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| |  | TABLE OF CONTENTS
| April 2013 Volume 20, Issue 4 |  | | |  |  News and Views
Research Highlights
Review
Articles
Technical Report
| | | | | | | Advertisement | | Nature Structural & Molecular Biology
FOCUS ON EPIGENETIC DYNAMICS
This Focus explores emerging themes and the functional implications of epigenetic dynamics.
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| | | | News and Views |  Top | |  | | | | Review | Top | | | | Transcription-replication encounters, consequences and genomic instability pp412 - 418
Anne Helmrich, Monica Ballarino, Evgeny Nudler and Laszlo Tora
doi:10.1038/nsmb.2543
To ensure replication success, DNA polymerases must negotiate encounters with actively transcribing RNA polymerases that share the genome. This Review highlights the strategies used by prokaryotic and eukaryotic cells to minimize the consequences of collisions between replication forks and transcription complexes to effect faithful DNA replication without compromising gene expression.
| | Articles | Top | | | | Crystal structure of oligomeric β1-adrenergic G protein–coupled receptors in ligand-free basal state pp419 - 425
Jianyun Huang, Shuai Chen, J Jillian Zhang and Xin-Yun Huang
doi:10.1038/nsmb.2504
G protein–coupled receptors (GPCRs) mediate transmembrane signaling. The crystal structure of β1-adrenergic receptor in its ligand-free, basal state is now presented. The structure reveals an inactive conformation with two alternating dimer interfaces.
| | | | Evidence for monomeric actin function in INO80 chromatin remodeling pp426 - 432
Prabodh Kapoor, Mingming Chen, Duane David Winkler, Karolin Luger and Xuetong Shen
doi:10.1038/nsmb.2529
While the cytoplasmic functions of actin are well established, its nuclear roles remain poorly understood. Genetic and biochemical analyses of the nuclear actin-containing yeast INO80 chromatin-remodeling complex now demonstrate that actin functions as a monomer in the nucleus and contributes to INO80 remodeling activity, suggesting a mechanism fundamentally different from that of cytoplasmic actin.
See also: News and Views by Bartholomew
| | | | Atg12–Atg5 conjugate enhances E2 activity of Atg3 by rearranging its catalytic site pp433 - 439
Machiko Sakoh-Nakatogawa, Kazuaki Matoba, Eri Asai, Hiromi Kirisako, Junko Ishii, Nobuo N Noda, Fuyuhiko Inagaki, Hitoshi Nakatogawa and Yoshinori Ohsumi
doi:10.1038/nsmb.2527
In the yeast autophagy system, the Atg12–Atg5 conjugate acts as an E3 to promote the E2 activity of Atg3, which conjugates Atg8 to phosphatidylethanolamine. Now structural and biochemical analyses reveal that Atg12–Atg5 induces a rearrangement in the catalytic center of Atg3, which employs a threonine residue in addition to the active cysteine to catalyze the conjugation reaction.
| | | | A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells pp440 - 446
Per Johnsson, Amanda Ackley, Linda Vidarsdottir, Weng-Onn Lui, Martin Corcoran, Dan Grandér and Kevin V Morris
doi:10.1038/nsmb.2516
The PTEN tumor-suppressor gene is regulated by the PTENpg1 long noncoding RNA. A new study investigating a previously uncharacterized PTENpg1-encoded antisense RNA (asRNA) now reveals that the asRNA a isoform functions as a negative regulator of PTEN transcription by recruiting chromatin remodelers and catalyzing H3K27me3 formation, whereas the asRNA β isoform interacts with PTENpg1, thereby affecting PTEN levels post-transcriptionally.
| | | | Structure-function analyses of the human SIX1–EYA2 complex reveal insights into metastasis and BOR syndrome pp447 - 453
Aaron N Patrick, Joshua H Cabrera, Anna L Smith, Xiaojiang S Chen, Heide L Ford and Rui Zhao
doi:10.1038/nsmb.2505
SIX1–EYA form a bipartite transcription factor, essential for development, whose overexpression is linked to metastasis. The crystal structure of SIX1 bound to EYA2 reveals that the interaction is mediated by an α-helix of SIX1, and a single mutation can disrupt this association and SIX1's ability to promote EMT and metastasis.
| | | | Structure of active dimeric human telomerase pp454 - 460
Anselm Sauerwald, Sara Sandin, Gaël Cristofari, Sjors H W Scheres, Joachim Lingner and Daniela Rhodes
doi:10.1038/nsmb.2530
EM analyses reveal the three-dimensional structure of human telomerase. Along with functional biochemistry data, the work reveals that telomerase is dimeric in its active form. Each of the two TERT subunits can bind telomeric DNA substrates, and both active sites are required for function.
| | | | Structure of the MutLα C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site pp461 - 468
Emeric Gueneau, Claudine Dherin, Pierre Legrand, Carine Tellier-Lebegue, Bernard Gilquin, Pierre Bonnesoeur, Floriana Londino, Cathy Quemener, Marie-Hélene Le Du, Josan A Márquez, Mireille Moutiez, Muriel Gondry, Serge Boiteux and Jean-Baptiste Charbonnier
doi:10.1038/nsmb.2511
Defective mismatch-repair function is associated with hereditary nonpolyposis colorectal cancer (HNPCC), and mutations in the MLH1 subunit of the MutLα heterodimer MLH1–PMS1 underlie half of HNPCC cases. Structural analysis of the conserved C-terminal domain of Mlh1 from budding yeast shows that Mlh1 contributes to the functionally important Pms1 endonuclease site and provides a rationale for the deleterious impact of MLH1 mutations.
| | | | SOCS3 binds specific receptor–JAK complexes to control cytokine signaling by direct kinase inhibition pp469 - 476
Nadia J Kershaw, James M Murphy, Nicholas P D Liau, Leila N Varghese, Artem Laktyushin, Eden L Whitlock, Isabelle S Lucet, Nicos A Nicola and Jeffrey J Babon
doi:10.1038/nsmb.2519
The inhibitory protein SOCS3 plays a key part in hematopoiesis by regulating signaling induced by specific cytokines. The crystal structure of SOCS3 bound to JAK2 and a fragment of the interleulkin-6 receptor reveals how SOCS3 targets specific receptor–JAK complexes and how it exerts its inhibitory activity by blocking substrate binding.
| | | | Allosteric signaling and dynamics of the clamshell-like NMDA receptor GluN1 N-terminal domain pp477 - 485
Shujia Zhu, David Stroebel, C Andrea Yao, Antoine Taly and Pierre Paoletti
doi:10.1038/nsmb.2522
NMDA receptors are heterotetrameric ligand-gated ion channels, with each subunit containing two extracellular clamshell-like domains. The dynamics of GluN1 NTD and its role in NMDA-receptor function are now explored by using functional and computational approaches. GluN1NTD is highly mobile and influences the gating and pharmacological profile of the receptor.
| | | | Friedreich's ataxia–associated GAA repeats induce replication-fork reversal and unusual molecular junctions pp486 - 494
Cindy Follonier, Judith Oehler, Raquel Herrador and Massimo Lopes
doi:10.1038/nsmb.2520
Friedreich's ataxia is one of several hereditary neurodegenerative disorders caused expansion of trinucleotide repeats, but the mechanism of their genomic propagation is unknown. A new plasmid-based system to probe human replicative intermediates reveals that GAA/TTC repeats interfere with replication, thus suggesting that repeat expansion occurs by postreplicative mechanisms.
| | | | Characterization of prion-like conformational changes of the neuronal isoform of Aplysia CPEB pp495 - 501
Bindu L Raveendra, Ansgar B Siemer, Sathyanarayanan V Puthanveettil, Wayne A Hendrickson, Eric R Kandel and Ann E McDermott
doi:10.1038/nsmb.2503
The protein CPEB, required for learning-related synaptic plasticity in the snail Aplysia, has been suggested to convert from a soluble to a prion-like state. Now these conformational forms of Aplysia CPEB are directly observed, with the prion form showing enhanced binding to target mRNAs.
| | | | Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases pp502 - 507
Florian Rosenthal, Karla L H Feijs, Emilie Frugier, Mario Bonalli, Alexandra H Forst, Ralph Imhof, Hans C Winkler, David Fischer, Amedeo Caflisch, Paul O Hassa, Bernhard Lüscher and Michael O Hottiger
doi:10.1038/nsmb.2521
ADP-ribosylation is an important post-translational protein modification, yet enzymes capable of removing the protein-proximal ADP-ribose were unknown. Human macrodomain proteins MacroD1, D2 and C6orf130 are now shown to catalyze mono-ADP-ribose removal. MacroD2 is also shown to reverse the inhibition of GSK3A caused by ARTD10-catalyzed mono-ADP-ribosylation.
See also: News and Views by Gamble
| | | | A family of macrodomain proteins reverses cellular mono-ADP-ribosylation pp508 - 514
Gytis Jankevicius, Markus Hassler, Barbara Golia, Vladimir Rybin, Martin Zacharias, Gyula Timinszky and Andreas G Ladurner
doi:10.1038/nsmb.2523
ADP-ribosylation catalyzed by PARPs and sirtuins is an important post-translation modification. Macrodomain proteins MacroD1 and D2 are now shown to preferentially bind mono-ADP-ribosylated proteins and to act as proximal ADP-ribosylhydrolases. The crystal structure of the MacroD2–ADPr complex suggests a catalytic mechanism for the reaction.
See also: News and Views by Gamble
| | | | Staufen1 dimerizes through a conserved motif and a degenerate dsRNA-binding domain to promote mRNA decay pp515 - 524
Michael L Gleghorn, Chenguang Gong, Clara L Kielkopf and Lynne E Maquat
doi:10.1038/nsmb.2528
Human Staufen1 (STAU1) functions in mRNA decay and other cellular processes. Structural and functional studies reveal that a new, conserved motif together with a degenerate double-stranded RNA–binding domain mediate STAU1 dimerization through a 'domain-swapping' interaction and that dimerization is important for efficient STAU1-mediated decay in vivo.
| | Technical Report | Top | | | | Detecting endogenous SUMO targets in mammalian cells and tissues pp525 - 531
Janina Becker, Sina V Barysch, Samir Karaca, Claudia Dittner, He-Hsuan Hsiao, Mauricio Berriel Diaz, Stephan Herzig, Henning Urlaub and Frauke Melchior
doi:10.1038/nsmb.2526
SUMOylation is a dynamic protein post-translational modification that regulates many eukaryotic proteins. Now a methodology using commercially available monoclonal antibodies coupled to MS analysis leads to the enrichment and identification of endogenous targets for SUMO1 and for SUMO2/3 in HeLa cells and mouse liver. This protocol can be adapted for other tissues and organs.
| | | Top | | | | Advertisement | | Nature Special: G protein-coupled receptors
In this updated online Special we present a selection of recently published Nature papers that involve the structures of various GPCRs.
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