Volume 30 Issue 10, October 2023

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.

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.

The Review provides an overview of ion-channel insecticide targets, with a focus on their mechanisms of action, and offers a perspective for structure-based development of insecticides.

Here, the authors present droplet-based Paired-Tag, an improved method to concomitantly map histone modifications and gene expression at single-cell resolution. They functionally benchmark the method and demonstrate its advantages in mammalian cells and primary brain tissues.

Here the authors show that Fanconi anemia repair proteins protect against LINE-1 retrotransposition, particularly during early development when the primary protective pathway of transcriptional silencing is inactive.

Here the authors describe the backbone structural dynamics of K-Ras in its active state by solution NMR. Comparing wild-type K-Ras to oncogenic mutants unveils cooperative transitions to a highly dynamic excited state that advances our understanding of the GTPase activities of K-Ras.

Here, the authors show that DYNLL1 accumulates at DNA double-strand breaks via 53BP1, where it inhibits MRE11-dependent end resection by disrupting its dimerization, and it restricts recruitment of the Shieldin complex.

Here, the authors use cryo-EM and machine-learning-based tools to analyze structurally heterogeneous ribosome assembly intermediates. They uncover a new proofreading function of the bacterial methyltransferase KsgA, wherein this assembly factor recognizes and drives partial disassembly of translationally incompetent particles, thereby affording these intermediates another opportunity to assemble in an active form.

Gangwar et al. describe the cumulative effect of the potentiating CNIH2 and inhibitory γ5 auxiliary subunits on GluA2 AMPA receptor activation and desensitization gating, polyamine block and noncompetitive inhibition by antiepileptic drug perampanel.

Capper et al. uncover how bicarbonate binds to the anion exchanger 1 (AE1), elucidate how drugs inhibit AE1 via distinct mechanisms, and generate a series of AE1 inhibitors using structure-based drug discovery.

Here, using structural and biochemical data, the authors provide a comprehensive overview of Okazaki fragment maturation in Escherichia coli, demonstrating a relay of events among the involved enzymes regulating an efficient four-point molecular handover.

The proteasome core particle (CP) assembles through the fusion of two half-CP precursors, yielding a complete but immature CP structure. Here the authors identify by cryogenic electron microscopy the structure of a post-fusion assembly intermediate, revealing how associated factors collaborate to chaperone CP assembly and maturation.

Here the authors show that the m⁶A modification on mRNAs mediates their length-dependent enrichment in stress granules, and that mRNAs with longer exons—which usually harbor more m⁶A sites—are preferentially enriched in the granules.

This study shows that CRISPRi mediates precise transcriptional pausing, which can be followed by transcription termination. The pausing effect is asymmetric, only being induced when dCas9-bound guide RNA anneals to the non-template DNA strand.

Mitochondrial DNA is critical for cell function, but how growing cells maintain stable concentrations is unclear. Seel et al. find that cells couple mitochondrial DNA copy number directly to cell volume through nuclear-encoded limiting factors, whose amount increases with cell volume.

Goekbuget et al. characterize the role of the developmentally essential transcriptional repressor FOXD3 in limiting transcription of highly active genes upon entry into S phase to promote faithful DNA replication and to protect genome integrity.

Here authors present SAMOSA-ChAAT, a method for resolving how chromatin-interacting proteins restructure individual chromatin fibers, in high throughput and at scale. They provide evidence that the imitation switch family remodeling enzymes sense nucleosome density to program internucleosomal spacing on individual molecules.

Here the authors present a functional, tagged version of Rad51, which allows dynamic, in vivo studies of Rad51–ssDNA nucleoprotein filament (NPF) formation. NPFs display notable flexibility, which allows them to implement an efficient search strategy for homolog sequences amidst the crowded nucleus.

Here the authors develop CRISPR–ChIP to enable the identification of factors required for chromatin regulation. Using this new method, they unveil a functional partitioning of H3K79 methylation into two distinct regulatory units, with important implications in MLL leukemia.