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Nature Structural & Molecular Biology

Kris G Alavattam, So Maezawa, Akihiko Sakashita, Haia Khoury, Artem Barski, Noam Kaplan, Satoshi H Namekawa
Germ cells manifest a unique gene expression program and regain totipotency in the zygote. Here, we perform Hi-C analysis to examine 3D chromatin organization in male germ cells during spermatogenesis. We show that the highly compartmentalized 3D chromatin organization characteristic of interphase nuclei is attenuated in meiotic prophase. Meiotic prophase is predominated by short-range intrachromosomal interactions that represent a condensed form akin to that of mitotic chromosomes. However, unlike mitotic chromosomes, meiotic chromosomes display weak genomic compartmentalization, weak topologically associating domains, and localized point interactions in prophase...
February 18, 2019: Nature Structural & Molecular Biology
Lucas Patel, Rhea Kang, Scott C Rosenberg, Yunjiang Qiu, Ramya Raviram, Sora Chee, Rong Hu, Bing Ren, Francesca Cole, Kevin D Corbett
In meiotic prophase, chromosomes are organized into compacted loop arrays to promote homolog pairing and recombination. Here, we probe the architecture of the mouse spermatocyte genome in early and late meiotic prophase using chromosome conformation capture (Hi-C). Our data support the established loop array model of meiotic chromosomes, and infer loops averaging 0.8-1.0 megabase pairs (Mb) in early prophase and extending to 1.5-2.0 Mb in late prophase as chromosomes compact and homologs undergo synapsis...
February 18, 2019: Nature Structural & Molecular Biology
Fuyang Li, Quan Wang, Ja-Hwan Seol, Jun Che, Xiaoyu Lu, Eun Yong Shim, Sang Eun Lee, Hengyao Niu
Ribonucleoside monophosphates (rNMPs) mis-incorporated during DNA replication are removed by RNase H2-dependent excision repair or by topoisomerase I (Top1)-catalyzed cleavage. The cleavage of rNMPs by Top1 produces 3' ends harboring terminal adducts, such as 2',3'-cyclic phosphate or Top1 cleavage complex (Top1cc), and leads to frequent mutagenesis and DNA damage checkpoint induction. We surveyed a range of candidate enzymes from Saccharomyces cerevisiae for potential roles in Top1-dependent genomic rNMP removal...
February 18, 2019: Nature Structural & Molecular Biology
Masashi Narita
No abstract text is available yet for this article.
January 31, 2019: Nature Structural & Molecular Biology
Leona D Samson
No abstract text is available yet for this article.
January 31, 2019: Nature Structural & Molecular Biology
Olesya O Panasenko, Syam Prakash Somasekharan, Zoltan Villanyi, Marina Zagatti, Fedor Bezrukov, Ravish Rashpa, Julien Cornut, Jawad Iqbal, Marion Longis, Sarah H Carl, Cohue Peña, Vikram G Panse, Martine A Collart
The assembly of large multimeric complexes in the crowded cytoplasm is challenging. Here we reveal a mechanism that ensures accurate production of the yeast proteasome, involving ribosome pausing and co-translational assembly of Rpt1 and Rpt2. Interaction of nascent Rpt1 and Rpt2 then lifts ribosome pausing. We show that the N-terminal disordered domain of Rpt1 is required to ensure efficient ribosome pausing and association of nascent Rpt1 protein complexes into heavy particles, wherein the nascent protein complexes escape ribosome quality control...
January 28, 2019: Nature Structural & Molecular Biology
Xiao-Min Liu, Shu-Bing Qian
No abstract text is available yet for this article.
January 28, 2019: Nature Structural & Molecular Biology
Joana S Sousa, Janet Vonck
No abstract text is available yet for this article.
January 28, 2019: Nature Structural & Molecular Biology
Teddy Jégu, Roy Blum, Jesse C Cochrane, Lin Yang, Chen-Yu Wang, Maud-Emmanuelle Gilles, David Colognori, Attila Szanto, Sharon K Marr, Robert E Kingston, Jeannie T Lee
The noncoding RNA Xist recruits silencing factors to the inactive X chromosome (Xi) and facilitates re-organization of Xi structure. Here, we examine the mouse epigenomic landscape of Xi and assess how Xist alters chromatin accessibility. Xist deletion triggers a gain of accessibility of select chromatin regions that is regulated by BRG1, an ATPase subunit of the SWI/SNF chromatin-remodeling complex. In vitro, RNA binding inhibits nucleosome-remodeling and ATPase activities of BRG1, while in cell culture Xist directly interacts with BRG1 and expels BRG1 from the Xi...
January 21, 2019: Nature Structural & Molecular Biology
Daniela Rhodes
No abstract text is available yet for this article.
January 21, 2019: Nature Structural & Molecular Biology
Laura J Blair, Olivier Genest, Mehdi Mollapour
No abstract text is available yet for this article.
January 7, 2019: Nature Structural & Molecular Biology
Sorbhi Rathore, Jens Berndtsson, Lorena Marin-Buera, Julian Conrad, Marta Carroni, Peter Brzezinski, Martin Ott
Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes III2 IV and III2 IV2 , at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation...
December 31, 2018: Nature Structural & Molecular Biology
Royce A Wilkinson, Coleman Martin, Artem A Nemudryi, Blake Wiedenheft
Cas9 is an endonuclease that can be programed to autonomously deliver diverse effectors to specified genetic addresses. High-resolution structures of this protein and its associated CRISPR RNA guide explain the molecular mechanisms of CRISPR-RNA-guided DNA recognition and provide a molecular blueprint that has facilitated structure-guided functional remodeling. Here we retrace events that led from early efforts to understand the central role of Cas9 in CRISPR-mediated adaptive immunity to contemporary efforts aimed at developing and deploying this enzyme for programmable genetic editing...
December 31, 2018: Nature Structural & Molecular Biology
Andrew M Hartley, Natalya Lukoyanova, Yunyi Zhang, Alfredo Cabrera-Orefice, Susanne Arnold, Brigitte Meunier, Nikos Pinotsis, Amandine Maréchal
Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is found solely in an SC with cytochrome bc1 (complex III, CIII). Here, we present the cryogenic electron microscopy (cryo-EM) structure of S. cerevisiae CIV in a III2 IV2 SC at 3.3 Å resolution. While overall similarity to mammalian homologs is high, we found notable differences in the supernumerary subunits Cox26 and Cox13; the latter exhibits a unique arrangement that precludes CIV dimerization as seen in bovine...
December 31, 2018: Nature Structural & Molecular Biology
Marion Blin, Benoît Le Tallec, Viola Nähse, Mélanie Schmidt, Caroline Brossas, Gael A Millot, Marie-Noëlle Prioleau, Michelle Debatisse
Common fragile sites (CFSs) are loci that are hypersensitive to replication stress and hotspots for chromosomal rearrangements in cancers. CFSs replicate late in S phase, are cell-type specific and nest in large genes. The relative impact of transcription-replication conflicts versus a low density in initiation events on fragility is currently debated. Here we addressed the relationships between transcription, replication, and instability by manipulating the transcription of endogenous large genes in chicken and human cells...
December 31, 2018: Nature Structural & Molecular Biology
Neel H Shah, John Kuriyan
The functionally tolerated sequence space of proteins can now be explored in an unprecedented way, owing to the expansion of genomic databases and the development of high-throughput methods to interrogate protein function. For signaling proteins, several recent studies have shown how the analysis of sequence variation leverages the available protein-structure information to provide new insights into specificity and allosteric regulation. In this Review, we discuss recent work that illustrates how this emerging approach is providing a deeper understanding of signaling proteins...
December 31, 2018: Nature Structural & Molecular Biology
Timothy L Dosey, Zhao Wang, Guizhen Fan, Zhixian Zhang, Irina I Serysheva, Wah Chiu, Theodore G Wensel
Cation channels of the transient receptor potential (TRP) family serve important physiological roles by opening in response to diverse intra- and extracellular stimuli that regulate their lower or upper gates. Despite extensive studies, the mechanism coupling these gates has remained obscure. Previous structures have failed to resolve extracellular loops, known in the TRPV subfamily as 'pore turrets', which are proximal to the upper gates. We established the importance of the pore turret through activity assays and by solving structures of rat TRPV2, both with and without an intact turret at resolutions of 4...
December 31, 2018: Nature Structural & Molecular Biology
Yu-Hung Chen, Sarah Keegan, Malik Kahli, Peter Tonzi, David Fenyö, Tony T Huang, Duncan J Smith
Although DNA replication is a fundamental aspect of biology, it is not known what determines where DNA replication starts and stops in the human genome. We directly identified and quantitatively compared sites of replication initiation and termination in untransformed human cells. We found that replication preferentially initiates at the transcription start site of genes occupied by high levels of RNA polymerase II, and terminates at their polyadenylation sites, thereby ensuring global co-directionality of transcription and replication, particularly at gene 5' ends...
December 31, 2018: Nature Structural & Molecular Biology
Jeffrey S Mugridge, Jeff Coller, John D Gross
The original and corrected figures are shown in the accompanying Publisher Correction.
December 21, 2018: Nature Structural & Molecular Biology
Alexandra G Knorr, Christian Schmidt, Petr Tesina, Otto Berninghausen, Thomas Becker, Birgitta Beatrix, Roland Beckmann
The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. Nevertheless, it is unclear how these enzymes act in concert with the translating ribosome. Here, we report the structure of a native ribosome-NatA complex from Saccharomyces cerevisiae. NatA (comprising Naa10, Naa15 and Naa50) displays a unique mode of ribosome interaction by contacting eukaryotic-specific ribosomal RNA expansion segments in three out of four binding patches...
December 17, 2018: Nature Structural & Molecular Biology
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