Volume 21 Issue 1, January 2014

Every RNA polymerase II transcript receives a 5′-end 7-methylguanosine (m⁷G) cap, which is rapidly bound by the nuclear cap–binding complex (CBC). Two recent studies now reveal that the CBC associates with a variety of effector proteins that enable it to interrogate nascent RNA, discriminating between distinct RNA subclasses and routing them either toward distinct maturation pathways or toward decay. Thus, the CBC has an early role in policing cellular RNA.

The long-awaited crystal structure of Saccharomyces cerevisiae DNA polymerase ε reveals a unique domain never before observed in B-family DNA polymerases. This novel domain endows polymerase ε with a capacity for highly processive DNA synthesis.

Enzymes that alter nucleosome structure or position are at the very center of gene and genome regulation, and understanding how, and to what extent, these diverse activities collaborate and control each other to shape the genome for dynamic regulation is a major challenge. A new study provides an important step in this direction by illustrating the cooperative nature of ATP-dependent chromatin-remodeling systems in mammalian cells.

The exosome complex has key roles in RNA processing and quality control. Single-particle EM analyses now provide compelling evidence for two distinct pathways by which substrate RNAs can pass through the exosome structure to reach the catalytic site for exonuclease digestion.

DNA replication begins with prereplication-complex formation at origins and is followed by helicase activation to unwind DNA at the replication fork. This Perspective compares bacterial DnaB and eukaryotic MCM2–7 helicase-loading mechanisms and discusses emerging data supporting current models of how two MCM2–7 complexes are loaded to form a double hexamer.

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.

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.

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.

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.

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.

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.

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.

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.