RNA localization adds a fundamental layer to gene expression by determining when and where translation-ready mRNAs become available, yet how this timing is coordinated with nuclear architecture and cell-cycle progression remains unclear. Here we identify a subnuclear RNA niche at the nuclear speckle periphery that couples intron retention to cell-cycle-timed RNA release. Using compartment-resolved transcriptional inhibition, sequence-based deep learning and single-molecule and super-resolution RNA imaging in human pluripotent stem cells, we define a class of nuclear RNAs with long-lived retained introns that persist for hours and are enriched in transcripts encoding regulators of genome maintenance and mitosis, including centromere and kinetochore assembly, DNA repair and telomere maintenance. Long-lived retained introns exhibit elevated GC content, predicted structural stability and enrichment for nuclear speckle-associated RNA-binding proteins. In interphase, these RNAs localize to a distinct nuclear speckle-peripheral RNA niche in a spatial arrangement conserved across cell types. During mitotic remodelling, they undergo coordinated, kinase-dependent splicing and are released into the cytoplasm of early G1 daughter cells. Together, these findings link cis-encoded intronic features, subnuclear organization and mitotic remodelling to temporal control of RNA fate. Biayna, Baranovskii and colleagues report that intron-retained RNAs derived from cell cycle- and genome maintenance-related genes are pooled at the periphery of nuclear speckles and undergo synchronous splicing at mitosis, thereby contributing to their temporal regulation.
Embryonic myeloid (EM) cells are the first immune-cell population to emerge during development and must disperse throughout the embryo to act as the first line of defence against infection. Although EM cells migrate directionally toward wounds, how they navigate through unwounded tissues during early colonization remains unclear. Here we show that EM cell dispersion in Xenopus embryos is driven, at least in part, by cell-on-cell migration, an important yet underappreciated phenomenon, guided by dynamic tissue flows. We have established a new ex vivo EM cell migration system that allows for live imaging, computational analyses and optogenetic manipulation. We find that local ectodermal tissue flows repolarize EM cell protrusions and bias their directional migration. Disrupting these flows, both ex vivo and in vivo, either genetically or mechanically, impairs EM cell dispersion. Our findings reveal that mechanical cues generated by surrounding tissue flows coordinate immune-cell migration during development, highlighting an overlooked mechanism by which collective tissue dynamics guide individual cell behaviour.
Interactions between epithelial cells and fibroblasts influence disease progression and treatment response in pancreatic ductal adenocarcinoma (PDAC). While the diversity of fibroblasts in PDAC is increasingly recognized, it remains unclear how these cells differ from fibroblasts found in pancreatic inflammation. Chronic pancreatitis is a stroma-rich inflammatory disease and a risk factor for PDAC, making it a useful setting to study how epithelial cells and fibroblasts change during disease. Here we compare fibroblast diversity and epithelial-stromal interactions in pancreatitis and PDAC using human samples, mouse models and mouse pancreatitis-derived epithelial organoids. We also developed pancreatitis and PDAC organoid co-cultures containing pancreatic stellate cells, fibroblasts and mesothelial cells. Combining in vitro and in vivo models better reflected human disease than mouse models alone. Overall, our findings reveal distinct epithelial and fibroblast features in pancreatitis and PDAC and provide models to identify disease-specific markers and therapeutic vulnerabilities.
Long recognized for its roles in autophagy and endosomal trafficking, phosphatidylinositol 3-kinase class III (PI3K-3) is now shown to also function in the nucleus. A recent study shows that PI3K-3 associates with the transcriptional machinery and a chromatin-modifying complex, and contributes to transcriptional adaptation during fasting.
Enhancer of zeste homolog 2 (EZH2) is frequently overexpressed in cancer, correlating with adverse clinical outcomes. However, how EZH2 overexpression supports tumorigenicity is not fully elucidated. Here we identify a previously unexplored tumour-promoting axis involving EZH2-SREBP2 association. EZH2 and SREBP2, a master regulator of lipid metabolism, cooperate to drive high expression of mevalonate pathway genes, enhancing cholesterol biosynthesis and sustaining tumour growth. Transcriptional activation domains of EZH2 and SREBP2 bind p300 directly, mediating proto-oncogene activation. Furthermore, we employed proteolysis targeting chimeras (PROTACs) to target this non-canonical EZH2 function. Independent EZH2-targeting PROTACs degrade both EZH2 and SREBP2, downregulating SREBP2-associated gene-expression programmes and inhibiting tumour growth. Collectively, this study unveils an EZH2-SREBP2 regulatory axis that promotes cholesterol biosynthesis and fuels tumorigenesis, shifting the current paradigm of EZH2's oncogenic functions.
Metabolic adaptation functions as an important selective bottleneck during tumour development. A study reveals that in response to glucose starvation, a metabolite from the TCA cycle is leveraged to enhance translation of the transcription factor NRF2, providing a critical adaptive response against disulfidptosis.
Exceptionally long genes and cis-regulatory enhancers are selectively activated in mammalian brain neurons, and these loci are mutation hotspots in neurological disorders. However, the organization of these large genomic elements at the level of chromosome folding, beyond local enhancer-promoter interactions, remains poorly understood. Here we report the discovery of a genomic subcompartment in the mouse cerebellum formed by near-megabase-long enhancers and their associated long genes encoding synaptic or signalling proteins. Genomic regions within this subcompartment are enriched in the outer half of the nucleus, whereas other transcriptionally active structures are enriched in the nuclear interior. Using an in vivo CRISPR genetic mini screen, we uncover a specific role for the transcription factor Etv1 in coupling the compartmentalization of neuronal long genes with their expression. Together, our study defines mechanisms that organize transcriptionally active genes across chromosomes in the mammalian brain.
Organelle membrane contact sites (MCSs) coordinate key cell activities and their alterations are associated with several high-incidence disorders, prompting an increasing interest in their study. However, the investigation of MCSs is challenging, mostly because of their nanometric size and dynamic nature. Here we highlight the methods that are available for analysing MCSs. We focus on advanced imaging techniques and discuss their advantages and limitations, providing practical guidance for researchers approaching this field. We propose to study MCSs through a combination of different methodologies, complementing their visualization with investigation of the associated functions. To this end, we also discuss the need to develop innovative biosensors.
Disulfidptosis is a form of regulated cell death triggered by disulfide stress resulting from glucose starvation. The capacity to evade disulfidptosis is crucial for tumour cells to withstand glucose-limited environments. Here we demonstrate that OGDH, a rate-limiting enzyme in citric acid cycle, is critical for conferring resistance to disulfidptosis. High expression of HSPA9 in melanoma protects OGDH from glucose deprivation-induced oxidative inactivation, thereby ensuring OGDH-generated succinyl-CoA for METTL3 succinylation. Succinylated METTL3 recognizes m6A modification on NRF2 mRNA to license NRF2 translation, TrxR1 expression and subsequent evasion of disulfidptosis. Combined suppression of HSPA9 and glucose uptake inhibits melanoma growth in mouse models. In patients with melanoma, expressions of HSPA9 and OGDH negatively correlate with the disulfidptosis signature and are associated with an unfavourable clinical prognosis. Therefore, our findings not only highlight the dependence of melanoma cells on the HSPA9-OGDH-METTL3-NRF2 axis for disulfidptosis evasion, but also propose a combined intervention strategy for melanoma therapy.
Ferroptosis, an iron-dependent form of cell death driven by lipid peroxidation, has emerged as a potential therapeutic strategy for therapy-resistant cancers. Glutathione peroxidase 4 and the selenoprotein biosynthesis pathway essential for its translation are key regulators of ferroptosis but lack effective therapeutic targeting. In a drug screening using a selenoprotein translation reporter, here we identify FMS-like tyrosine kinase 3 (FLT3) inhibitors as suppressors of selenoprotein translation that induce ferroptosis in FLT3-mutant acute myeloid leukaemia. Mechanistically, FLT3 inhibition disrupts selenocysteine recoding, in which a UGA stop codon is recoded as selenocysteine via the SECIS element and associated binding proteins. Notably, the antileukemic efficacy of the FLT3 inhibitor gilteritinib was markedly reduced by dietary vitamin E, which attenuated ferroptosis. This study highlights ferroptosis as a vulnerability in FLT3-mutant acute myeloid leukaemia and suggests that high vitamin E intake may compromise tyrosine kinase inhibitor efficacy partly by suppressing ferroptosis.
How tumour cells rewire metabolic processes in response to changing nutrient availability in the tumour microenvironment is complex. Here, Zhang et al. define a role for PGAM1 in promoting autophagy in response to nutrient deprivation that competes with its catalytic function in glycolysis, which may explain selection for PGAM1 overexpression in cancer.
Circadian clocks underlie daily rhythms in physiology by coordinating temporal patterns of gene expression and protein function throughout the body. At the core of this system in mammals is CLOCK/BMAL1, a ubiquitously expressed heterodimeric transcription factor complex that orchestrates tissue-specific circadian gene expression. The basis for this specificity remains unclear, but tissue-specific interactions at chromatin could provide one. Here we used chromatin immunoprecipitation coupled to mass spectrometry to map CLOCK/BMAL1-associated protein complexes on chromatin in mouse liver, kidney and lung. We detected 1,510 associated proteins, most of which were tissue-specific and not explained by protein abundance. Among these, we identified the homeodomain transcription factors PROX1, HNF1B and HOXA5 as tissue-enriched interactors that bind BMAL1, co-occupy most BMAL1 genomic sites and establish organ-restricted circadian transcription. Our findings demonstrate that tissue-specific transcription factors confer cellular identity on the core clock, thereby contributing to organ-specific patterns of rhythmic gene expression.
Microenvironment remodelling impacts tumour growth and metastasis, but whether remodelling promotes pre-malignant clonal fitness remains unknown. Here, using single-cell RNA-sequencing of the bone-marrow microenvironment in a mouse model of DNMT3A-mutant clonal haematopoiesis (CH), we identify mesenchymal stromal cells (MSCs) in a molecular state of cellular senescence. Elevated bone-marrow MSC senescence is also observed in humans with CH driven by several common somatic mutations. MSC senescence is induced by mutant haematopoietic cells in a contact-independent manner through production of soluble factors including TNF-α and IL-6. These cytokines activate a Stat3-driven pathway that is necessary and sufficient for MSC senescence induction. Genetic or pharmacological depletion of senescent non-haematopoietic cells reduces the burden of CH and delays progression to myeloid neoplasia. Our findings show that microenvironment remodelling modifies pre-malignant clonal fitness and identifies disruption of the crosstalk between pre-malignant cells and their niche as a cancer prevention strategy.
How genes are desilenced without erasure of repressive chromatin is a poorly understood phenomenon. A dominant mode of repression occurs through methylation of lysine 9 of histone H3 (H3K9me3), a mark that engages heterochromatin protein 1 (HP1) to drive chromatin compaction and transcriptional silencing. The erasure and replacement of this repressive mark with acetyl/acyl groups recruits positive factors such as BRD4/BET to elicit gene transcription. Here we report that, in Friedreich's ataxia, a synthetic gene regulator (SynGR1/SynTEF1) licenses transcription across repressive chromatin without removal or replacement of H3K9me3 or HP1. By recruiting BRD4/BET into repressive GAA repeats in frataxin (FXN), SynGR1 creates a paradoxical state wherein gene transcription and repressive chromatin coexist. Contrary to convention, we find that BRD4 partitions into phase separated HP1 condensates in vitro and into HP1 puncta in patient-derived cells, thus offering a mechanistic explanation for desilencing transcription without the dispersal of mesoscale repressive chromatin. More broadly, our study highlights the dynamic nature of repressive chromatin and the context dependence of epigenetic marks in regulating gene expression.
