Research articles

Using embryonic stem cells as a model system for studying the basic bimodal DNA methylation pattern in vivo, a new study now indicates that demethylation is not required for generating unmethylated regions such as CpG islands as part of the overall bimodal methylation pattern but is involved in resetting methylation patterns during somatic-cell reprogramming.

Non-CG methylation is abundant in plants, but its functions are poorly understood. A new study has uncovered the contributions of each non-CG methyltransferase, including the poorly characterized methyltransferase CMT2, to DNA methylation patterning and gene silencing. The results suggest that non-CG methyltransferases participate in self-reinforcing loop mechanisms with histone H3 K9 methylation and small RNAs to control gene silencing throughout the Arabidopsis genome.

Histone H2A is rapidly phosphorylated to γH2AX at the site of DNA double-strand breaks (DSBs). A new, genome-wide analysis in Saccharomyces cerevisiae reports a second histone phosphorylation, γH2B, and examines the modification kinetics and chromosomal distribution of both γH2AX and γH2B and their propagation from DSBs to other genomic loci.

Human Staufen1 (Stau1) is a double-stranded RNA-binding protein implicated in various post-transcriptional gene-regulatory processes. Genome-wide mapping of Stau1-binding sites, combined with Stau1 knockdown and overexpression analyses, has revealed a new role for Stau1 in regulating translation of GC-rich mRNAs by sensing overall transcript secondary structure.

A combination of single-particle EM and biochemical analyses provides direct evidence for two distinct, substrate-specific recruitment pathways that channel RNAs for degradation by the eukaryotic exosome.

To test the effect of transcription-generated torsional stress on nucleosome dynamics and RNA polymerase II (Pol II) kinetics in Drosophila cells, a new study reports a genome-wide sequencing-based assay to measure torsional states at the gene level. Inhibition of topoisomerases leads to rapid accumulation of torsional strain accompanied by changes in Pol II kinetics and destabilization of nucleosomes.

ATP-dependent chromatin remodeling is essential for the dynamic organization of chromatin structure. Genome-wide localization and activity analyses now suggest that remodeler complexes substantially overlap in the mouse genome and that many regions require the activity of more than one remodeler to regulate chromatin accessibility.

The type III secretion systems of infectious bacteria use the needle-like injectisome to secrete proteins from the bacterial cytoplasm into host cells. Cryo-electron tomography and single-particle cryo-EM reveal for the first time the path of unfolded protein substrates through the narrow bore of the injectisome.

Glucokinase activators are attractive therapeutics in diabetes, but their benefits can be offset by hypoglycemia, owing to the allosteric enhancement of the enzyme's glucose affinity. The biochemical and structural dissection of the interaction between glucokinase and a phosphomimetic of the BH3 α-helix derived from human BAD, a glucokinase-binding partner, demonstrates a new binding region and distinct mode of enzyme activation.

P-type ATPases adopt different conformations during their transport cycle, including autophosphorylated forms. The structure of type IB P-type ATPase CopA is now solved in its E2P state. Comparison with a previous E2Pi structure indicates that dephosphorylation is not coupled to ion extrusion, in contrast to mechanisms in type IIA SERCA. The findings explain the effect of disease-related mutations in human Cu⁺ transporters.

The first X-ray crystal structure of the catalytic core of Saccharomyces cerevisiae DNA polymerase ɛ with a primed DNA template and an incoming dNTP reveals a new 'P domain' that encircles the DNA and contributes to the high processivity of this replicative polymerase.

Activated G protein–coupled receptors promote GDP release by their cognate G proteins, through an allosteric mechanism that remains to be fully determined. Now DEER analyses are integrated with previously available structural data and computational work, thus generating a unified model for receptor-mediated G-protein activation.

The nuclear cap–binding complex (CBC) stimulates RNA maturation, but the mechanistic basis is not well understood. In vitro reconstitution experiments combined with functional analyses have revealed a new CBC complex containing ARS2, a major effector of CBC. ARS2 links the cap to 3'-end maturation for several RNA families, thus favoring the production of short RNAs.

How the nuclear exosome is targeted to nuclear RNA substrates is poorly understood. An affinity-capture MS approach and functional analyses now demonstrate a physical and functional connection between the human exosome and the cap-binding complex (CBC). A CBC-containing complex was found to promote transcription termination of several RNA types, thus suggesting a direct link to exosomal RNA degradation.

DNA damage that causes replication forks to stall can be bypassed via translesion synthesis (TLS). New work has identified a bifunctional human primase and TLS polymerase, PrimPol, that reinitiates DNA synthesis beyond the damage site by virtue of its unique primase activity, revealing a novel pathway of DNA-damage tolerance.

Although the DNA damage–induced ubiquitylation by RNF8 and/or RNF168 ubiquitin ligases is crucial for the DNA-damage response (DDR), the precise mechanisms of ubiquitylation-mediated chromatin modulation and recruitment of DNA-repair proteins 53BP1 and RAP80–BRCA1 are not fully understood. A new study now indicates that human demethylase JMJD1C regulates the RAP80–BRCA1 branch of this DDR pathway.

Single-molecule FRET studies of pre-mRNA dynamics within the spliceosome offer new insights into the mechanism of splicing by showing that Prp2 juxtaposes the 5' splice site and branch point elements, and that splicing factor Cwc25 enhances first step catalysis by stabilizing this proximal conformation.

TDP-43 regulates alternative splicing of the cystic fibrosis transmembrane regulator (CFTR) and is found in cytosolic granules associated with several neurodegenerative disorders. A new solution structure of the tandem RNA-recognition motifs (RRMs) that mediate interactions with its UG-rich RNA targets reveals a new RRM arrangement critical for TDP-43 function.

The Rbfox family of developmentally important splicing factors controls alternative splicing in a tissue-specific manner. Genome-wide analyses now show that more than half of Rbfox-binding sites are located distally from exons, that these distal sites are conserved and functionally important, and that long-range RNA-RNA secondary structures mediate distal splicing regulation by Rbfox.

A transcription activator–like effector nuclease (TALEN)-mediated knockout approach to delete human microRNA (miRNA) genes was used to generate a library of 540 TALEN pairs for 274 miRNA loci. As a case study, single and double knockouts for two related miRNAs, miR-141 and miR-200c, revealed intriguing functional differences.