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The EMBO Journal

Cover image for Vol. 30 Issue 22

November 16, 2011

Volume 30, Issue 22

Pages 4517–4691

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      Autophagy regulation by miRNAs: when cleaning goes out of service (pages 4517–4519)

      Francesco Cecconi

      Version of Record online: 16 NOV 2011 | DOI: 10.1038/emboj.2011.387

      Autophagy, the process of cellular self-digestion, is intricately controlled and defective regulation leads to multiple diseases. A study in this issue adds the tumour suppressor and inhibitor of autophagy miR-101 to the roster of regulatory mechanisms and identifies STMN1, RAB5A and ATG4D as targets functioning in autophagy.

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      When zip codes are in short supply (pages 4520–4522)

      Rotem Ben-Tov Perry and Mike Fainzilber

      Version of Record online: 16 NOV 2011 | DOI: 10.1038/emboj.2011.389

      The RNA-binding protein ZBP1 promotes the transport of regeneration-associated axonal mRNAs, and is a limiting and essential factor for adult axonal regeneration in vivo.

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      A kinesin-1 binding motif in vaccinia virus that is widespread throughout the human genome (pages 4523–4538)

      Mark P Dodding, Richard Mitter, Ashley C Humphries and Michael Way

      Version of Record online: 13 SEP 2011 | DOI: 10.1038/emboj.2011.326

      This study identifies a kinesin light chain binding motif, first analysed in a vaccinia virus protein, and subsequently found by bioinformatics in a large number of human proteins—several of which are shown to represent novel KLC interacting proteins.

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      Integrin adhesion and force coupling are independently regulated by localized PtdIns(4,5)2 synthesis (pages 4539–4553)

      Kyle R Legate, Seiichiro Takahashi, Navid Bonakdar, Ben Fabry, David Boettiger, Roy Zent and Reinhard Fässler

      Version of Record online: 16 SEP 2011 | DOI: 10.1038/emboj.2011.332

      Focal adhesion (FA) formation is regulated by the phosphoinositide lipid PI(4,5)P2. Here, genetic ablation of the FA-localized PIP kinase PIPKIγ reveals the critical importance of localized PI(4,5)P2 synthesis for integrin-mediated adhesion and force coupling to the actin cytoskeleton.

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      FoxO3A promotes metabolic adaptation to hypoxia by antagonizing Myc function (pages 4554–4570)

      Kim Steen Jensen, Tina Binderup, Klaus Thorleif Jensen, Ib Therkelsen, Rehannah Borup, Elise Nilsson, Hinke Multhaupt, Caroline Bouchard, Bjørn Quistorff, Andreas Kjær, Göran Landberg and Peter Staller

      Version of Record online: 13 SEP 2011 | DOI: 10.1038/emboj.2011.323

      This paper characterizes FoxO3A as required for hypoxic suppression of mitochondrial mass, oxygen consumption, and ROS production. Mechanistically, FoxO3A is shown to promote hypoxic cell survival by directly antagonizing c-Myc at nuclear encoded mitochondrial genes.

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      IRF6 is a mediator of Notch pro-differentiation and tumour suppressive function in keratinocytes (pages 4571–4585)

      Gaetana Restivo, Bach-Cuc Nguyen, Piotr Dziunycz, Elodie Ristorcelli, Russell J H Ryan, Özden Yalçin Özuysal, Matteo Di Piazza, Freddy Radtke, Michael J Dixon, Günther F L Hofbauer, Karine Lefort and G Paolo Dotto

      Version of Record online: 9 SEP 2011 | DOI: 10.1038/emboj.2011.325

      Using molecular and genetic approaches, this study identifies the interferon regulatory factor 6 (IRF6) as an essential and direct mediator of Notch/CSL pro-differentiation and tumour suppressive functions in keratinocytes.

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      Jarid1b targets genes regulating development and is involved in neural differentiation (pages 4586–4600)

      Sandra U Schmitz, Mareike Albert, Martina Malatesta, Lluis Morey, Jens V Johansen, Mads Bak, Niels Tommerup, Iratxe Abarrategui and Kristian Helin

      Version of Record online: 21 OCT 2011 | DOI: 10.1038/emboj.2011.383

      The histone demethylase Jarid1b (Kdm5b/Plu1) removes H3K4 dimethyl and trimethyl marks from chromatin. Here, Jarid1b is shown to be dispensable for embryonic stem cell (ESC) self-renewal but required for silencing of stem and germ cell genes during neuronal differentiation of ESC.

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      The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline (pages 4601–4615)

      Attilio Pane, Peng Jiang, Dorothy Yanling Zhao, Mona Singh and Trudi Schüpbach

      Version of Record online: 27 SEP 2011 | DOI: 10.1038/emboj.2011.334

      The identity and function of many factors involved in the piRNA pathway remain unknown. Here, in Drosophila, cutoff plays a role in regulating piRNA cluster transcript levels and biogenesis together with the heterochromatin protein Rhino.

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      Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference (pages 4616–4627)

      Natalia Beloglazova, Pierre Petit, Robert Flick, Greg Brown, Alexei Savchenko and Alexander F Yakunin

      Version of Record online: 18 OCT 2011 | DOI: 10.1038/emboj.2011.377

      Cas3 is an essential protein required for CRISPR-based bacteriophage immunity in bacteria. This study describes the structure, biochemical activity, and catalytic mechanism of Cas3.

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      microRNA-101 is a potent inhibitor of autophagy (pages 4628–4641)

      Lisa B Frankel, Jiayu Wen, Michael Lees, Maria Høyer-Hansen, Thomas Farkas, Anders Krogh, Marja Jäättelä and Anders H Lund

      Version of Record online: 13 SEP 2011 | DOI: 10.1038/emboj.2011.331

      Regulation of autophagy is of fundamental importance to the cell. This study identifies miR-101 as key negative regulator of autophagy and STMN1, RAB5A and ATG4D as relevant targets.

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      Temporal orchestration of circadian autophagy rhythm by C/EBPβ (pages 4642–4651)

      Di Ma, Satchidananda Panda and Jiandie D Lin

      Version of Record online: 6 SEP 2011 | DOI: 10.1038/emboj.2011.322

      This study reveals that C/EBPβ expression is regulated by the circadian clock and feeding/fasting rhythms. C/EBPβ regulates the transcription of autophagy-related genes and its circadian expression underlies the rhythmic regulation of autophagy in mouse liver.

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      Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1 (pages 4652–4664)

      Thorsten Althoff, Deryck J Mills, Jean-Luc Popot and Werner Kühlbrandt

      Version of Record online: 9 SEP 2011 | DOI: 10.1038/emboj.2011.324

      The respiratory chain complexes of the mitochondrial inner membrane are organized as three higher-order multi-enzyme complexes. This study puts forward the first cryo-EM map for one of these supercomplexes and provides insight into possible pathways for efficient electron transfer.

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      Limited availability of ZBP1 restricts axonal mRNA localization and nerve regeneration capacity (pages 4665–4677)

      Christopher J Donnelly, Dianna E Willis, Mei Xu, Chhavy Tep, Chunsu Jiang, Soonmoon Yoo, N Carolyn Schanen, Catherine B Kirn-Safran, Jan van Minnen, Arthur English, Sung Ok Yoon, Gary J Bassell and Jeffery L Twiss

      Version of Record online: 30 SEP 2011 | DOI: 10.1038/emboj.2011.347

      This study looks at the contributions of RNA localization and local translation to axon growth and regeneration. Axonal transport of β-actin and GAP-43 mRNAs and axonal regeneration are determined by the availability of the RNA binding protein, ZBP1.

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      Obesity resistance and increased hepatic expression of catabolism-related mRNAs in Cnot3+/− mice (pages 4678–4691)

      Masahiro Morita, Yuichi Oike, Takeshi Nagashima, Tsuyoshi Kadomatsu, Mitsuhisa Tabata, Toru Suzuki, Takahisa Nakamura, Nobuaki Yoshida, Mariko Okada and Tadashi Yamamoto

      Version of Record online: 6 SEP 2011 | DOI: 10.1038/emboj.2011.320

      This paper identifies the CNOT3 subunit of the CCR4–NOT deadenylase complex as the first molecular sensor to integrate cellular energy metabolism and specific mRNA processing.