marcy

    Analysis of the metallicities of more than 400 stars hosting 600 candidate extrasolar planets shows that the planets can be categorized by size into three populations — terrestrial-like planets, gas dwarf planets with rocky cores and hydrogen–helium envelopes, and ice or gas giant planets — on the basis of host star metallicity.

  • Contribution of semi-arid ecosystems to interannual variability of the global carbon cycle

    • Benjamin Poulter
    • David Frank
    • Philippe Ciais
    • Ranga B. Myneni
    • Niels Andela
    • Jian Bi
    • Gregoire Broquet
    • Josep G. Canadell
    • Frederic Chevallier
    • Yi Y. Liu
    • Steven W. Running
    • Stephen Sitch
    • Guido R. van der Werf

    The unusually large land carbon sink reported in 2011 can mostly be attributed to semi-arid vegetation growth in the Southern Hemisphere following increased rainfall and long-term greening trends.

    See also
  • Storm-induced sea-ice breakup and the implications for ice extent

    • A. L. Kohout
    • M. J. M. Williams
    • S. M. Dean
    • M. H. Meylan

    Concurrent observations at multiple locations indicate that storm-generated ocean waves propagating through Antarctic sea ice can transport enough energy to break first-year sea ice hundreds of kilometres from the ice edge, which is much farther than would be predicted by the commonly assumed exponential wave decay.

  • A Palaeozoic shark with osteichthyan-like branchial arches

    • Alan Pradel
    • John G. Maisey
    • Paul Tafforeau
    • Royal H. Mapes
    • Jon Mallatt

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    • Srdjan Maksimovic
    • Masashi Nakatani
    • Yoshichika Baba
    • Aislyn M. Nelson
    • Kara L. Marshall
    • Scott A. Wellnitz
    • Pervez Firozi
    • Seung-Hyun Woo
    • Sanjeev Ranade
    • Ardem Patapoutian
    • Ellen A. Lumpkin

    The cellular basis of touch has long been debated, in particular the relationship between sensory neurons and non-neuronal cells; a mouse study uses optogenetics to identify their distinct and collaborative roles, with skin-derived Merkel cells both transducing touch and actively tuning responses of touch-sensitive neurons.

  • Piezo2 is required for Merkel-cell mechanotransduction

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    • Sanjeev Ranade
    • Andy D. Weyer
    • Adrienne E. Dubin
    • Yoshichika Baba
    • Zhaozhu Qiu
    • Matt Petrus
    • Takashi Miyamoto
    • Kritika Reddy
    • Ellen A. Lumpkin
    • Cheryl L. Stucky
    • Ardem Patapoutian

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  • Scalable control of mounting and attack by Esr1+ neurons in the ventromedial hypothalamus

    • Hyosang Lee
    • Dong-Wook Kim
    • Ryan Remedios
    • Todd E. Anthony
    • Angela Chang
    • Linda Madisen
    • Hongkui Zeng
    • David J. Anderson

    Activation of Esr1+ neurons of the mouse ventromedial hypothalamus initiates graded social behavioural responses–weak activation triggers close investigation (sniffing) during a social encounter that often leads, with continued stimulation, to mounting behaviours by males towards either gender; mounting behaviour transitions to aggressive attacks with greater stimulation intensity.

  • A single female-specific piRNA is the primary determiner of sex in the silkworm

    • Takashi Kiuchi
    • Hikaru Koga
    • Munetaka Kawamoto
    • Keisuke Shoji
    • Hiroki Sakai
    • Yuji Arai
    • Genki Ishihara
    • Shinpei Kawaoka
    • Sumio Sugano
    • Toru Shimada
    • Yutaka Suzuki
    • Masataka G. Suzuki
    • Susumu Katsuma

    It is known that in the silkworm (Bombyx mori), males have two Z sex chromosomes whereas females have Z and W and the W chromosome has a dominant role in female determination; here a single female-specific W-chromosome-derived PIWI-interacting RNA is shown to be the feminizing factor in B. mori.

    See also
  • Dichloroacetate prevents restenosis in preclinical animal models of vessel injury

    • Tobias Deuse
    • Xiaoqin Hua
    • Dong Wang
    • Lars Maegdefessel
    • Joerg Heeren
    • Ludger Scheja
    • Juan P. Bolaños
    • Aleksandar Rakovic
    • Joshua M. Spin
    • Mandy Stubbendorff
    • Fumiaki Ikeno
    • Florian Länger
    • Tanja Zeller
    • Leonie Schulte-Uentrop
    • Andrea Stoehr
    • Ryo Itagaki
    • Francois Haddad
    • Thomas Eschenhagen
    • Stefan Blankenberg
    • Rainer Kiefmann
    • Hermann Reichenspurner
    • Joachim Velden
    • Christine Klein
    • Alan Yeung
    • Robert C. Robbins
    • Philip S. Tsao
    • Sonja Schrepfer

    During development of myointimal hyperplasia in human arteries, smooth muscle cells have hyperpolarized mitochondrial membrane potential (ΔΨm), high proliferation and apoptosis resistance; PDK2 is a key regulatory protein whose activation is necessary for myointima formation, and its blockade with dichloroacetate prevents Δψm hyperpolarization, facilitates apoptosis and reduces myointima formation in injured arteries, without preventing vessel re-endothelialization, possibly representing a novel strategy to prevent proliferative vascular diseases.