BMC Molecular and Cell Biology

Background: The spatial organization of the human genome emerges from an enzyme-guided self-assembly process in which chromatin has a bidirectional relationship with transcription. Central to this architecture are chromatin packing domains, 50-200 nm structures exhibiting mass-scaling behavior. Nascent domains arise through transcription and cohesin/CTCF-mediated loop extrusion, while their maturation depends on conditions that permit differential access of epigenetic enzymes to their dense cores and continuously lower density periphery, resulting in the accumulation of heterochromatic marks in domain cores and euchromatic marks outside of the domain cores. In turn, packing domains support transcription by creating an "ideal zone" peripherally to their cores due to a nonmonotonic dependence of transcription rate on local chromatin density. Results: We investigated the role of heterochromatin protein 1 alpha (HP1), a key chromatin crosslinking factor with affinity to H3K9me3 marks, in maintaining packing domain organization. Paradoxically, short-term HP1 degradation resulted in overall downregulation of genes, contrasting with the canonical view that repression of heterochromatin allows chromatin to become more accessible for transcription. While some packing domains persisted, heterochromatic cores of dense packing domains were disrupted. When exposed to hypoxia, HP1-depleted cells exhibited a dampened transcriptional response, showcasing that when domain maturation is disrupted, stress response pathways are not effectively activated. Conclusions: This work highlights HP1 crosslinking as an essential component of domain maturation, as HP1 loss disrupts domain geometry and inhibits efficient transcriptional reprogramming. Our findings suggest an intriguing perspective on the potential relationship between chromatin architecture and gene regulation that could inform chromatin engineering-based treatments.

Introduction: Endothelial-mesenchymal transition (EndoMT) is a dynamic endothelial cell-state transition increasingly implicated in fibrosis, vascular dysfunction, inflammation and cancer. Despite expansion of EndoMT-focused transcriptomic research, EndoMT representation remains limited to broader epithelial-mesenchymal transition (EMT) frameworks in standard gene set repositories. Methods: To address the absence of a general-purpose EndoMT gene set for transcriptomic enrichment analysis, we developed an open EndoMT gene set resource and accompanying R package. A literature-informed EndoMT gene set was curated and directionally assigned to EndoMT UP and EndoMT DOWN signatures according to reported or hypothesised expression during partial EndoMT, defined here as an active transitional state rather than a complete mesenchymal endpoint, to improve capture of EndoMT-associated transcriptional changes across different stages of the process. Genes were annotated by marker subtype and implemented as Gene Matrix Transposed files distributed through the R package, together with exported R objects and gene-level metadata. Benchmarking was performed using bulk RNA-seq data sets GSE118446, comprising seven-day IL-1l{beta}/TGF-{beta}2-treated human umbilical vein endothelial cells (HUVECs) and human pulmonary arterial endothelial cells, and GSE342578, comprising three-day TGF-{beta}1/2/3-treated HUVECs; single-cell RNA-seq data set GSE237895, comprising seven-day TGF-{beta}1-treated and SNAI1-overexpressing HUVECs; and endothelial cell and cancer-associated fibroblast populations from human metastatic melanoma single-cell RNA-seq data set GSE72056. Results: In GSE118446, EndoMT UP was positively enriched and EndoMT DOWN negatively enriched in chronically IL-1{beta}/TGF-{beta}2-treated endothelial cells, concordant with experimentally validated EndoMT induction, while partial EndoMT-associated enrichment was detected in single ligand-treatment. In contrast, EndoMT UP was negatively enriched following acute TGF-{beta}1/2/3 treatment, suggesting temporal differences between acute TGF-{beta} stimulation and chronic EndoMT induction. In GSE237895 mesenchymal-like endothelial cells, EndoMT UP was positively enriched and EndoMT DOWN negatively enriched in both TGF-{beta}1-treated and SNAI1-overexpressing models. EndoMT gene sets also discriminated endothelial and mesenchymal/stromal transcriptional states in GSE72056 metastatic melanoma. Marker subtype and Gene Ontology Biological Process analyses provided additional exploratory resolution of EndoMT-associated components beyond MSigDB Hallmark EMT. Discussion: The EndoMT R package provides a dedicated, accessible and interoperable resource for EndoMT-focused transcriptomic enrichment analysis. Benchmarking demonstrates utility for detecting established, partial and divergent EndoMT-associated states, supporting broad applicability across EndoMT biology research.

Oncogenic mutations are known to occur at non-random rates and specific hotspots, yet the structural and thermodynamic factors underlying these hotspots remain poorly understood. This study presents molecular dynamics simulations of 22 cancer hotspots across 10 oncogene families, simulated as histone-DNA complexes. Across 18 of 22 mutations, thermodynamic effects were predominantly localized to within 6 [A] of the DNA-histone interface (mean capture 104%), with van der Waals interactions driving the effect at the thermodynamic extremes, indicating that oncogenic mutations alter nucleosome binding through precise local contact changes rather than global structural rearrangements. Further, analysis revealed a gene-family correlated pattern in thermodynamic stability. RAS family mutations showed a consistent trend toward nucleosome stabilization (mean {Delta}{Delta}G = -4.82 kcal mol-1), while kinase domain mutations trended toward destabilization (mean {Delta}{Delta}G = +40.12 kcal mol-1), a difference reaching statistical significance in this exploratory analysis (Mann-Whitney U, p = 0.008). This interface-specific mechanism, combined with the gene-family-correlated thermodynamic pattern, provides a biophysical framework for understanding nucleosome-level contributions to cancer hotspot mutation biology.

Oxidative phosphorylation (OxPhos) and substrate-level phosphorylation (SLP) are the primary biochemical mechanisms for ATP generation in mammalian cells. Increased dependency on SLP can arise from either transient (e.g., Crabtree effect) or chronic (e.g., Warburg effect) suppression of OxPhos. We evaluated the steady-state bioenergetics of quiescent and proliferating mouse cells matched in genetic background and cell biology, including primary thioglycollate-elicited peritoneal macrophages, malignant VM-M3 glioma with macrophage characteristics, and malignant CT-2A astrocytoma. Data are presented showing: 1) OxPhos insufficiency was the primary bioenergetic hallmark of proliferating malignant cells. 2) Dysregulated proliferation was associated with lower metabolic flexibility under nutrient stress than was growth arrest or regulated proliferation. 3) The Crabtree effect was present in macrophages and involved a glucose- and time-dependent suppression of OxPhos coupled to ATP production through SLP and resistance to mitochondrial inhibitors; lowering glucose concentration or substituting glucose with respiratory fuels increased OxPhos and restored sensitivity to mitochondrial inhibitors. 4) The Warburg effect in tumor cells involved a persistent SLP dependency and resistance to mitochondrial inhibitors under equivalent glucose-replete conditions. 5) OxPhos could sustain the regulated proliferation of non-tumor cells in the absence of a Warburg effect. Collectively, our findings emphasize that comparisons between normal and cancer cell metabolism require long-term experimental endpoints that ensure steady-state ATP sufficiency.

In our past study on human cilia from primary ciliary dyskinesia (PCD) patients using cryo-electron tomography and mass spectrometry, defects in the DNAH5 gene were proven to cause the loss of the entire outer dynein arm along with other proteins. This phenomenon was not observed in the unicellular green alga Chlamydomonas. In this study, we examined the loss of ciliary components caused by defects in various genes, based on proteomic and structural analyses of motile cilia from multiple PCD patients. The absence of single outer arm dynein genes causes a loss or significant decrease in other inner and outer arm dyneins. Interestingly, some patients with outer dynein defects show decreased intraflagellar transport (IFT) proteins, suggesting an influence of cargo components or assembly on transport. These phenomena were not observed in Chlamydomonas, suggesting a more complex mechanism of ciliogenesis in humans despite the high similarity in the final 3D architecture of the 9+2 axoneme. Defects in certain central pair proteins unexpectedly reduced components on the doublets as well. Our results demonstrate protein-protein interactions during stages of human motile ciliogenesis that are more complex than those in unicellular organisms.

Prospero-related homeobox (Prox) genes encode a family of transcription factors that play essential roles in the development of several organs and systems, including the central nervous system, lymphatic endothelium, musculature, and liver. Despite their developmental importance, the evolutionary history of the vertebrate Prox gene family remains poorly understood. In this study we combined phylogenetic and synteny analysis to characterise the evolution of the Prox family in vertebrates. Our results reveal that two to three Prox subfamilies were already present in the last common ancestor of jawed vertebrates. We clarify the identity and evolutionary relationships of well-studied members of this family and identify multiple independent losses of Prox2 and Prox3 genes in specific vertebrate lineages. Furthermore, we uncover evidence for the existence of a fourth Prox gene in the ancestral vertebrate genome, which was subsequently lost. Overall, this study provides the first comprehensive analysis of the evolutionary history of the vertebrate Prox gene family and establishes a foundations for future studies on the functional roles of these genes.

Nucleolar alterations are characteristic features of cancer cells; however, how changes in the overall morphology relate to internal subcompartment organization and ribosomal RNA (rRNA) dynamics remains unclear. In this study, the nucleolar organization of non-transformed MCF-10A mammary epithelial cells and MDA-MB-231 breast cancer cells was quantitatively compared. MDA-MB-231 cells exhibited differences in nucleolar morphology, accompanied by altered spatial organization of the dense fibrillar component and granular component, and accelerated intranucleolar trafficking of nascent rRNA. Pharmacological perturbation with SU056 shifted multiple structural and dynamic parameters toward an MCF-10A-like profile. Conversely, transient physicochemical perturbation with 1,6-hexanediol induced several MDA-MB-231-like nucleolar features in MCF-10A cells, which returned to their untreated profile after washout. These findings support the view that cancer-associated nucleolar alterations are an integrated reorganization across morphological, spatial, and dynamic dimensions. The observed reversibility further indicates that cancer-associated nucleolar organization can be remodeled in response to perturbations. By linking the morphology, subcompartment organization, and nascent rRNA dynamics within a common framework, this study provides a basis for exploring the establishment, maintenance, and remodeling of distinct nucleolar profiles in cancer.

Pannexin 1 (PANX1) is a channel-forming glycoprotein that has been implicated in regulating melanoma cell properties such as growth, migration, and invasion. Here we report that the CRISPR-Cas9 mediated ablation of PANX1 or channel inhibition with probenecid shifted A375-P cell cycle distribution towards G2/M, while channel inhibition with spironolactone stalled cell cycle progression at the G1/S checkpoint regardless of PANX1 expression. Bulk RNA sequencing revealed cell cycle related gene expression was downregulated with PANX1 targeting strategies and this was exacerbated when PANX1 deficient cells were treated with spironolactone. When grown as spheroids, we found the deletion and inhibition of PANX1 disrupted spheroid compaction, with spheroids displaying poorly defined borders and reduced circularity. The deletion of PANX1 increased spheroid fragmentation, and this phenotype was intensified when spheroids devoid of PANX1 were treated with spironolactone, highlighting a potential synthetic lethal effect. Using liquid chromatography mass spectrometry, we sought to determine whether PANX1 had binding partners that may act to stabilize spheroid integrity and found that PANX1 co-immunoprecipitated various cell adhesion molecules such as {beta}-actin and F-actin-capping protein subunit -1, suggesting PANX1 and its interacting partners may stabilize cell-cell contacts. When control and PANX1 ablated cells were grown in chick chorioallantoic membrane xenografts to assess their tumour growth characteristics, we discovered that the deletion of PANX1 reduced tumour surface area and viability. Our findings indicate that PANX1 regulates cell cycle progression and the structural architecture of A375-P melanoma tumours, highlighting the therapeutic utility of targeting PANX1 in melanoma.

Palmitate-associated lipotoxic stress activates the endoplasmic-reticulum stress sensor protein IRE1, but how IRE1 signaling influences genotoxic-stress responses in triple-negative breast cancer remains unclear. Here, we investigated IRE1 and XBP1 signaling in MDA-MB-231 cells exposed to palmitate and etoposide. Under combined lipotoxic and genotoxic stress, XBP1 depletion increased DNA-damage accumulation in IRE1 wild-type cells but not in IRE1-deficient cells, whereas IRE1 re-expression reduced DNA damage. Pharmacologic IRE1 RNase inhibition also increased etoposide-associated DNA damage, supporting a protective role for IRE1 RNase-dependent signaling. IRE1 status and XBP1 manipulation differentially affected H2A.X and {gamma}H2A.X abundance, indicating context-dependent regulation of chromatin-associated DNA-damage signaling. At the RNA level, H2A.X was enriched in IRE1 immunoprecipitates, and the H2A.X-linked DNA-damage-response transcripts HUWE1 and BRCA2 also associated with IRE1 under combined stress. These findings link palmitate-activated IRE1-XBP1 signaling to genome-protective responses during genotoxic stress and identify a network of IRE1-associated DNA-damage-response transcripts in triple-negative breast cancer cells. Direct IRE1-mediated cleavage of these transcripts remains to be established.

In eukaryotic cells, the positive transcription elongation factor b (P-TEFb) plays a critical role in the transition of RNAPII from the paused state to actively transcribing mode. Although three different cyclin (Cyc) T (CycT1, T2a, and T2b) interact with CDK9 to form functional P-TEFb, a majority of P-TEFb complexes are comprised of the CycT1 and CDK9. To analyze the role of the CycT1 subunit of P-TEFb on cellular transcription, we established HEK293T cells lacking CycT1 proteins (CycT1-KO cells). While no apparent growth defects were observed with CYcT1-KO cells, the level of CDK9 was decreased and no compensatory over-expression of CycT2 was observed, suggesting that the reduced level of functional P-TEFb complexes is sufficient for the normal cell growth. Reporter gene assays indicate that NF-kappaB-dependent transcription induced by PMA was impaired in CycT1-KO cells although the function of NF-kappaB (P65) per se was not affected. On the other hand, AP1-dependent transactivation induced by PMA was unaffected in CycT1-KO cells. Moreover, transcription stimulated by JQ1, a strong P-TEFb inducer, was reduced in CycT1-KO cells. Data of biochemical analysis indicate that P-TEFb with CycT1 (P-TEFb (CDK9:CycT1)) was efficiently released from 7SKsnRNP by JQ1 while P-TEFb (CDK9:CycT2) was not affected by JQ1. Transcriptome analysis indicated that the lack of CycT1 had a minor effect on the steady-state transcription. However, expression of JQ1-dependent genes was severely reduced in CycT1-KO cells. Interestingly, referring to gene expression profiles of 33 different types of cancer revealed that 11 out of 13 top JQ1-dependent genes were also highly upregulated in Pancreatic Adenocarcinoma. From these results, we conclude that although many genes can be regulated by both P-TEFb (CDK9:CycT1) and P-TEFb (CDK9:CycT2), CycT1 plays a critical role in regulating highly inducible genes, which are also aberrantly regulated in a particular type of cancer.

Abstract Background Liposarcoma is a rare cancer, comprising four major histological subtypes: well-differentiated, dedifferentiated, myxoid and pleomorphic liposarcoma. Therapeutic options remain limited for advanced disease, and additional biomarkers that may support biological characterization, diagnosis, or risk stratification are needed. Methods Bulk RNA sequencing (RNA-seq) was performed on paired tumour and adjacent non-tumour tissues from an analysable subset of 16 patients (22 tumour specimens) within a clinicopathological cohort of 21 patients. Differential gene expression analysis, principal component analysis, gene set enrichment (GSEA) analysis and single-sample GSEA (ssGSEA) were used to define subtype-specific transcriptional programs and imprinted-gene dysregulation. PEG10 expression was validated by RT-qPCR and RNA fluorescence in situ hybridization (FISH), and its cellular localization was explored by combined FISH and immunofluorescence for P53, vimentin, Ki67, and CD34. PEG10 expression in liposarcoma was further investigated in an external single-cell RNA-sequencing dataset of dedifferentiated liposarcoma. An exploratory survival analysis was performed in the pan-sarcoma TCGA-SARC cohort. Results Transcriptomic profiling identified distinct subtype-specific gene expression patterns and broad dysregulation of imprinted genes in liposarcoma compared with adjacent non-tumour tissue. Among all the imprinted genes, PEG10 showed a marked tumour-to-normal expression difference and good discriminatory performance between tumour and normal tissues in the discovery cohort (AUC=0.867). In the TCGA sarcoma cohort high PEG10 expression was associated with shorter overall survival. Immuno-FISH and single-cell analyses revealed that PEG10 was predominantly detected in tumour and proliferating cell populations. Importantly, PEG10 expression was higher in high-grade tumours. In bulk RNA-seq data, PEG10 expression correlated with hypoxia, extracellular matrix remodelling and invasion ssGSEA signatures. In the external single-cell RNA-seq dataset PEG10high tumours showed a reduced immune cell infiltration. Conclusions This study provides an integrated transcriptomic characterisation of liposarcoma and identifies PEG10 as a candidate tumour-associated biomarker linked to aggressive disease features. The diagnostic and prognostic value of PEG10 requires validation in larger, independent, subtype-balanced liposarcoma cohorts, and its potential therapeutic relevance requires direct functional investigation.

Dysfunctions in transcription cause severe human diseases. In eukaryotes, transcription initiation by RNA polymerase (Pol) II requires the formation of the pre-initiation complex (PIC) composed of general transcription factors (GTFs), Pol II, and an essential multiprotein coactivator, Mediator. In vitro experiments with GTFs and Pol II have depicted a linear sequence of PIC assembly. However, PIC assembly paths in vivo at the genomic scale and Mediator's role in these paths remain poorly understood. One strategy characterizes ChIP-seq occupancy alterations in Mediator mutants, but analysis of these data still lacks a formalized interpretation framework. In this study, we address this need by developing a quantitative framework that scores candidate assembly paths according to their ability to explain these alterations. This framework combines a model of PIC assembly based on a system of differential equations with parameter optimization based on a penalized criterion. We applied this new framework to datasets from two yeast Mediator mutants, in the Med17 and Med10 subunits. Our results show that the best-supported PIC assembly paths differ from those inferred in vitro. In particular, we show that it is important to distinguish the core TFIIH module from the TFIIK kinase module, and that similar paths starting with Mediator or TBP receive different levels of support. Furthermore, although multiple paths fit the data equally well, they differ markedly for specific gene groups. Taken together, the results show that the path can depend on the gene, and are also compatible with more than one path being operational in vivo for a single gene. This work improves our understanding of PIC assembly paths and transcription initiation, and opens perspectives for future modeling and experimental studies.

Purpose. To determine which proposed keratoconus (KC) mechanisms carry its genetic susceptibility and how it relates to corneal structure, and which describe its corneal tissue. Methods. Six mechanism modules and two attribution sets (transforming growth factor-{beta} [TGF-{beta}] and canonical type-2 atopy) were tested for enrichment in three independent European KC genome-wide association studies (GWAS) and in GWAS of central corneal thickness (CCT) and corneal resistance factor (CRF), with colocalization at matrix loci. Tissue expression was pooled across nine arms from eight studies with control-source meta-regression; activator protein-1 (AP-1)/immediate-early regulatory activity was scored in 107 donors, spatial expression in 21, and serum responses in human and rabbit stromal cells. Results. Extracellular matrix (ECM) was the only module enriched in all three KC sources (P [≤] 5.46 x 10-) and for CCT, CRF, and thickness-independent CRF (P [≤] 2.07 x 10-). COL5A1 shared causal variants with CCT in all three sources (posterior probability 0.985-0.991), and FNDC3B and COL1A1 with CRF or its thickness-independent component (0.961-0.986). Pooled, KC corneas had lower general and corneal-local inflammatory and stress/immediate-early expression (log2 fold-change -0.97, -0.98, -0.82; P [≤] 0.049). In whole-cornea and stromal tissue, ECM expression reversed between postmortem-donor and pathological controls (log2 fold-change +0.36, -2.34), whereas inflammatory and TGF-{beta} programs were lower against both. AP-1/immediate-early regulatory activity was lower in four donor cohorts (Hedges' g -1.50) and stress/immediate-early expression in two spatial cohorts; serum raised immediate-early readouts in human and rabbit cells. Conclusions. KC combines matrix-mechanical genetic susceptibility with a low-inflammatory, low-immediate-early corneal state whose matrix expression direction depends on the control source. Because this susceptibility is genetically shared with corneal thickness and resistance, interventions on the inherited disease are judged by corneal structure and mechanics.

Two rounds of whole-genome duplication (2R-WGD) in the vertebrate lineage are thought to have driven gene diversification. Mammals have four genes encoding five nebulin superfamily proteins (LASP1, LASP2/NEBL, NEB, and NRAP) hypothesised to have arisen from invertebrate LASP via WGD. Here, we examined the evolutionary fate of the nebulin superfamily after an additional WGD, teleost-specific genome duplication (TGD). Genome and transcriptome analysis of zebrafish (Danio rerio) and medaka (Oryzias latipes), of which the complete genomes were recently determined, showed only lasp family genes retained duplicate copies. Zebrafish retained two LASP2/NEBL-derived ohnologs; one (LASP2L) had been misidentified as a nebulette gene in the Zebrafish Information Network (ZFIN) despite lacking nebulette-specific exons. Another (LASP2/NEBL) is newly identified in this study because it lies in a newly determined region of the latest genome assembly. Contrastingly, medaka retained two LASP1 ohnologs and one LASP2/NEBL. The duplicated lasp family proteins showed overlapping and specific tissue expression patterns. We confirmed all three zebrafish lasp proteins bound actin and co-localized with actin-rich structures when ectopically expressed in cultured fibroblasts. This supports that TGD-derived lasp duplicates underwent lineage-specific retention and expression divergence in teleosts whilst conserving core actin-binding properties.

Chromosome was "self-assembled" into a complex three-dimensional topology in the nucleus, which provided the structural basis for important biological processes such as gene expression regulation and cell differentiation. The current understanding of the three-dimensional organization of the genome is based on high-throughput sequencing and imaging technologies to visualize the conformation of chromatin in its native environment. This study proposes a new research perspective and technical means to use fusion genes to determine the interaction information and three-dimensional structure of chromosomes. This three-dimensional information provided by the fusion gene spectrum not only shows the universality of the spatial layout of chromosomes, but also increases the interpretability of the occurrence of fusion genes. The chromatin conformation capture data of multiple tissues and periods is significantly correlated with the strength of fusion genes. For example, the frequency of trans-interaction between chromosomes 11 and 17 was the highest, and the frequency of fusion gene occurrence corresponding to KMT2A on chromosome 11 was the highest. Therefore, we infer that this structural universality is a common feature of the human genome, which provides a theoretical basis and data for predicting chromosome fusion events.

Uterine leiomyomas, commonly known as fibroids, are benign tumors of the female reproductive tract. They are the most common tumor of the female reproductive system and the leading cause of hysterectomy in the United States. Progesterone, estrogen, and their receptors are important drivers for the development and growth of leiomyomas. How estrogen drives leiomyoma growth remains unclear. We have previously shown that simvastatin can inhibit leiomyoma growth by modulating intracellular calcium. This suggests that calcium signaling is important for leiomyoma growth. We therefore hypothesized that estrogen may drive leiomyoma growth by stimulating calcium release through the membrane estrogen receptor GPR30 (also known as GPER). We found that estrogen dose-dependently induced calcium release in leiomyoma cells. The GPR30-specific agonist G-1 also induced calcium release, indicating that GPR30 mediates estrogen-mediated calcium release. The GPR30 antagonist G-15 blocked estrogen-induced calcium release and significantly reduced leiomyoma proliferation. Our results demonstrate that GPR30 is a major driver of estrogen-dependent growth in leiomyoma cells by modulating intracellular calcium. These findings may have high therapeutic relevance to leiomyomas and other estrogen-dependent tumors.

Skeletal muscle is a dynamic tissue able to regenerate in response to injury. This regeneration relies primarily on the activation of precursor cells, known as muscle stem cells (MuSC). Upon activation, skeletal MuSC re-enter the cell cycle and proliferate as myoblasts, which subsequently either differentiate and fuse to form new fibers or return to quiescence to maintain long-term regenerative capacity. From primary human myoblasts, we generated reserve cells (RCs), quiescent cells similar to MuSC, and investigated their activation after stimulation with a growth medium containing serum. Here, we show that Orai3 calcium channel is primarily expressed in RC, where it promotes RC activation in a calcium-independent manner. We demonstrate that Orai3 does not contribute to store-operated calcium entry (SOCE) or calcium response induced by serum stimulation in RC cells, supporting the hypothesis that Orai3 plays a unique role in RC, distinct from its calcium channel activity. Using a protein proximity assay (BioID), we identified the large scaffold protein AHNAK2 as a potential partner of Orai3. AHNAK2 is expressed at high level in myotubes, and has a similar effect on RC activation than Orai3. Both Orai3 and AHNAK2 are necessary for proper myoblast differentiation and RC activation, while acting through different signaling pathways. Specifically, we show that Orai3 directly influences the RC fate, whereas AHNAK2 facilitates RC activation via signals derived from myotubes. These findings provide new insights into the molecular mechanisms underlying the activation and quiescence of human MuSC.

Microtubules, composed of - and {beta}-tubulin polymers, are essential components of the eukaryotic cytoskeleton. They maintain cellular shape and structural integrity and play critical roles in cell division and in intracellular vesicular transport. In Plasmodium, the parasite that causes malaria, nuclear replication during the liver stage is among the fastest known in eukaryotic cells and relies heavily on microtubules for DNA segregation and cytoskeletal organization. Despite their importance, the role of microtubules in liver stage development remains largely unexplored. Here, we investigated microtubule dynamics during liver stage development using a combination of cell and molecular biology techniques, expansion microscopy, and live-cell imaging. By employing antibodies specific for {beta}-tubulin post-translational modifications (PTMs), we found that the Plasmodium sporozoites subpellicular microtubules (SSPM) persist during liver infection, giving rise to liver stage parasite microtubule bundles (LSPMB). These LSPMB form multimeric tubulin structures within hepatocytes and are redistributed to the hemi-spindle poles of parasite nuclei during schizogony. Deletion of the C-terminal region encompassing all known Plasmodium -tubulin PTM sites prevented sporozoite migration from the mosquito midgut to the salivary glands, effectively blocking parasite transmission. Using Plasmodium microtubule-specific depolymerisation drugs, we found that while LSPMB are stable in sporozoites, they exhibit dynamic behavior during hepatocyte infection. Given the regulatory role of PTMs in microtubule dynamics, we generated parasite mutants by substituting and deleting key {beta}-tubulin C-terminal residues involved in PTMs. Substitution of the polyglutamylation site with alanine and deletion of the C-terminal tyrosination/detyrosination motifs impaired parasite growth during liver infection. Together, our findings reveal extensive microtubule remodeling during liver stage development and establish -tubulin C-terminal modifications as critical regulators of both intracellular development and parasite transmission of Plasmodium parasites.

Chromatin profiling methods, such as ChIP-seq (chromatin immunoprecipitation followed by sequencing), are used to characterize the genomic localization of DNA-associated proteins. While ChIP and ChIP-seq have been used for decades, an orthogonal approach, CUT&Tag (Cleavage Under Targets and Tagmentation), is gaining popularity as an efficient and cost-effective alternative. Although previous comparative studies note discrepancies in signal-to-noise ratios and detection bias at certain genomic regions, many differences between ChIP-seq and CUT&Tag results remain largely unreconciled. Here, we systematically investigate the disagreeing signals captured by these two methods across well annotated genomic regions. We assess multiple histone mark profiles generated by different groups in two cell lines (K562 and MCF-7). Overall, our analysis indicates that compared to ChIP-seq, CUT&Tag may have limited sensitivity in low-GC environments and, as previously observed, increased signal in hyper-accessible chromatin. Notably, within GC-poor regions of active gene bodies and Polycomb-repressed domains, CUT&Tag exhibits a loss of H3K36me3 and H3K27me3 signal, respectively, where occupancy of these histone marks is otherwise expected. Further, active promoters with discrepant H3K4me3 and H3K27ac signal between the two assays differ systematically in GC content and chromatin accessibility. Promoters differentially enriched for CUT&Tag signal relative to ChIP-seq generally show higher, broader GC-content profiles and higher DNase-seq and ATAC-seq signal, while promoters enriched for ChIP-seq signal harbor the opposite characteristics. A local bias for high GC content and/or chromatin accessibility in CUT&Tag may also explain its differing signal patterns at nucleosome-depleted regions (NDRs) compared to ChIP-seq and MNase-seq promoter profiles. Altogether, our results highlight that studies focused on profiling the intensity and structure of histone modification occupancy can be sensitive to potential biases of CUT&Tag to GC content and chromatin accessibility. These characteristics should be accounted for when selecting a chromatin profiling approach, analyzing and interpreting data as well as drawing biological conclusions.

Gene duplication is an important evolutionary mechanism contributing to genomic innovation and adaptation. While the long term fate of duplicated genes has been extensively studied, immediate effects such as those resulting from increase in gene dosage remain understudied. Of particular interest is the question of how expression level relates to the optimum after a duplication, as it could fall short, exceed or directly reach the optimal expression. In this study, we investigated the relationship between expression and fitness for 11 genes previously reported to increase fitness when duplicated in Saccharomyces cerevisiae to compare the expression level achieved by duplication to the one maximizing fitness. While most of the studied genes show little fitness variation across the expression levels tested, we found that ESP1, which encodes a separase essential to anaphase initiation, exhibits a clear fitness optimum at an expression level above the native single-copy state. However, the expression level associated with gene duplication exceeds the optimum. We find that ESP1 overexpression is associated with a reduced cell size and a lower proportion of the cell cycle spent in G2 phase, consistent with its role in cell cycle progression. We propose that the duplication of ESP1 accelerates the cell cycle, resulting in smaller, faster-dividing cells. When measured in different environments, the fitness functions also exhibit similar shapes, with slight variation in the optimal expression. Our findings highlight how gene duplication can confer an immediate selective advantage through dosage increase while being non-optimal, reversing the directionality of natural selection on expression level after duplication.