Longitudinal monitoring of cytoplasmic RBP-RNA interactions and transcriptome in living cells by engineered protein nanocages

Hu et al. develop POND-seq, a nanocage-based strategy that exports RNA information from living cells without disruption. This approach enables repeated sampling of the same cell population to track tr...

cell.com

Sequential reading of a stepwise-shortened peptide immobilized on nanopore - Nature

A nanopore-based ‘chop and measure’ method sequences peptides at single-amino-acid resolution by using enzymatic digestion to progressively shorten the N terminus one residue at a time,...

doi.org

Animal retrozymes are nonautonomous sequences of Penelope-like elements

Hammerhead ribozymes (HHRs) are small catalytic RNAs found across diverse life forms. In animals, they can occur as dispersed copies or in tandem genomic arrangements. These tandemly organized forms, ...

biorxiv.org

Somatic mutations reveal the ontogeny of microglia in human aging - Nature

Nature - Somatic mutations reveal the ontogeny of microglia in human aging

nature.com

A pre-rRNA positive feedback loop drives malignant ribosome biogenesis - preLights

Tumor-driving signals turn pre-rRNA into a recruitment hub for the enzyme CK2, boosting nucleolar fusion and ribosome production

prelights.biologists.com

Co-option of retrotransposons promotes antibody diversification

A longstanding mystery in antibody diversification is how AID specifically targets immunoglobulin V genes. Ancient LINE-1 retrotransposons embedded within the immunoglobulin locus provide a recruitment platform for the HUSH complex and AID to drive somatic hypermutation.

dlvr.it

Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics

This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...

nature.com

Cap-specific second nucleotide ribose methylase CMTR2 is required for transcriptome transition during mammalian germline development

Eukaryotic RNA polymerase II transcripts carry a signature m7G cap (Cap0) structure that is co-transcriptionally added to the 5’ end, and is essential for translation and RNA stability. Higher eukaryotes carry additional essential ribose methylations on the first and second cap-proximal nucleotides, termed as Cap1 and Cap2, respectively. The ubiquitous Cap1 modification protects cellular RNAs from being recognized by the innate immune sensors. Cap2 is also implicated in such an innate immune role, but here we use our genetic analyses of two human cell lines and three mouse tissues to reveal that loss of CMTR2 does not result in activation of the innate immune response. Germline deletion of mouse CMTR2 shows that it is required for male and female fertility. While mutant germ cells proceed into the meiotic pachytene spermatocyte stage, their transcriptome fails to keep pace and transition from the preceding leptotene/zygotene stages. Such a meiotic role is not conserved in other vertebrates like zebrafish, as cmtr2 mutants are fertile, instead it has a role in defining sex, as all mutants are exclusively males. Taken together, our study reveals that CMTR2 does not influence innate immune response in human cells and mouse tissues, but shapes gene expression during developmental transitions. ### Competing Interest Statement The authors have declared no competing interest. Novartis Foundation for Medical-Biological Research, 24B138 Swiss National Science Foundation, https://ror.org/00yjd3n13, 310030_215346, 310030_207468, 51NF40_205601 Lalor Foundation, https://ror.org/03vpdge44

doi.org

Exchange dynamics and kinetic control of gene regulation complexes

Nature Reviews Molecular Cell Biology, Published online: 30 July 2026; doi:10.1038/s41580-026-00991-zRecent evidence reveals how gene expression complexes form transient assemblies that continually exchange their subunits under kinetic control. This Perspective proposes that these dynamics form the basis of RNA processing and gene regulation.

dlvr.it

Fat body CLOCK restrains innate immunity and maintains survival under dietary stress in Drosophila

Both aging and a high-fat diet (HFD) dampen circadian gene transcription rhythms and promote chronic inflammation. How aging and HFD interact to affect peripheral molecular clocks and circadian behavi...

doi.org

Analog intrinsic recoding measures RNA dynamics without chemical conversion

Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...

biorxiv.org

A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins

Abstract. Efficient purification of specific RNAs from lysates remains a major challenge. Existing methods, such as MS2 tagging or oligonucleotide hybridiz

doi.org

Compendium of RNA modifications for bacterial stress adaptation | Microbiology and Molecular Biology Reviews

SUMMARYRNA modifications in the tRNA, rRNA, and mRNA constitute a widespread layer of post-transcriptional gene regulation, commonly known as the epitranscriptome. In bacteria, tRNA and rRNA modifications are well documented and play essential roles in tRNA folding, rRNA maturation, translation, and peptidyl transfer. Although mRNA modifications have been extensively characterized in eukaryotes, their functional implications for mRNA fate in prokaryotes remain uncertain, and their identities and locations are the subject of an emerging field of research. Importantly, RNA modification is a dynamic process, and variation in the presence and abundance of these modifications has significant consequences for bacterial physiology. Here, we discuss current knowledge of modified RNA nucleotides in bacteria, with a particular focus on their roles in bacterial adaptation to environmental stress.

journals.asm.org

Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Sequencing of species that can be cultured in the laboratory results in a bias in taxon sampling. This study uses cost-effective, amplification-free, low-input sequencing methods to assemble genomes o...

journals.plos.org

Gene regulatory innovations from transposable elements in primate cerebellum development - Nature Communications

The roles of transposable elements in primate brain development remain underexplored. Here, the authors identify transposable elements with ancestral regulatory potential that have been co-opted as ci...

nature.com

Independent Evolution of Sex Chromosomes and Male Pregnancy–Related Genes in Two Seahorse Species

Abstract. Unlike birds and mammals, many teleosts have homomorphic sex chromosomes, and changes in the chromosome carrying the sex-determining locus, terme

academic.oup.com

UTR-ly unexpected: RNA chaperones tame intrinsically disordered proteins

How do cells ensure that complex, multidomain proteins fold correctly? Luo et al. reveal a self-contained solution. The 3′UTR of an mRNA co-translationally chaperones the protein it encodes, preventin...

cell.com

Evolution of CTCF binding sites in the human genome

Abstract. The CCCTC-binding factor (CTCF) is a master regulator of topologically associating domains (TADs), which shape 3D genome architecture and gene re

doi.org

A conserved architectural domain shapes centromere evolution in Drosophila

Centromeres ensure faithful chromosome segregation despite being embedded within rapidly evolving repetitive DNA, a contradiction known as the centromere paradox. While centromere identity is defined ...

biorxiv.org

Genetic background shapes the transcriptional activity and phenotypic contribution of a horizontally acquired region in yeast

Abstract. Horizontal Gene Transfer (HGT) is the movement of genetic material across species. In Saccharomyces cerevisiae, a DNA segment known as Region B w

academic.oup.com

Crush-resistant air sacs allow insect larvae to exploit aquatic habitats at extreme depth

The absence of aquatic insects from pelagic marine habitats has been attributed to their air-filled tracheal respiratory system, which could implode at depth while undertaking diel vertical migrations...

science.org

The +1 nucleosome functions in RNA Pol II transcription initiation and the transition to elongation

By combining biochemical assays and electron cryo-microscopy, Zhan, Abril-Garrido, et al. elucidated key steps of transcription initiation and the transition to elongation in the presence of the +1 nucleosome. The authors demonstrated for the first time that the +1 nucleosome has an active role in the initiation-elongation transition.

dlvr.it

Mobility shapes plasmid GC content evolution

Plasmids are frequently AT-rich relative to their bacterial hosts. Despite this tendency towards lower GC content, plasmid and host chromosome GC content are positively correlated across diverse collections of plasmid-host pairs. However, the evolutionary processes underlying this pattern remain unclear. The classic model of amelioration predicts that horizontally acquired DNA gradually converges on host nucleotide composition. However, because plasmids can repeatedly transfer between bacterial hosts, the opportunity for such host-associated evolution may depend on their transmission dynamics. Using 50,936 plasmid-host pairs from a public sequence database, we found that the apparent global correlation between plasmid and host chromosome GC content was largely driven by differences between bacterial species rather than within species. We therefore accounted for plasmid and host population structure when testing how plasmid mobility shaped host-associated compositional evolution. We compared two contrasting regimes: a population of 3,682 Enterobacterales plasmids distributed across diverse host backgrounds, and six long-term host-associated plasmids from a Rhizobium leguminosarum lineage with INSeq-determined gene essentiality data. In the Enterobacterales population, GC content variation was overwhelmingly explained by plasmid lineage rather than host phylogeny, and conjugative plasmids showed greater similarity to their host chromosomes than mobilisable or non-mobilisable plasmids. In the Rhizobium leguminosarum plasmids, synonymous-site composition was more similar to the host chromosome among genes required across multiple host life stages. Together, these results support a model in which plasmid mobility influences the opportunity for host-associated evolutionary processes to alter nucleotide composition. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 319534/Z/24/Z St. John's College, University of Oxford, UK

doi.org