Cell and organismal growth is controlled not only by the availability of nutrients, but also the ability to dynamically sense and respond to changes in metabolic demand. We have identified a protein, TMEM263 (also known as C12orf23) as a new mechanistic link between growth and lipid metabolism. TMEM263 was discovered in a screen as an ER-resident protein, and we have characterised its role as both necessary and sufficient for lipid droplet formation. TMEM263 has two transmembrane domains that fold into a hairpin structure which are essential for its localisation to the ER and to lipid droplets. Functionally, we propose that TMEM263 can interact with and support the condensation of neutral lipids in a bilayer to promote lipid droplet formation and growth. Consistently, loss of TMEM263 in cells and in zebrafish significantly impairs lipid droplet formation. Loss of TMEM263 protein function in vivo is associated with organismal growth defects and proportional dwarfism and our study provides a mechanistic understanding linking these phenotypes to impaired lipid droplet biology.

Upstream open reading frames (uORFs) are a widespread class of translated regions (translons) occurring in 5′ leaders of mRNAs and serving critical roles in post-transcriptional regulation. However, their specific biological activities in human cells remains to be fully elucidated. Here, we conducted a genome-wide CRISPR-Cas9 loss-of-function screen of 978 uORFs identified with ribosome profiling, across human cell lines of distinct origin (HAP1, A549 and HEK293T). A total of 155 uORFs were identified as being essential for cell proliferation. These uORFs showed a high cell-type specificity, with only a few being universally essential. Subsequent analysis has revealed that the primary reason underlying the uORF essentiality is not encoded micropeptides, but rather cis -regulatory mechanisms. Moreover, uORFs located within short 5′ UTRs were disproportionately sensitive to frameshift-inducing indels, which frequently lead to the uORF extension and overlap with the coding region (CDS), resulting in translational repression. Finally, by intersecting regions of essential uORF with ClinVar and dbSNP datasets, we identified naturally occurring variants with the potential to disrupt their function and contribute to disease phenotypes. These findings highlight a pervasive and underappreciated layer of translational control in human cells and establish uORFs as critical cis -regulatory elements with potential relevance to human health.

Rapid identification of viral infections and specific variants in patient samples requires a simple and multiplexed RNA detection method that does not rely on DNA sequencing. Although recent direct detection assays based on CRISPR-Cas13a offer rapid RNA detection by avoiding reverse transcription and DNA amplification required of goldstandard PCR assays, these assays are not easily multiplexed to detect multiple viruses or variants without dividing the sample into separate reactions. Here we show that Cas13a acting on single target RNAs exhibits variable nuclease activity that depends on the interaction between the target RNA and crRNA. To exploit this feature for multiplexed detection, we devised a crRNA modification strategy that enables programmable tuning of Cas13a nuclease enzymatic rates. Using a droplet-based Cas13a assay, we demonstrate that kinetic signatures can be harnessed to differentiate among respiratory viruses and SARS-CoV-2 variants in contrived and clinical samples. This kinetic barcoding strategy can be extended to additional RNA targets through simple modification of crRNAs.

Collective animal behaviors arise from a complex interplay between internal physiological states and external environmental cues. In Caenorhabditis elegans , favorable conditions promote dispersal, while stressors like food scarcity or overcrowding trigger aggregation. Here, we describe a distinct behavior termed as swarming, where C. elegans move and feed in aggregates despite abundant food availability. While environmental factors have been implicated in this behavior, the underlying genetic and molecular mechanisms remain unclear. We identify a novel role for the conserved calsyntenin protein CASY-1 in regulating swarming. Through genetic, behavioral, and optogenetic approaches, we show that CASY-1 functions in sensory neurons to modulate the neuropeptide pigment-dispersing factor (PDF) signaling. Mutants in casy-1 show impaired PDF-1 signaling and reduced inhibition of the serotonin pathway, a known regulator of social behaviors. This dysregulation, along with its associated mechanosensory and foraging defects, likely contributes to the swarming phenotype. Our findings reveal a putative neuromodulatory pathway critical for swarming behavior in C. elegans .

Apomixis, a process of clonal reproduction through seed, has the potential to significantly change agriculture by enabling a clonal seed propagation system for hybrid crops. Here, we demonstrate that hybrid seed from synthetically induced apomictic sorghum hybrids can be generated and maintained across multiple seed generations. This was achieved through the combination of avoidance of meiosis and induced parthenogenesis. Avoidance of meiosis was generated by the CRISPR/Cas9 knockout of the sorghum meiosis genes Spo11, Rec8, and OsdL1 and OsdL3. Parthenogenesis was induced in the resultant diploid egg cell using a maize egg cell promoter to express the Cenchrus ASGR-BBML2 gene coding sequence. Two strategies incorporating these components were used to induce synthetic apomixis in two different sorghum hybrids. Each hybrid used Tx623 as a female parent and either Tx430 or the African landrace Macia as a male parent. Seed yields in the induced apomictic hybrids were consistent and stable for multiple generations following self-pollination but reduced relative to the sexual hybrids. Sorghum contains two copies of the Osd1 gene that function in meiotic non-reduction. CRISPR/Cas9 knockout of both OsdL1 and OsdL3 loci was sufficient to produce clonal hybrid progeny in conjunction with the other apomixis induction components, but this led to a significant reduction in seed set. By contrast, a single in-frame edit of either OsdL1 or OsdL3 significantly improved seed set of clonal hybrid progeny. Fine-tuning OsdL activity appears to be essential to optimizing fertility. As the efficiency of seed set in the induced synthetic sorghum apomicts was lower than that of the sexual hybrid control, additional improvements are required to unlock the agronomic potential of synthetically induced apomictic sorghum in the field.

Heterochromatin is a repressive epigenetic state that suppresses transcription and safeguards genomic integrity. However, the full mechanism of how it is regulated remains elusive. Here, we focus on a previously described Pol II variant called rpb2-N44Y, which has a single substitution mutation within the Rpb2 subunit of Pol II that reduces RNAi-dependent heterochromatin. Through CRISPR-mediated site-directed mutagenesis, we find that rpb2-N44Y is a gain-of-function mutation. Furthermore, the heterochromatin defects of the rpb2-N44Y mutant requires a subunit of the Elongator complex called Elongator Protein 1 (Elp1), a protein that canonically promotes in mcm5s2U34 tRNA modifications. Intriguingly, we find that loss of Elp1, but not of other Elongator subunits such as Elp3, can robustly suppress heterochromatin defects in the rpb2-N44Y mutant. Elp1 acts independently of the mcm5s2 U34 tRNA modification to suppress RNAi-dependent heterochromatin at the pericentromere and the levels of small interfering RNAs (siRNAs) at affected heterochromatin. Overall, our study reveals two distinct Rpb2-centric pathways, via RNAi or Elp1, that can positively or negatively regulate heterochromatin, respectively. Furthermore, our findings reveal the first evidence of a chromatin function for Elp1 that is distinct from its canonical role in tRNA modifications. This work expands our understanding of how Elp1 can influence chromatin biology.

ABSTRACT Transcription in eukaryotes is regulated by chromatin-based mechanisms that control nucleosome occupancy, chromatin modifications, and transcription factor binding. We have previously shown that the transcription factor ADNP forms the ChAHP complex with the chromatin remodeler CHD4 and HP1 proteins, acting as a site-specific regulator of transcription and antagonist of CTCF binding. However, the molecular basis of these functions remained unclear. Here, we demonstrate that the CHD4 subunit is essential to antagonize CTCF and silence transcription of transposons, while HP1 proteins are dispensable. Although the remodeling activity of CHD4 is not required for ChAHP chromatin association, it is critical for both transposon repression and CTCF antagonism. Our findings support a model wherein ADNP recruits chromatin remodeling activity in a sequence-specific manner, enabling transcriptional control and local modulation of chromatin architecture.

Long-read sequencing enables the incorporation of isoform-level expression into single-cell transcriptomic studies, offering detail beyond those accessible with short-read methods. Although insightful, these approaches have typically been costly and yielded limited data for each individual cell. Recent advances in library preparation approaches and sequencing throughput have brought long-read single-cell studies closer to the mainstream. Here, we present a comparative analysis of commercial approaches for single-cell long-read sequencing. We have performed parallel analyses of the same cDNA material, generated using the 10X genomics platform, on Illumina short-read, and PacBio and Oxford Nanopore long-read platforms. We also demonstrate the impact of CRISPR-based depletion of libraries, to remove highly expressed transcripts, prior to long-read sequencing in these experiments. By analysing single-source cDNA libraries in parallel, we enable a direct comparison of each platform, evaluating standard metrics alongside concordance in clustering and cell type identification. While each approach generates usable gene and isoform expression data, we identify limitations common across platforms, primarily linked to cDNA synthesis inefficiencies and read filtering strategies. Our work demonstrates the increasing utility of single-cell long-read sequencing for isoform-resolved analyses, such as direct immunoglobulin chain reconstruction without additional amplification, and the detection of alternative splicing patterns across immune cell subtypes in CD45, a key gene for immune cell activation and differentiation. Our benchmarking of current platform options provides a foundation for researchers looking to adopt single-cell long-read sequencing into their transcriptomic studies, providing a framework for its integration into diverse biological questions.

The recent discovery of TIGR-Tas (Tandem Interspaced Guide RNA–Targeting Systems) marks a major advance in the field of genome editing, introducing a new class of compact, programmable DNA-targeting systems that function independently of traditional CRISPR-Cas pathways. TIGR-Tas effectors use a novel dual-spacer guide RNA (tigRNA) to recognize both strands of target DNA without requiring a protospacer adjacent motif (PAM). These Tas proteins introduce double-stranded DNA cuts with characteristic 8-nucleotide 3′ overhangs and are significantly smaller than Cas9, offering delivery advantages for in vivo editing. Structural analyses reveal homology to box C/D snoRNP proteins, suggesting a previously unrecognized evolutionary lineage of RNA-guided nucleases. This review positions TIGR-Tas at the forefront of a new wave of RNA-programmable genome-editing technologies. In parallel,I provide comparative insight into the diverse and increasingly modular CRISPR-Cas systems, including Cas9, Cas12, Cas13, and emerging effectors like Cas3, Cas10, CasΦ, and Cas14. While the CRISPR-Cas universe has revolutionized molecular biology, TIGR-Tas systems open a complementary and potentially more versatile path for programmable genome manipulation. I discuss mechanistic distinctions, evolutionary implications, and potential applications in human cells, synthetic biology, and therapeutic genome engineering.

Human induced pluripotent stem cells (iPSCs) present a powerful approach to study human brain physiology and disease, yet robust, pure GABAergic induction has remained difficult. Here we present improved, single-step, transposon-based GABAergic induction with Ascl1/Dlx2, which yields pure GABAergic neurons, in contrast to lentiviral approaches, and was tested across three independent iPSC lines. Proteomic and electrophysiological characterization at different developmental time points showed that these neurons gain a proteomic profile that maps to different cortical interneuron subtypes, particularly VIP+ interneurons, and display typical GABAergic synaptic properties, producing large, synchronous and picrotoxin-sensitive currents. During early development synaptic strength increased threefold, which was accompanied by enhanced expression of multiple GABA- specific presynaptic gene sets, but few changes in postsynaptic gene sets. Synaptic strength continued to improve during late development but with only minor proteomic changes. Co-seeding with NGN2 neurons created stable networks of predefined excitation/inhibition ratios, with corresponding synapse ratios. Taken together, transposon-based GABAergic induction yields pure, mature GABAergic neurons suitable for studying gene sets involved in synaptic maturation and to build excitation/inhibition networks for disease modelling.

SUMMARY Horizontal gene transfer plays a key role in bacterial evolution, yet its efficiency under natural conditions, especially between genetically distinct strains, remains unclear. Using Staphylococcus aureus as a model, we found that gene transfer via various mechanisms is significantly restricted between strains from different clonal complexes (CCs), with the notable exception of lateral transduction, which occurs at high frequency. Interestingly, some strains exhibited a “promiscuous” ability to accept diverse mobile genetic elements. These strains were defective in the key immune defences of S. aureus , specifically the Type I restriction-modification systems that normally protect against foreign DNA. A broader analysis revealed that such immune-deficient mutants are widespread within S. aureus populations. Our study uncovered a trade-off that explains their persistence in nature: although these mutants are more susceptible to phage attack, they gain an evolutionary advantage by acquiring beneficial genes - such as those conferring antibiotic resistance - which enhance survival under selective pressure. These immune-deficient cells act as gateways for foreign DNA, which, once integrated and advantageous, can spread within the same CC. Our findings highlight an unexpected role for immune-deficient bacteria in facilitating the emergence of novel virulence factors and antibiotic resistance, emphasising their importance in shaping bacterial evolution.

Maintenance of T cell population size, which is important for immune homeostasis, is controlled by interleukin-7 (IL-7) and low-affinity TCR/MHC interactions that provide limited survival cues. Using arrayed CRISPR screening of miR-17∼92 targets, Bio-ID proximity labeling and proteomics we identified Tmem127 as an essential regulator of the T cell surface proteome. We validated interaction with the common gamma chain (IL-2Rγ) in a multi-protein complex. Tmem127 reduces IL-7 receptor surface expression to restrict homeostatic proliferation, thereby controlling naïve and central memory T cell population sizes. Tmem127 germline knockout (KO) mice display splenomegaly, accelerated experimental autoimmune encephalomyelitis and Tmem127-deficient bone marrow displays a competitive advantage over wildtype cells. Thus, we identified Tmem127 as an important regulator of the common gamma chain and immune homeostasis.

ABSTRACT Developmental decisions rely on cells making accurate transcriptional responses to signals they receive, as with Notch pathway activity. Local condensates or transcription factor hubs are a proposed mechanism for facilitating gene activation by nuclear complexes. To investigate their importance in endogenous Notch signalling, we deployed multi-colour live-imaging to measure Notch transcription-complex enrichment at a target gene locus in combination with the transcription dynamics. The co-activator Mastermind (Mam) was present in signalling-dependent nuclear foci, during Notch active developmental stages. Tracking these highly-dynamic Mam hubs together with transcription in the same nucleus, revealed that their condensation precedes and correlates with the profile of transcription and becomes stabilized if transcription is inhibited. Manipulations to signalling levels had concordant effects on hub intensities and transcription profiles, altering their probability and amplitude. Together the results argue that signalling induces the formation of transcription hubs whose properties are instrumental in the quantitative gene expression response to Notch activation.

Dengue virus (DENV) continues to pose a major global health burden, yet therapeutic options remain limited due to the virus's capacity for immune evasion, serotype variability, and persistence. While exosomes have been implicated as vehicles for viral dissemination and immune evasion, the cellular mechanisms underlying their generation during DENV infection remain poorly defined. Here, we identify the endoplasmic reticulum (ER)-associated host protein Reticulon 3 (RTN3), particularly its short isoform RTN3S, as a critical regulator of replication-competent viral cargo loading during infectious exosome biogenesis in DENV infection. Using hepatic and monocytic cell models, we revealed that RTN3S expression is induced upon infection and that RTN3S directly associates with DENV replication complexes, facilitating the packaging of replication-competent viral RNA and host proteins into infectious exosomes. Loss of RTN3 function via CRISPR-Cas9 markedly attenuated exosome production and reduced the transfer of infectious viral components to recipient naïve cells. Mutational analyses of RTN3S further revealed that both its N-terminal amphipathic and C-terminal domains are essential for exosomal loading of viral material. Single-cell RNA-sequencing of peripheral blood mononuclear cells (PBMCs) from DENV-infected individuals confirmed RTN3 upregulation in monocytes, particularly in those displaying intermediate/classical phenotypes, and revealed a transcriptional signature linking RTN3 to ER stress, vesicle trafficking, and impaired antiviral responses. These findings uncover a previously unrecognized RTN3-centered mechanism by which DENV hijacks the host exosomal machinery to propagate infection and potentially escape immune surveillance. Thus, our findings demonstrate a novel function for RTN3 in orchestrating the biogenesis of infectious exosomes, providing mechanistic insight and identifying a new therapeutic axis for combating flavivirus infections through host-directed approaches.

Selenocysteine (Sec), the 21st amino acid, is co-translationally inserted at UGA codons via a specialized machinery requiring SECIS elements, Sec-tRNA^Sec, eEFSec, and SECIS-binding protein 2 (SBP2). While SBP2 is essential for Sec incorporation in vitro and in vivo, the function of its paralog, SECISBP2L, remains incompletely defined. In this study, we investigated the distinct roles of SBP2 and SECISBP2L in the human hepatocellular carcinoma cell line HepG2, which expresses a broad selenoproteome. Using CRISPR-Cas9 genome editing, we generated SBP2 and SECISBP2L edited cell lines. Consistent with previous findings, SBP2 targeting impaired selenoprotein mRNA and protein expression, whereas SECISBP2L targeting did not. However, transcriptomic profiling by RNA-seq revealed that SECISBP2L targeting induced differential expression of over 800 genes, with significant enrichment in pathways related to extracellular matrix organization and cell adhesion. In contrast, SBP2 targeting produced a distinct transcriptomic signature enriched for metabolic and ion transport processes. Notably, only limited overlap in differentially expressed genes was observed between the two knockout models. Mass spectrometry and immunoblot data indicated that CRISPR-targeted SECISBP2L cells produce a truncated protein via internal translation initiation, suggesting that observed gene expression changes may be attributable to loss of a portion of the SECISBP2L N-terminus. These findings support a model in which SECISBP2L plays a noncanonical role in regulating gene expression independent of selenoprotein synthesis. Given prior associations between SECISBP2L downregulation or mutation and cancer progression, our data raise the possibility that SECISBP2L modulates cell adhesion and extracellular matrix gene networks relevant to metastatic potential. This work establishes a foundation for further mechanistic studies into SECISBP2L’s role in gene regulation and disease.

Abstract Synthetic lethality (SL) underlies the success of PARP1 inhibitors (PARPi) in treating homologous recombination (HR) deficient cancers, but extending this paradigm to other DNA damage response (DDR) deficiencies has proven challenging. We performed an in vivo CRISPR screen to identify DDR gene mutations that both enhance tumorigenesis and confer sensitivity to PARPi. Our screen identified FANCA deficiency as a driver of PARPi SL that was validated across diverse human cancer models. FANCA deficiency does not impair HR but disrupts Okazaki fragment maturation (OFM), causing lagging strand gaps and RPA exhaustion upon PARPi treatment. These effects require FANCA interaction with FEN1, independently of its canonical role in interstrand crosslink repair. We find FANCA-mediated FEN1 recruitment is required for OFM at oncogene-associated R loops during PARPi treatment. These findings establish a novel and non-canonical function for FANCA in FEN1-mediated OFM that can be leveraged for PARPi synthetic lethality in FANCA-mutant cancers.

During zygotic genome activation (ZGA) in Drosophila, broad domains of Polycomb-modified chromatin are rapidly established across the genome. Here, we investigate the spatial and temporal dynamics by which Polycomb group (PcG) histone modifications, H3K27me3 and H2Aub, emerge during early embryogenesis. Using ChIP-seq and live imaging of CRISPR-engineered GFP-tagged PcG components, we show that PRC2-dependent H3K27me3 accumulates adjacent to a subset of E(z)-bound prospective Polycomb Response Elements (PREs) beginning in nuclear cycle 14 (NC14), with patterns indicative of nucleation followed by spreading. Surprisingly, PRE-binding factors Pho, Combgap, and GAGA-factor are excluded from interphase nuclei prior to NC10 despite nuclear localization of E(z) throughout early interphases. Loss-of-function studies further demonstrate that GAGA-factor is largely dispensable for PcG domain establishment, whereas the pioneer factor Zelda is required for proper deposition of H3K27me3 and H2Aub at a subset of Polycomb domains. The role of Zelda at Polycomb domains is context-dependent; a large subset of targets requires Zelda not for PcG factor recruitment, but instead to license a loaded PRE to deposit H3K27me3 and H2Aub. Our findings support a model where licensing of PcG domains is an initial step in the regulatory processes governing Polycomb-regulated developmental genes.

Distorted GABAergic neurodevelopment is believed to underscore cortical network dysfunction that lies at the heart of neurodevelopmental disorders (NDD) such as autism and schizophrenia. GABAergic neuron diversity is sculptured by cortical environmental cues during protracted postmitotic differentiation. However, the mechanism by which the NDD environment influences GABAergic neuronal development remains largely unknown. Oxysterols are oxidized metabolites of cholesterol that can interact with developmental signaling pathways. Using an iPSC model recapitulating human forebrain GABAergic neuron development and single-cell transcriptomic profiling, we show that 24S, 25-epoxysterol, an NDD-affected oxysterol highly enriched in the fetal brain, promotes neurogenesis, and disturbs the composition of GABAergic neuronal subtypes. Moreover, pharmacological and genetic interrogation identified the liver X receptor as a regulatory pathway mediating the action of 24S, 25-epoxysterol. These findings provide insights into the roles of cholesterol metabolism in neuronal development and a potential mechanism by which dysregulated brain oxysterols contribute to the pathogenesis of NDD.

Transcriptome profiling of bladder cancer has revealed distinct basal-like and luminal-like molecular subtypes, which may be correlated with pathological subtypes of different patient outcomes. However, whether these molecular subtypes originate from the corresponding cell types in the normal urothelium and whether different cells of origin influence bladder cancer progression remain unclear. Here, we conducted cell-type-specific lineage tracing in CRISPR/Cas9-induced mouse bladder cancer models of Pten and Trp53 targeting. We show that although basal, intermediate, and superficial umbrella cells can all serve as the cell of origin for bladder cancer, transformed umbrella cells were gradually displaced by tumor cells from inner layers, particularly transformed basal cells, which had highest stemness. Histological and single cell RNA-sequencing data comparing basal- and intermediate-cell-induced bladder tumors revealed that basal-induced tumors displayed higher heterogeneity, and contained unique cell clusters including Krt14+Ki67+ highly proliferative basal cells, squamous cell carcinoma, and transitioning cells towards the Gata3+ luminal subtype. Trajectory analysis confirmed the cell lineage differentiation hierarchy uncovered in lineage tracing. Moreover, human bladder cancer molecular subtype signatures were highly enriched in mouse tumor cell clusters of the corresponding cell of origin, and a gene signature derived from the unique basal-induced clusters is predictive of worse patient outcome. Overall, our results support that the basal and luminal molecular subtypes of bladder cancer have the corresponding cells of origin as their basis, and that urothelial basal cells are intrinsically more competitive than intermediate and umbrella cells in generating aggressive bladder cancer subtypes.

Extrachromosomal circular DNA (eccDNA) of chromosomal origin is present in all eukaryotic organisms and tissues that have been tested. Populations of eccDNA exhibit immense diversity and a characteristically low degree of overlap between samples, suggesting low inheritance of eccDNA between cells or a deficiency in the methods by which eccDNA is detected. This study revisits the Circle-seq approach for enrichment of eccDNA to address these limitations, hypothesizing that experimental procedures significantly contribute to the observed low eccDNA overlap. We optimized the protocol by reducing the time needed to complete the procedure. Linear DNA is digested by increasing Exonuclease V activity. We employed CRISPR-Cas9 for mitochondrial linearization, which proved superior to using restriction enzymes. A key finding is the critical role of random hexamer primer concentration and genomic DNA input in Rolling circle amplification (RCA) for generating high-quality long amplicons from eccDNA (concatemeric tandem copy [CTC]), essential for confident de novo eccDNA construction from long-read sequencing data. Lower primer concentrations substantially increased the percentage of CTC-derived eccDNA and improved the overlap of identified eccDNAs in technical replicates. Applying this revised approach to human myeloma and breast cancer cell lines, as well as xenograft models, demonstrated >50% overlap in detected eccDNA, a substantial improvement over the <1% overlap observed in previous studies. Additionally, the oncogenic signature of eccDNAs can be identified across all replicates. These findings provide guidelines for developing standardized procedures for eccDNA profiling, advancing our understanding of eccDNA biology, and its potential clinical applications.

Mutations of EIF2AK4 , which encodes the eIF2α kinase GCN2, cause a severe inherited form of pulmonary hypertension called pulmonary veno-occlusive disease (PVOD). Some pathogenic variants of GCN2 are amenable to pharmacological reactivation by low concentrations of ATP-pocket binding inhibitors. Kinase inhibition at modestly elevated concentrations limits the clinical utility of these drugs against PVOD. We therefore performed an in cellulo chemical screen for GCN2 activators and identified three structurally distinct compounds with low micromolar stimulatory activities. Unlike previously described GCN2 activators, one of these molecules activated GCN2 independently of GCN1. Modelling supported by structure activity screens suggested it binds within the ATP-pocket of GCN2, but unlike existing ligands does not protrude inward into the allosteric pocket or outward into the solvent. This overcomes a key requirement of other GCN2 activators.

ABSTRACT Short interspersed nuclear elements (SINEs) are abundant non-autonomous transposable elements derived from RNA polymerase III (POL III)-transcribed short non-coding RNAs. SINEs retain sequence features recognized by the POL III machinery and constitute a substantial portion of vertebrate genomes. Despite their impact on genome stability and evolution, the mechanisms governing SINE transcription remain poorly understood. Although DNA methylation and heterochromatin formation have been implicated in their repression, we find these pathways play only a minor role in mouse embryonic stem cells. Instead, we identify the ChAHP complex as a key repressor of SINE B2 elements. ChAHP directly inhibits POL III transcription by blocking TFIIIB recruitment without affecting TFIIIC binding. This selective interference prevents transcription initiation and highlights a distinct regulatory mechanism. Our findings establish ChAHP as a non-canonical repressor of POL III-dependent SINE transcription, offering new insights into the control of this pervasive class of non-coding genomic elements.

The sequestration of the malaria parasite Plasmodium falciparum in the microvasculature is a major driver of severe malaria, but its pathogenic mechanisms still remain unknown. Advancements in induced pluripotent stem cell (iPSC) technologies offer unique opportunities to study parasite interactions with blood vessels in a well-defined host environment. However, endothelial iPSC-differentiation methods often result in cells with mixed epithelial identity. Here, we have generated an iPSC line with inducible and simultaneous expression of ETS transcription factors (ETV2, FLI1, ERG), which resulted in improved endothelial cell identity and strong barrier function. These cells display a high affinity to infected red blood cells. Exposure to parasite products caused significant endothelial metabolic changes and splicing alterations. Furthermore, it disrupted the iPSC-endothelial barrier, as a consequence of transcriptional downregulation of key barrier processes, and alteration of severe malaria biomarkers. Our novel iPSC-based approach represents a new in vitro platform to study the pathogenesis of vascular infections.

Abstract Deficiency of the Monocarboxylate Transporter 8 (MCT8) severely impairs thyroid hormone (TH) transport into the brain, disrupting brain development as well as peripheral TH homeostasis. Studies assessing MCT8 expression patterns and tissue-specific pathologies induced by local TH-deficiency are often inconclusive due to unreliable antibody staining and the lack of functional tools to specifically target MCT8-expressing cells. For this purpose, we generated non-inducible Mct8-Cre and tamoxifen-inducible Mct8-CreERT2 mice. Mct8-Cre;Sun1-sfGFP mice demonstrated ubiquitous Sun1-sfGFP expression, due to early recombination driven by Mct8 gene expression at the stage of trophoblast implantation. Tamoxifen injection in 6-week-old Mct8-CreERT2 mice induced reporter expression specifically in Mct8-expressing cells in the brain and peripherally in liver, kidney, and thyroid, without leaky reporter expression in vehicle controls. Using vDISCO tissue clearing and 3D-imaging of GFP-nanobody-boosted mice, we further identified the sublingual salivary gland and the prostate as prominent Mct8-expressing organs. Nuclei from Mct8-expressing cells could selectively be enriched using fluorescence-activated nuclei sorting on Mct8-CreERT2;Sun1-sfGFP mice and characterized as choroid plexus cells and tanycytes. Our new inducible Mct8-CreERT2 line provides researchers with a tool to reliably mark, enrich, and characterize Mct8-expressing cells and to genetically modify genes specifically in these cells to study thyroid hormone transport and function.

Abstract Primary aldosteronism (PA), also known as Conn’s syndrome or adrenal aldosterone producing adenoma (APA), is predominantly caused by functional adrenal tumors and is a common cause of secondary hypertension. The KCNJ5 gene mutations are frequently associated with APA, leading to increased aldosterone production. This study investigates the effect of KCNJ5 mutations on CYP11A1 and the aldosterone biosynthesis pathway. We created two model cell lines by introducing homozygous p.L168R and p.G151R mutations in the KCNJ5 gene to SW13 cell line using CRISPR/Cas9 technology. The mutations were verified succeed through Sanger sequencing and multi-omics analysis. Aldosterone and its biosynthesis intermediates were quantitatively analyzed, and the expression of CYP11A1 mRNA in wild-type and mutant cell lines was detected through qPCR. Increased concentrations of aldosterone, pregnenolone, progesterone, and corticosterone in the KCNJ5 mutated cell lines were observed compared to the wild type, while cholesterol levels remained unchanged. qPCR results showed increased CYP11A1 mRNA expression in KCNJ5 mutant cells. Therefore, KCNJ5 mutations promote aldosterone synthesis by enhancing CYP11A1 activity, which catalyzes the conversion of cholesterol to pregnenolone, a critical step in the aldosterone biosynthesis pathway. This study highlights the potential of CYP11A1 as a therapeutic target for treating APA-induced secondary hypertension.