Friday, March 3, 2017

Nature Structural & Molecular Biology Contents: 2017 Volume #24 pp 195 - 336

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Nature Insight Frontiers in Biology

This year's Frontiers in Biology Insight features Reviews on how genomics is helping to uncover the peopling of the world, the interplay between morphogens and morphogenesis in determining organismal shape, the factors that influence the immune response to cancer, advances in single-cell genomics, and the effects of base modifications in messenger RNA.

March 2017 Volume 24, Issue 3

News and Views
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News and Views


Unearthing worm replication origins   pp195 - 196
Takayo Sasaki and David M Gilbert
Unlike in animals in which gastrulation marks the onset of zygotic transcription and a transition from random to site-specific localization of replication origins, transcription and origin specification in Caenorhabditis elegans are in place before gastrulation. Nonetheless, origin-site redistribution takes place after gastrulation, and is coordinated with changes in the sites of active transcription.

See also: Article by Rodriguez-Martinez et al.



Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation   pp197 - 204
Simao T da Rocha and Edith Heard
This Review highlights recent breakthroughs in X-chromosome inactivation and discusses how the multitasking RNA Xist can structurally and functionally transform an active chromosome into uniquely organized facultative heterochromatin.

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Structural basis of dual Ca2+/pH regulation of the endolysosomal TRPML1 channel   pp205 - 213
Minghui Li, Wei K Zhang, Nicole M Benvin, Xiaoyuan Zhou, Deyuan Su et al.
Crystal structures of the linker region of TRPML1 reveal that the luminal domain forms a tetrameric pore. Along with electrophysiology studies, this work provides insight into the mechanism of channel regulation by Ca2+ and H+.

Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1   pp214 - 220
Chengying Ma, Shan Wu, Ningning Li, Yan Chen, Kaige Yan et al.
The cryo-EM structure of pre-60S purified via Nmd3 provides molecular insights into the roles of assembly factors Nmd3, Lsg1, Tif6 and Reh1 in the last steps of ribosomal large-subunit maturation.

Cotranslational folding of spectrin domains via partially structured states   pp221 - 225
Ola B Nilsson, Adrian A Nickson, Jeffrey J Hollins, Stephan Wickles, Annette Steward et al.
Using a family of spectrin domain variants and a combination of structural, biochemical and biophysical approaches, it is shown that cotranslational folding cannot be predicted on the basis of the folding behavior of isolated proteins.

Xist-dependent imprinted X inactivation and the early developmental consequences of its failure   pp226 - 233
Maud Borensztein, Laurene Syx, Katia Ancelin, Patricia Diabangouaya, Christel Picard et al.
Single-cell RNA sequencing of preimplantation mouse embryos demonstrates that lack of paternal Xist leads to genome-wide transcriptional misregulation in the early blastocyst and a failure to activate the extraembryonic pathway.

The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses   pp234 - 242
Barbara Hummel, Erik C Hansen, Aneliya Yoveva, Fernando Aprile-Garcia, Rebecca Hussong et al.
The molecular chaperone HSP90 is found to affect the expression of mouse endogenous retrovirus elements and neighboring genes through the KAP1-SETDB1 epigenetic-repression machinery.

G-quadruplex structures within the 3′ UTR of LINE-1 elements stimulate retrotransposition   pp243 - 247
Aleksandr B Sahakyan, Pierre Murat, Clemens Mayer and Shankar Balasubramanian
Guanine-rich sequences with a tendency to form G4 structures are a hallmark of hominoid-specific L1 retrotransposons, and their stabilization increases L1 mobility, thus potentially affecting genome evolution.

Eukaryotic Rad50 functions as a rod-shaped dimer   pp248 - 257
Young Bong Park, Marcel Hohl, Michal Padjasek, Eunyoung Jeong, Kyeong Sik Jin et al.
Structural, biochemical and in vivo analyses reveal that Rad50 zinc-hook and coiled-coil domains form a novel dimerization interface essential for Mre11-complex function in DNA damage response and repair.

RdRP-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway   pp258 - 269
Xufei Zhou, Xuezhu Feng, Hui Mao, Mu Li, Fei Xu et al.
A genetic screen in C. elegans identifies a suppressor of siRNA and a new subset of 22G-RNAs that act through the nuclear RNAi pathway to downregulate pre-rRNA under stress conditions.

Structural basis of the specificity of USP18 toward ISG15   pp270 - 278
Anja Basters, Paul P Geurink, Annika Rocker, Katharina F Witting, Roya Tadayon et al.
The specificity of USP18's deconjugating activity toward ISG15, a ubiquitin-like protein induced by interferon, is revealed by structural and biochemistry studies of the mouse proteins.

STAT2 is an essential adaptor in USP18-mediated suppression of type I interferon signaling   pp279 - 289
Kei-ichiro Arimoto, Sara Lochte, Samuel A Stoner, Christoph Burkart, Yue Zhang et al.
STAT2, previously known as a positive effector of interferon signaling, is now shown to participate in negative feedback and suppression of this signaling pathway, by recruiting USP18 to the type I IFN receptor subunit IFNAR2.

The gastrula transition reorganizes replication-origin selection in Caenorhabditis elegans   pp290 - 299
Marta Rodriguez-Martinez, Natalia Pinzon, Charles Ghommidh, Emmanuelle Beyne, Herve Seitz et al.
Nascent-strand mapping of active DNA replication origins before and after gastrulation in C. elegans reveals that replication initiation is coordinated with transcriptional programs during embryonic development.

See also: News and Views by Sasaki & Gilbert

Open-ringed structure of the Cdt1-Mcm2-7 complex as a precursor of the MCM double hexamer   pp300 - 308
Yuanliang Zhai, Erchao Cheng, Hao Wu, Ningning Li, Philip Yuk Kwong Yung et al.
A high-resolution cryo-EM structure of the heptameric Cdt1-Mcm2-7 complex of the replicative helicase from budding yeast suggests a /`spring-action/' DNA-unwinding mechanism.

Mechanism and timing of Mcm2-7 ring closure during DNA replication origin licensing   pp309 - 315
Simina Ticau, Larry J Friedman, Kanokwan Champasa, Ivan R Correa Jr, Jeff Gelles et al.
smFRET analysis and colocalization spectroscopy reveal the mechanism of DNA entry into the Mcm2-7 helicase ring during replication origin licensing.

Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1   pp316 - 324
Zuanning Yuan, Alberto Riera, Lin Bai, Jingchuan Sun, Saikat Nandi et al.
A 3.9-A-resolution cryo-EM structure of the S. cerevisiae OCCM replicative helicase loading complex bound to DNA shows how ORC and Cdc6 recognize DNA origins, and reveals details of how the Mcm2-7 hexamer ring is loaded onto the DNA helix.



Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation   pp325 - 336
Ivo A Hendriks, David Lyon, Clifford Young, Lars J Jensen, Alfred C O Vertegaal et al.
A comprehensive analysis of the human SUMO proteome, in HeLa and U2OS cell lines and under different conditions, identifies new SUMOylated sites and reveals cross-talk between SUMO and other post-translational modifications, such as phosphorylation.

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