Articles in 2016

Genetic and biochemical assays reveal that carbon monoxide produced by heme catabolism influences circadian rhythm in mammals by altering the activity of transcription factor CLOCK–BMAL1 at clock-gene targets.

Large-scale sequencing approaches reveal that the genetic code of Euplotes ciliates supports widespread ribosomal frameshifting at stop codons, and that additional mechanisms are required for efficient translation termination.

Barcoded HIV ensembles (B-HIVE) provides a new approach to map HIV integration sites and to determine how genomic context influences proviral transcription activity and response to latency-reversing agents.

Quantitative assessment of transcription, splicing, degradation, localization and translation of coding and noncoding genes allows classification of RNAs on the basis of their metabolism and may aid in inference of lncRNA function.

Comparative analysis of RNA-seq and ribosome profiling data show that a major fraction of exon-skipping events in transcripts with medium-to-high abundance are engaged by ribosomes and therefore are likely to be translated.

spFRET microscopy analysis reveals how FACT reversibly uncoils DNA from nucleosomes during remodeling, thus modulating DNA accessibility in vitro and in vivo.

Opposing effects of 8-oxodGTP on telomerase activity – promoting elongation by destabilizing G4 structures or inhibiting elongation by acting as a chain terminator – explain the differential sensitivity of cells with short telomeres to oxidative stress.

During protein synthesis, the growing nascent polypeptide chain acts as a positive or negative regulator of the rate of peptide-bond formation and ribosomal fidelity, and influences the efficiency of downstream protein-folding and targeting events. At a recent international meeting held on the banks of Lake Kawaguchi in Japan, scientists and students investigating diverse aspects of nascent-chain biology met to discuss their latest findings in the scenic presence of Mount Fuji.

A conserved long noncoding RNA expressed at the 5S rDNA ribosomal locus has acquired a novel function in alternative-splicing regulation in primates, owing to the insertion of a mobile Alu element. This discovery opens new perspectives regarding the roles of transposable elements in expanding the human transcriptome and may be applied as a biotechnology tool to drive gene-specific changes in alternative splicing.

Drosophila Skywalker regulates the GTPase Rab35, thereby controlling the turnover of synaptic-vesicle proteins. A new crystal structure of the TBC domain of Skywalker reveals an unexpected phosphoinositide-binding pocket, which is critical for synaptic function and is disrupted in DOORS syndrome–causing mutations in the human Skywalker homolog TBC1D24.

The degradation of mRNAs involves removal of the 5′ protective cap via a decapping-enzyme complex, in a largely irreversible process that commits the transcript for destruction. Understanding how the decapping reaction is catalyzed and regulated are major goals in the field. New data suggest how the chemistry of decapping is controlled and orchestrated within the cell.

Applying SHAPE-seq to analyze cotranscriptional folding of the B. cereus crcB fluoride riboswitch at nucleotide resolution shows that the folding pathway undergoes a ligand-dependent bifurcation that influences terminator formation via coordinated structural transitions.

The ribosome-assembly factor Mrt4 prevents untimely recruitment of the RNA-export receptor Mex67–Mtr2 to the nascent 60S ribosomal subunit, thereby ensuring appropriately timed nuclear export.

Cryo-EM analyses of yeast TRiC (CCT) reveal conformational changes induced by ATP binding and a staggered mode of nucleotide binding to the different subunits.

The RNA-binding protein CPEB1 drives post-transcriptional changes in the host transcriptome and poly(A)-tail lengthening of viral RNAs, processes essential for productive HCMV infection.

Perinuclear localization of CED-3 zymogen in C. elegans germ cells and interaction with nuclear-pore protein NPP-14 inhibit autocatalytic activation of CED-3, a central event in apoptosis.

Analyses of Hsp90 mutants show no correlation between the speed of ATP turnover and chaperone activity in vivo, indicating that timing of conformational transitions, rather than cycle speed, is essential for Hsp90 function.

Methicillin resistance in the clinically important bacterium Staphylococcus aureus (MRSA) has evolved in multiple S. aureus lineages through acquisition of chromosomally integrating mobile genetic elements named SCCmec. Now Rice and colleagues show that the conserved SCCmec cch gene encodes an active DNA helicase, thus suggesting that extrachromosomal replication is part of the enigmatic SCCmec horizontal-transfer mechanism.

Here, we announce two policy changes across Nature journals: data-availability statements in all published papers and official Worldwide Protein Data Bank (wwPDB) validation reports for peer review.

A potent toxin present in the venom of a fish-hunting cone snail is a minimized insulin (Con-Ins G1) lacking key residues involved in the receptor binding of most insulins. New data show that Con-Ins G1 nevertheless binds potently to the human insulin receptor, owing to a rearrangement that compensates for the lack of a critical binding residue.