|Nature Structural aamp; Molecular Biology - Issue - nature.com science feeds|
Traditionally, maintenance of gene silencing by the Polycomb group proteins has been thought to involve recruitment of Polycomb repressive complex (PRC) 1 by PRC2-mediated trimethylation of K27 on histone H3. Three recent studies challenge this model by demonstrating that monoubiquitination of histone H2A, which is catalyzed by PRC1 complexes, can recruit PRC2 and potentiate its catalytic activity.
ATP is continuously synthesized inside mitochondria and exported to the cytoplasm via transporter and channel proteins residing in the inner and outer mitochondrial membranes, respectively. In this issue of Nature Structural aamp; Molecular Biology, a new crystal structure of the mitochondrial channel protein VDAC-1 provides the basis for a detailed simulation study that unravels the mechanism by which ATP diffuses across the outer mitochondrial membrane at a fast rate.
Post-transcriptional mRNA regulation is often attained by lengthening or shortening the 3′ poly(A) tail of a transcript. Eukaryotic mRNAs show a spectrum of deadenylation rates, thus allowing intricate control of gene expression, but the mechanisms that determine such rates are unclear. Three new studies highlight the structural and biochemical features of a key enzyme in removing poly(A) tails, the PAN2–PAN3 complex, providing clues to how different mRNA deadenylation rates can be achieved.
Cancer-associated mutations in the pseudokinase domain (JH2) of JAK2 lead to constitutive activation of its tandem kinase domain (JH1). Molecular dynamics simulations, supported by mutational analysis, provide a model for JH2-JH1 interactions that explains many of the JAK2-activating disease mutations.
Chang and colleagues report the involvement of a Dicer-microRNA-cMyc signaling axis in the transcriptional regulation of a large set of long noncoding RNAs (lncRNAs). These lncRNAs are specifically dependent on cMyc, as compared to divergently transcribed protein-coding genes.
Conti and colleagues present the crystal structure of the yeast deadenylase Pan2–Pan3 core complex, revealing a 1:2 stoichiometry and indicating how deadenylase and pseudokinase domains work together to promote RNA deadenylation.
Structural analyses reveal the asymmetric assembly of Neurospora crassa PAN2–PAN3 complex and, along with functional work on the proteins from different species, indicate an essential role for PAN3 in coordinating PAN2-mediated deadenylation with subsequent steps in mRNA decay.
A new study using fertilized mouse eggs shows that nuclear pore complex (NPC) formation is dependent on nucleosome assembly. Preventing de novo histone deposition on sperm chromatin results in formation of a paternal nuclear envelope lacking NPCs, thus indicating a role for nucleosomes beyond DNA packaging.
A new system to monitor the effects of nucleosome depletion in Xenopus egg extracts reveals that nucleosomes are required for spindle assembly and for recruitment of nuclear pore complex (NPC) components to the nuclear envelope for NPC formation.
VDAC channels permeate metabolites from the mitochondrial intermembrane space to the cytosol. Markov state modeling, an approach used in protein-folding simulations, is now applied to examine ATP-permeation rates and pathways through mouse VDAC1.
The X-ray crystal structure and biochemical analysis of a triple helix formed between the expression and nuclear retention element (ENE) and the 3′ poly(A) tail of the human long noncoding RNA MALAT-1 reveals the basis of its stability and how it confers resistance to degradation.
The first comprehensive analysis of the meiotic translational program of Schizosaccharomyces pombe by deep sequencing of ribosome-protected fragments identifies new translated sequences and highlights differences in the translational changes occurring during sexual differentiation of fission and budding yeasts.
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Guettou et al. describe structural studies on a bacterial homolog of PepT1 and PepT2 peptide transporters—nutrient transporters responsible for all peptide transport across the plasma membrane—in complex with three di- or tripeptides. The data suggest how the transporter's broad peptide specificity is achieved.
Eukaryotic initiation factor 5b (eIF5B) is essential for translation initiation. Spahn and colleagues now report cryo-EM structures of the mammalian 80S initiation complex associated with eIF5B that redefine eIF5B as a tRNA reorientation factor.
A screen identifies 15 genes that modulate CUG-repeat toxicity in C. elegans, including those encoding RNA-export and clearance factors. Toxic RNAs are recognized by the NMD pathway via their 3' UTR GC content.
MAP kinases recognize pathway-specific substrates via docking interactions. NMR analyses now reveal that docking interactions also stimulate ATP binding and phosphotransfer activity of p38α via an allosteric mechanism.
Structural elucidation of the RNA aptamer 'Spinach' reveals that a new G-quadruplex structure forms the fluorophore-binding site that confers the ability of the RNA to function as a GFP mimic.
Roquin controls T-cell activity through interactions with mRNAs of stimulatory receptors. Structural and functional elucidation of its RNA-binding domain reveals how it interacts with constitutive decay elements in the 3' UTR of its targets to regulate their expression.
Roquin recognizes the CDE element in mRNAs to promote their decay. Crystal structures of human Roquin ROQ domain in complex with RNA reveals two distinct RNA-binding sites for stem-loop RNA and dsRNA.
Eukaryotic DNA replication is carried out by two DNA polymerases, Polɛ and Pol δ. An in vitro–replication system reconstituted with purified yeast components identifies the factors that selectively recruit each polymerase for leading- or lagging-strand synthesis.
Mammalian RPRD proteins bind the phosphorylated CTD of RNA pol II with different affinities. Structural elucidation and characterization of their CTD interaction domains reveal the basis of RPRD binding preferences and a role in directing CTD dephosphorylation.
Plk4 regulates centriole duplication. Two centrosomal scaffold proteins, Cep192 and Cep152, are shown to interact with Plk4 in a temporally and spatially regulated manner, and structural analyses reveal that these interactions are mutually exclusive.
A randomized RNA library is used to determine the specificities of RNA recognition by PUF repeats. The code is then used to design a protein that targets endogenous human cyclin B1 mRNA and activates its translation.
Two sibling DNA polymerases synthesize most of the eukaryotic nuclear genome. A new study provides insights into the distinct protein interactions that deliver these replicases for asymmetric leading- and lagging-strand replication and reveals possible cross-talk between DNA replication and other cellular processes.