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donderdag 7 december 2017

Nature Structural & Molecular Biology Contents: 2017 Volume #24 pp 1007 - 1163

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Nature Structural & Molecular Biology

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December 2017 Volume 24, Issue 12

News and Views
Focus issue on Mechanobiology 

Nature Reviews Molecular Cell Biology presents a focus issue highlighting the importance of mechanotransduction — the conversion of mechanical forces into biochemical signals — in morphogenesis, tissue regeneration and disease, including tumorigenesis. The articles discuss our understanding of how mechanical forces are transduced into the cell, including the nucleus, to regulate gene expression, and the therapeutic potential of modulating the mechanobiology of cells and tissues. 

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Nature Collection: 2017 Nobel Prize in Physiology or Medicine

The 2017 Nobel Prize in Physiology or Medicine was awarded to Jeffrey C. Hall, Michael Rosbash and Michael W. Young for their pioneering work in Drosophila that elucidated the molecular mechanisms controlling circadian rhythm. 

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Poster on: The expanding CRISPR toolbox 

The CRISPR-Cas9 system can do a lot more than gene editing. This Poster, from Nature Methods, explores the newest possibilities of CRISPR. 

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News and Views


Polθ helicase: drive or reverse   pp1007 - 1008
Judith L Campbell and Hongzhi Li
The helicase intrinsic to DNA polymerase θ (Polθ), the versatile mediator of microhomology-based repair of DNA double-strand breaks and stalled replication forks, is now revealed to be a member of an elite group of proteins known as annealing helicases. This small family of enzymes remodels DNA intermediates in multiple repair processes that are crucial to preserving genome stability and warding off cancer and aging.

See also: Article by Mateos-Gomez et al.

One flexible loop in OST lassos both substrates   pp1009 - 1010
Shiteshu Shrimal, Natalia A Cherepanova and Reid Gilmore
The crystal structure of an oligosaccharyltransferase in complex with a sugar donor and an acceptor peptide provides insight into the mechanism of protein glycosylation and reveals how lipid-linked oligosaccharides are positioned in the enzyme active site.

See also: Article by Napiorkowska et al.

Poly(A) tails: longer is not always better   pp1010 - 1011
Luciana A Castellano and Ariel A Bazzini
Deadenylation of mRNAs is generally associated with translational inhibition and mRNA decay. A study now reports that, unexpectedly, highly expressed genes tend to have shorter poly(A) tails and suggests that poly(A) tails can be 'pruned', generating a 30-nucleotide-biased phased distribution, likely due to protection by poly(A)-binding proteins.

See also: Article by Lima et al.


Catching DNA with hoops—biophysical approaches to clarify the mechanism of SMC proteins   pp1012 - 1020
Jorine Eeftens and Cees Dekker
In this Review, the authors consider how single-molecule biophysical approaches can inform our understanding of the ring-shaped structural maintenance of chromosome (SMC) complexes and their function in chromosome organization.

Structural & Molecular Biology
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The ribosome moves: RNA mechanics and translocation   pp1021 - 1027
Harry F Noller, Laura Lancaster, Jie Zhou and Srividya Mohan
The mechanics and mechanisms of ribosomal translocation, including the conformational rearrangements in the ribosome and the roles of EF-G and tRNAs, are discussed in this Perspective by Mohan, Noller and colleagues.

Nature Collection: 2017 Nobel Prize in Chemistry 

Nature Research present this Collection of articles celebrating the 2017 Nobel Prize in Chemistry to Jacques Dubochet, Joachim Frank and Richard Henderson, recognised "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution". 

Access the collection here >> 

Produced with support from: 
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Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA   pp1028 - 1038
Xueyin Wang, Richard D Paucek, Anne R Gooding, Zachary Z Brown, Eva J Ge et al.
Biochemical reconstitution of PRC2 interactions with chromatinized templates demonstrates that protein-free linker DNA dominates the PRC2-nucleosome interaction, while RNA inhibits binding.

DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation   pp1039 - 1047
Jeongyoon Choi, Andreas Linus Bachmann, Katharina Tauscher, Christian Benda, Beat Fierz et al.
The DNA-binding activity of the winged-helix domain of PHF1 stabilizes PRC2 on chromatin, thereby permitting efficient H3K27 trimethylation.

Histone propionylation is a mark of active chromatin   pp1048 - 1056
Adam F Kebede, Anna Nieborak, Lara Zorro Shahidian, Stephanie Le Gras, Florian Richter et al.
Histone H3 lysine 14 is propionylated and butyrylated in vivo in a metabolic-state-dependent manner and these modifications promote high levels of transcription.

Short poly(A) tails are a conserved feature of highly expressed genes   pp1057 - 1063
Sarah Azoubel Lima, Laura B Chipman, Angela L Nicholson, Ying-Hsin Chen, Brian A Yee et al.
Although deadenylation induces translational inhibition and mRNA decay, well-expressed transcripts are now shown to possess short, well-defined poly(A) tails, suggesting that pruned tails may be ideal for protective and translational functions.

See also: News and Views by Castellano & Bazzini

Dissecting the telomere-inner nuclear membrane interface formed in meiosis   pp1064 - 1072
Devon F Pendlebury, Yasuhiro Fujiwara, Valerie M Tesmer, Eric M Smith, Hiroki Shibuya et al.
Structural and functional analyses of human TRF1 in complex with meiosis-specific protein TERB1 reveal the basis for telomere tethering to the inner nuclear membrane and offer insight into the mechanism of dissociation in late pachytene.

Telomeric TERB1-TRF1 interaction is crucial for male meiosis   pp1073 - 1080
Juanjuan Long, Chenhui Huang, Yanyan Chen, Ying Zhang, Shaohua Shi et al.
Disrupting the interaction between telomere protein TRF1 with meiosis-specific protein TERB1 impairs the pairing of X and Y chromosomes via their telomere-adjacent pseudoautosomal regions in pachytene, leading to spermatocyte apoptosis and male infertility in mice.

Dynamic regulation of CD28 conformation and signaling by charged lipids and ions   pp1081 - 1092
Wei Yang, Weiling Pan, Shuokai Chen, Nicola Trendel, Shutan Jiang et al.
CD28 signaling motifs are sequestered within the membrane via interactions with phospholipids. TCR activation increases the local Ca2+ concentration, which disrupts CD28-lipid interactions.

A consensus model of human apolipoprotein A-I in its monomeric and lipid-free state   pp1093 - 1099
John T Melchior, Ryan G Walker, Allison L Cooke, Jamie Morris, Mark Castleberry et al.
Apolipoprotein A-I (apoA-I) is the scaffold protein that is essential for the assembly and function of HDL particles. A structural model for monomeric, lipid-free apoA-I, based on previous and new data, is now presented.

Molecular basis of lipid-linked oligosaccharide recognition and processing by bacterial oligosaccharyltransferase   pp1100 - 1106
Maja Napiorkowska, Jeremy Boilevin, Tina Sovdat, Tamis Darbre, Jean-Louis Reymond et al.
The crystal structure of the single-subunit oligosaccharyltransferase PglB in complex with acceptor peptide and a synthetic lipid-linked oligosaccharide analog reveals a key intermediate in the reaction mechanism.

See also: News and Views by Shrimal et al.

Preribosomes escaping from the nucleus are caught during translation by cytoplasmic quality control   pp1107 - 1115
Anshuk Sarkar, Matthias Thoms, Clara Barrio-Garcia, Emma Thomson, Dirk Flemming et al.
Abnormal pre-60S particles are able to escape nuclear quality control and join mature 40S subunits to catalyze cytoplasmic protein synthesis, but the resulting translation defects trigger the cytoplasmic surveillance machineries RQC and the Ski-exosome.

The helicase domain of Polθ counteracts RPA to promote alt-NHEJ   pp1116 - 1123
Pedro A Mateos-Gomez, Tatiana Kent, Sarah K Deng, Shane McDevitt, Ekaterina Kashkina et al.
Biochemical and cellular analyses reveal that the helicase activity of DNA polymerase theta (Polθ) antagonizes RPA to promote DNA strand annealing and double-strand break repair via alt-NHEJ in mouse ES cells.

See also: News and Views by Campbell & Li

Extrachromosomal telomere repeat DNA is linked to ALT development via cGAS-STING DNA sensing pathway   pp1124 - 1131
Yi-An Chen, Yi-Ling Shen, Hsuan-Yu Hsia, Yee-Peng Tiang, Tzu-Ling Sung et al.
The cGAS-STING cytoplasmic-DNA-sensing pathway is activated by accumulation of extrachromosomal telomere repeats, and this proliferation-inhibition mechanism is defective in ALT cancer cells.

Programming asynchronous replication in stem cells   pp1132 - 1138
Hagit Masika, Marganit Farago, Merav Hecht, Reba Condiotti, Kirill Makedonski et al.
Asynchronous replication-timing patterns undergo programmed switching between maternal and paternal alleles in embryonic and adult stem cells.

TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning   pp1139 - 1145
Eric J Tomko, James Fishburn, Steven Hahn and Eric A Galburt
During transcription initiation, Ssl2, the dsDNA translocase of TFIIH, opens a 6-bp DNA bubble, suggesting a two-step model wherein Ssl2 triggers a 6-bp open complex that RNA polymerase II expands via NTP-dependent RNA transcription.

Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states   pp1146 - 1154
Xiaoyuan Zhou, Minghui Li, Deyuan Su, Qi Jia, Huan Li et al.
Cryo-EM analyses of human TRPML3 reveal this channel in three different states—closed, agonist-activated and low-pH-inhibited—and suggest mechanisms for regulation.

Encoding optical control in LCK kinase to quantitatively investigate its activity in live cells   pp1155 - 1163
Ardiyanto Liaunardy-Jopeace, Ben L Murton, Mohan Mahesh, Jason W Chin and John R James
Engineering an LCK mutant, in which an active-site lysine is replaced by a photocaged equivalent via genetic code expansion, allows quantitation of phosphorylation kinetics in situ and provides insights into LCK activation dynamics.

npj Molecular Phenomics is an online-only, open access journal that provides a forum for cutting-edge scientific advances in the emerging field of phenomics, the study of the physical and chemical characteristics of an individual in quantitative terms.

Part of the Nature Partner Journals series, npj Molecular Phenomics is published in partnership with Fudan University. The journal is now open for submissions.

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40 years of Sanger DNA sequencing 

Research and Commentary reflecting on the evolution and future of Sanger DNA sequencing 

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