Nucleosomes — the basic unit of chromatin architecture — have intrinsic biophysical features of large-scale genome organization.

In this Tools of the Trade article, Abdallah (Gilbert lab) describes the development of direct analysis of ribosome targeting (DART), a tool designed to explore 5' UTR sequences for their potential to efficiently initiate translation.

In this Tools of the Trade article, Zhang and Mille-Fragoso (Gao lab) describe a synthetic receptor platform that is activated by the binding of specific ligands, which triggers RNA editing, enabling the translation of an output protein.

Repair of DNA double-strand breaks requires chromatin opening; however, the mechanisms involved were unclear. This work shows that sequential histone deamidation and acetylation modifications induce chromatin decompaction by reducing positive charge at the DNA–nucleosome interface.

A distinct population of adipose progenitor cells contributes to the accumulation of visceral white adipose tissue in middle-aged male mice.

A 2012 study discovered that RNA–binding proteins are more numerous and diverse than previously thought, many having non-canonical RNA-binding domains.

Pia Cosma recounts the development of STORM, which was the first microscopy method to break the diffraction limit of light.

Evandro De-Souza discusses an article by Dillin and Taylor that revealed the importance of neurons in organism-wide stress responses and the role of such cell-nonautonomous stress responses in ageing.

A study that helped explain how lack of sequence conservation can go hand in hand with functional conservation.

The authors of a new study characterize blebbisomes, large extracellular vesicles that contain functional mitochondria and other organelles and have significant roles in inter-cellular communication and the tumour microenvironment.

This study shows that zotatifin selectively inhibits the translation of prostate cancer oncogene transcripts by restructuring their 5′ untranslated regions. In mice, this agent reversed treatment resistance, which led to improved survival.

Carrie Bernecky describes why the first solved structure of RNA polymerase II was important for transcription researchers, structural biologists, and beyond.

Correction to: Nature Reviews Molecular Cell Biology https://doi.org/10.1038/s41580-024-00780-6, published online 11 October 2024.

Subunits of mitochondrial and cytosolic ribosomes need to be targeted to their correction cellular location. A study identified a mitochondrial avoidance segment in a eukaryotic cytosolic ribosome subunit that prevents its mislocalization to mitochondria.

Synonymous mutations can promote tumorigenesis by perturbing m6A modification of tumour suppressor mRNAs.

In this Tools of the Trade article, Wang and Cheng (Deng Lab) describe an improved protocol for the generation of human pluripotent stem cells by chemical reprogramming based on the targeting of epigenetic obstacles.

In this Tools of the Trade article, Zhang and Owyong (Hong lab) discuss the development of a fluorescent probe that binds disordered proteins in situ and allows their enrichment and identification using a mass-spectrometry-based workflow.

In this Tools of the Trade article, Goronzy (Guttman lab) describes the development of ChIP-DIP, a high-throughput, split-pool barcoding method that enables genome-wide profiling of hundreds of regulatory proteins, transforming our ability to study the regulation of gene activity across cell types and biological contexts.

This study uncovered how extracellular vesicles carrying gasdermin D pores propagate pyroptosis between cells, exacerbating inflammation.

In this Tools of the Trade article, Zong (Zhou lab) describes how using genetic code expansion enabled the precise incorporation of post-translational modifications such as lysine lactylation into proteins, allowing the authors to investigate their role in cellular processes.

Centromeres are silenced in aged cells by the epigenetic downregulation of centromere transcription.

Intriguing findings in yeast suggested that centromeres ‘tag’ DNA as self and allow its condensation during mitosis; vice versa, if a certain DNA is condensed during mitosis, it harbours a centromere.

This study provides a framework to predict whether protein complexes assemble co- or post-translationally based solely on protein structures.

Marina Lusic recounts seminal papers that showed that nuclear pore complexes and association with the nuclear lamina can shape borders between genomic domains and gene regulation.

A calcium-dependent pathway induces stress granule formation and promotes cell survival following lysosomal damage.

Sites of N6-methyladenosine (m6A) in the coding region of mRNAs can induce a distinct, translation-dependent decay pathway involving mRNA translocation to P-bodies.

Zhao et al. describe how nuclear deformation during confined cell migration affects chromatin organization and biomolecular condensates. Chromatin heterogeneity in the trailing nuclear half creates a permissive environment for condensate formation, with potential roles in nuclear mechanics and chromatin interactions.

Obesity-induced transcriptional and epigenetic alterations persist following weight loss, which negatively affects adipose tissue function and increases the propensity to regain weight.

This year marks the 30th anniversary of the publication of a novel approach to measuring protein–protein interactions (PPIs) in living cells, called the ubiquitin-based split-protein sensor (USPS), the inspiration for the protein-fragment complementation assays (PCAs) that followed. Here I provide a brief history of PCAs and discuss advances in their applications and possible future developments. Stephen

The cellular environment is critical to protein function. How is information from many cellular components decoded in order to fine-tune biological activity? New models of biomolecular recognition raise the possibility that proteins engage in specific, yet fuzzy, interactions with their functional partners, which can provide a readout mechanism of the cellular context. Manipulating the cellular context

In this Tools of the Trade article, Cao (Baskin lab) discusses the development of MARS, which enables mitosis-specific recruitment of enzymes to the plasma membrane, exploiting the cell cycle’s natural regulation of PLEKHA5 phosphorylation.

It is now well established that ancient proteins endure, and remain informative, much longer than DNA. Accordingly, sequencing of ancient proteins is currently the only viable methodology for retrieving the genetic data required to resolve evolutionary relations between vertebrate species that disappeared millions of years ago. Ancient proteins can provide phylogenetic information at a timescale that

Tunnelling nanotubes, which are actin-based protrusions different from filopodia and cytokinetic bridges, connect cells in the zebrafish embryo, enabling the transport of proteins and organelles.

Evidence shows that RNA trafficking is a key communication mechanism across kingdoms and species, but how RNAs are secreted and trafficked and how they function within the recipient organisms remain unclear. Here, we discuss how understanding inter-organismal RNA communication can assist in disease management in both agriculture and medicine. Cross-species host–pathogen or mutualistic RNA communication