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Commentary

A 3D cellular context for the macromolecular world Open pp841 - 845

Ardan Patwardhan, Alun Ashton, Robert Brandt, Sarah Butcher, Raffaella Carzaniga, Wah Chiu, Lucy Collinson, Pascal Doux, Elizabeth Duke, Mark H Ellisman, Erik Franken, Kay Grünewald, Jean-Karim Heriche, Abraham Koster, Werner Kühlbrandt, Ingvar Lagerstedt, Carolyn Larabell, Catherine L Lawson, Helen R Saibil, Eduardo Sanz-García, Sriram Subramaniam, Paul Verkade, Jason R Swedlow & Gerard J Kleywegt

doi:10.1038/nsmb.2897

We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community.


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News and Views

The timing is right pp846 - 847

R Magnus N Friis & Michael C Schultz

doi:10.1038/nsmb.2898

Yeast cells display synchronized oscillation between phases of high and low oxygen consumption accompanied by a program of cyclical gene expression. A study monitoring mRNA levels, histone modifications and chromatin occupancy of histone modifiers during the yeast metabolic cycle (YMC) at high temporal resolution reveals both 'just-in-time' supply of YMC gene products and new patterns of chromatin reconfiguration associated with transcriptional regulation.

See also: Article by Kuang et al.


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Articles

Energetic dissection of Gleevec's selectivity toward human tyrosine kinases pp848 - 853

Roman V Agafonov, Christopher Wilson, Renee Otten, Vanessa Buosi & Dorothee Kern

doi:10.1038/nsmb.2891

Chemotherapeutic drug Gleevec (imatinib) is a potent and specific inhibitor of Abl kinase. NMR and fast kinetic analyses now reveal that Abl undergoes an induced-fit conformational change upon Gleevec binding.


High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast pp854 - 863

Zheng Kuang, Ling Cai, Xuekui Zhang, Hongkai Ji, Benjamin P Tu & Jef D Boeke

doi:10.1038/nsmb.2881

Analyses of transcription and chromatin states during the yeast metabolic cycle reveal the links between different chromatin modifications and gene expression. The data also show that chromatin-modifier occupancies do not precisely match modification patterns.

See also: News and Views by Friis & Schultz


Structure of cohesin subcomplex pinpoints direct shugoshin-Wapl antagonism in centromeric cohesion pp864 - 870

Kodai Hara, Ge Zheng, Qianhui Qu, Hong Liu, Zhuqing Ouyang, Zhe Chen, Diana R Tomchick & Hongtao Yu

doi:10.1038/nsmb.2880

The crystal structure of a human cohesin subcomplex, SA2–Scc1, guides mutagenesis analyses to dissect the antagonistic roles of shugoshin and Wapl in regulating centromeric functions during mitosis.


Mechanochemical basis of protein degradation by a double-ring AAA+ machine pp871 - 875

Adrian O Olivares, Andrew R Nager, Ohad Iosefson, Robert T Sauer & Tania A Baker

doi:10.1038/nsmb.2885

A single-molecule optical-trapping approach is used to examine protein unfolding and translocation by double-ring AAA+ machine ClpA. Although ClpA can unfold some substrates faster than ClpX can, it translocates the unfolded polypeptide more slowly.


TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release pp876 - 883

Heeyoun Bunch, Xiaofeng Zheng, Adam Burkholder, Simon T Dillon, Shmulik Motola, Gabriel Birrane, Christopher C Ebmeier, Stuart Levine, David Fargo, Guang Hu, Dylan J Taatjes & Stuart K Calderwood

doi:10.1038/nsmb.2878

The protein TRIM28 is identified as a factor that modulates RNA polymerase II pausing and transcriptional elongation at a large number of mammalian genes. This function is regulated by transcription-coupled phosphorylation of TRIM28 at Ser824.


Visualization of recombination-mediated damage bypass by template switching pp884 - 892

Michele Giannattasio, Katharina Zwicky, Cindy Follonier, Marco Foiani, Massimo Lopes & Dana Branzei

doi:10.1038/nsmb.2888

A combination of two-dimensional gel electrophoresis and EM is used to isolate and characterize multiple template-switching intermediates generated in budding yeast during replication of damaged DNA.


Protein dynamics during presynaptic-complex assembly on individual single-stranded DNA molecules pp893 - 900

Bryan Gibb, Ling F Ye, YoungHo Kwon, Hengyao Niu, Patrick Sung & Eric C Greene

doi:10.1038/nsmb.2886

New single-molecule imaging analyses reveal how dynamic interactions of RPA, Rad52 and Rad51 on single-stranded DNA direct assembly of the presynaptic complex that promotes strand invasion during homologous recombination.


Rbfox3 controls the biogenesis of a subset of microRNAs pp901 - 910

Kee K Kim, Yanqin Yang, Jun Zhu, Robert S Adelstein & Sachiyo Kawamoto

doi:10.1038/nsmb.2892

The RNA-binding protein Rbfox is an established regulator of alternative splicing. Here, Kawamoto and colleagues identify transcriptome-wide targets of Rbfox3 in neuronal cells and tissues to uncover an unexpected role in pri-miRNA processing


Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex pp911 - 918

Piotr Wysoczański, Cornelius Schneider, ShengQi Xiang, Francesca Munari, Simon Trowitzsch, Markus C Wahl, Reinhard Lührmann, Stefan Becker & Markus Zweckstetter

doi:10.1038/nsmb.2889

A solution NMR structure of the pre-mRNA retention and splicing (RES) core complex from budding yeast now reveals how the trimer stabilizes the RRM of its Snu17 subunit to promote pre-mRNA interactions within the spliceosome.


The RNA exosome promotes transcription termination of backtracked RNA polymerase II pp919 - 926

Jean-François Lemay, Marc Larochelle, Samuel Marguerat, Sophie Atkinson, Jürg Bähler & François Bachand

doi:10.1038/nsmb.2893

New in vivo analyses in Schizosaccharomyces pombe suggest that the RNA exosome promotes transcription termination by targeting the 3' end of nascent transcripts associated with 'backtracked' RNA polymerase II, revealing a new link between mRNA surveillance and termination.


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Resource

Uncovering global SUMOylation signaling networks in a site-specific manner pp927 - 936

Ivo A Hendriks, Rochelle C J D'Souza, Bing Yang, Matty Verlaan-de Vries, Matthias Mann & Alfred C O Vertegaal

doi:10.1038/nsmb.2890

High-resolution MS identifies >4,300 SUMOylation sites in >1,600 proteins in human cells under standard growth conditions and after proteasome inhibition or heat shock. The data reveal cross-talk between SUMO and other post-translational modifications.


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Technical Report

Multiple in vivo pathways for Escherichia coli small ribosomal subunit assembly occur on one pre-rRNA pp937 - 943

Neha Gupta & Gloria M Culver

doi:10.1038/nsmb.2887

Using the M2 stem-loop region to tag 16S pre-rRNA allows one-step isolation of assembly intermediates of the small ribosomal subunit from wild-type Escherichia coli. Characterization of these RNPs reveals multiple independent pathways for rRNA maturation.


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