|Nature Structural aamp; Molecular Biology - Issue - nature.com science feeds|
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
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.
High-resolution MS identifies ggt;4,300 SUMOylation sites in ggt;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.
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.
|Nature Structural aamp; Molecular Biology - AOP - nature.com science feeds|
The X-ray crystal structure of ScaDMT, a bacterial member of the solute carrier 11 transporter family, identifies conserved residues within the substrate-binding site that confer metal-ion selectivity.
U2AF is known to affect 3A-splice-site selection. Here, Fu and colleagues use genome-wide analysis of U2AF-RNA interactions to define U2AF's key roles in gene expression and regulated splicing in normal and disease states.
Histone variant macroH2A1 represses gene expression in heterochromatin. New data show that it can also stimulate transcription by cooperating with PARP-1 to promote CBP-mediated H2B acetylation and that this regulatory function is lost in cancer cells.
CAG-repeat expansion in the housekeeping gene ATXN7 causes the neurodegenerative disorder SCA7. Now ATXN7 protein is found to promote transcription and expression of miR-124, which in turn mediates cross-talk between lnc-SCA7 and ATXN7 transcripts.
A genome-wide screen of gene targeting by an adeno-associated virus vector in human cells reveals that target sites are preferentially located where transcription occurs in the opposite direction from DNA replication, suggesting that colliding polymerases promote homologous recombination.
Crystal structures of MhsT, a bacterial member of the neurotransmitter/sodium symporter family, in an occluded, inward-facing state with bound sodium and substrate reveal conformational changes during the transport cycle that provide new insights into the mechanism of cytoplasmic sodium release.
Structural and biochemical analyses of full-length human BRCA2 reveal how it facilitates RAD51-mediated homologous recombination to repair DNA double-strand breaks.
Crystal structures of the extracellular domain of human nAChR, in its apo form and with antagonists methyllycaconitine orα-bungarotoxin bound, are presented. The structures provide insight into the channel-opening mechanism of nAChRs and their pharmacological properties.
An X-ray crystal structure of substrate-bound Neisseria PnuC, a bacterial member of the SWEET family of transporters, provides key insights into the translocation mechanism and potential evolution of these membrane proteins.