Reviews & Analysis

Cryo-electron microscopy of brain tissue from two individuals with Down syndrome showed amyloid-β (Aβ) and tau filaments identical to those found in individuals with sporadic or dominantly inherited Alzheimer disease (AD), but also two types of Aβ₄₀ filaments with distinct structures different from those previously reported in AD and cerebral amyloid angiopathy.

The androgen receptor forms nuclear condensates associated with gene transcription. Investigating the molecular basis of condensate formation led us to discover an approach for optimizing small molecules that inhibit the receptor in a currently untreatable form of prostate cancer.

We describe how transcription start site (TSS) choice of thousands of genes results in transcript isoforms with potential for distinct post-transcriptional regulation affecting translation and cell behavior. We show that dynamic switching between initiation sites defines cancer proliferation, differentiation and treatment response, indicating start site determination as a potential diagnostic tool.

An Ago2^HA/HA mouse model combined with super-resolution microscopy, molecular and biochemical assays allowed us to stringently characterize AGO2 regulation in vivo. We found that in quiescent splenocytes, AGO2 localizes almost exclusively to the nucleus, where it binds to the RNA of young mobile transposons and represses their expression through its catalytic domain.

The human ATPase p97 (also known as VCP) unfolds protein substrates by translocating them through its central channel. This process is highly regulated by numerous adapter proteins. Structures of p97 in complex with the unusual adapter UBXD1 reveal how this protein coordinates p97 hexamer remodeling and ring opening by expansive interactions across multiple p97 protomers.

The release of inorganic phosphate (P_i) from actin marks old actin filaments for disassembly. By combining cryo-electron microscopy (cryo-EM) with in vitro reconstitution and molecular dynamics simulations, we show how actin filaments release P_i through a ‘molecular backdoor’ and demonstrate that this arrangement is distorted in a disease-linked actin variant.

In vitro reconstitution of recognition of 80S ribosomes by CCR4–NOT, cryo-electron microscopy (cryoEM), crosslinking mass spectrometry and biochemical characterization reveal that CCR4–NOT specifically identifies ribosomes stalled during translation elongation. CCR4–NOT occupies the ribosomal exit site (E site) and locks the ribosomal L1 stalk in an open conformation to enforce the stalled state.

Here we report Droplet Paired-Tag, a rapid and robust method to simultaneously profile histone modifications and gene expression in single cells at scale. The new procedure provides researchers with a tool for studying the epigenome and gene regulation in complex tissues and disease pathogenesis.

Using designed ankyrin repeat proteins (DARPins) technology, we discovered an α-helical conformation of the third variable (V3) loop on the human immunodeficiency virus 1 (HIV-1) envelope glycoprotein that renders the virus susceptible to broad neutralization at an intermediate entry stage after binding the CD4 receptor. Our results highlight the potential of post-attachment neutralization and enable exploitation of this helical region for inhibitor and vaccine design.

We engineered a tagged version of the yeast Rad51 recombinase and used this tool to monitor DNA double-strand break repair in living cells. We could observe how a broken DNA fragment can scout the nucleus to identify a similar sequence and use it as a template for repair.

By studying the folding of chromosomes relative to nuclear bodies in single-cell models, we reveal specialized subnuclear microenvironments linked to specific gene functions. Our models provide insights into a variety of structural features of the genome and unveil key structure–function correlations.

mRNAs that encode insulin in humans, mice, salmon and the fly Drosophila melanogaster are marked by methylated adenosines in the 3′ untranslated region (UTR). In D. melanogaster, these methylated adenosines are necessary for robust translation of the insulin mRNA into protein. In their absence, flies cannot regulate energy homeostasis and develop diabetes-like hallmarks.

Genome-scale CRISPR–Cas9 screens have identified genetic backgrounds that are vulnerable to inhibition of the SUMO modification pathway in human cells. These findings reveal that protein SUMOylation is essential for cell proliferation owing to a key role in complementary catenane resolution pathways that operate in interphase and mitosis to resolve intertwined DNA structures.

The activity of genes is controlled by regulatory DNA sequences, which interact and communicate with their target genes over long genomic distances. New analyses show that the Mediator complex contributes to the formation of these long-range interactions in the genome.

Cryo-electron microscopy (EM) structures and molecular dynamics simulations of organic cation transporters (OCTs) in ligand-free and drug-bound states provide insights into drug recognition by OCTs. As OCTs are largely responsible for the hepatic uptake and renal clearance of hundreds of drugs, these results will help to inform future drug design and development efforts.

The correction of errors during mitochondrial DNA replication by the proofreading function of DNA polymerase-γ is crucial for maintaining the integrity of the mitochondrial genome and the production of cellular energy. Using cryo-electron microscopy, several steps of the DNA polymerase-γ proofreading pathway have been revealed at near-atomic resolution.

Single-molecule live-cell imaging of the transcription dynamics in budding yeast cells revealed that the remodeling of different nucleosomes in the promoter of a gene regulates various kinetic steps of transcription. The measurements also showed that the TATA-binding protein competes with promoter-associated nucleosomes around the TATA element to activate transcription.

We determined the structure of the Polα–primase complex trapped in a DNA elongation state. Cryo-electron microscopy showed that primase has a role in facilitating the timely termination of primer DNA elongation by Polα by hanging on the primer–template complex.

Endogenous retroviruses (ERVs), a type of transposable element (TE), have been incorporated throughout evolution into the human genome. We show that many ERVs regulate placental gene expression, which may have helped fuel the rapid evolution of the placenta and could have implications for pregnancy complications.

The cryo-EM structure of a natural AlkB–AlkG fusion from Fontimonas thermophila reveals the mechanistic basis for its selectivity towards, and functionalization of, alkane terminal C–H groups. AlkB contains an alkane entry tunnel and a diiron active site, and AlkG docks through electrostatic interactions and transfers electrons to the diiron center for catalysis.