Biology subjects

Unal, E.

Publications and source records attributed to Unal, E..

14 recordsLinked to original sources

bioRxiv2026

APOBEC3 activity and polymerase-ε deficiency are associated with distinct IDH1 R132 hotspot mutations

IDH1 R132 mutations are among the most frequent hotspot mutations in cancer, but their mutational origins have remained unclear. Here, we provide evidence that IDH1 R132C, the predominant IDH1 mutation in cholangiocarcinoma, acute myeloid leukemia, and melanoma, likely arises through APOBEC3-mediated mutagenesis. IDH1 R132C is a TpC>TpT substitution on the lagging-strand DNA template within a hairpin-forming sequence context, consistent with APOBEC3 susceptibility. In vitro assays showed that APOBEC3A can deaminate the relevant cytosine, and APOBEC3A and APOBEC3B were relatively highly expressed in tumor types with recurrent IDH1 R132C mutations. IDH1 R132G, a TpC>TpG substitution at the same site, may similarly result from APOBEC3 activity. By contrast, IDH1 R132H, the predominant IDH1 mutation in lower grade glioma and glioblastoma, is a CpG>TpG substitution at a methylated cytosine on the leading-strand DNA template, a pattern more consistent with DNA polymerase epsilon replication error. Concordantly, tumor types enriched for IDH1 R132H showed relatively low POLE expression. Together, these in vitro and bioinformatic analyses provide insight into the distinct mutational mechanisms that likely underlie recurrent IDH1 hotspot mutations in cancer.

cancer biology↗

bioRxiv2026

APOBEC3-driven neoantigen-rich cancers co-opt 1q23.3 amplification for tumor-intrinsic immune cloaking

Hypermutational processes, including those driven by the APOBEC3 family of cytidine deaminases, generate abundant neoantigens yet give rise to tumors that evade immune recognition. Here, using multi-omics analyses followed by functional validation, we identified a tumor-intrinsic immune-cloaking mechanism in neoantigen-rich epithelial cancers, characterized by coordinated suppression of antigen presentation, immune-recruiting cytokines and immune-checkpoint programs. In bladder cancer, genome-wide copy-number analysis identified recurrent 1q23.3 amplification as a genomic feature of a neoantigen-high/CD8-low tumor state. Within this locus, NECTIN4 emerged as the dominant candidate effector, outperforming extrachromosomal DNA status as a predictor of immune-neoantigen discordance. Similar associations were observed across breast and lung cancers. Functional studies demonstrated that NECTIN4 was sufficient to establish a T-cell-poor tumor microenvironment and confer resistance to PD-1 blockade in immunocompetent mice. Mechanistically, NECTIN4 engaged a DDR1-SHP2 axis that suppressed STAT1 phosphorylation, silencing tumor-cell immune-engagement programs. NECTIN4 blockade restored STAT1 activity and reduced tumor growth, indicating that the cloaked state is pharmacologically reversible. Mutational signature, breakpoint motif, timing and clonality analyses, together with APOBEC3B expression and germline genetic evidence, linked APOBEC3-mediated mutagenesis to recurrent 1q23.3 amplification encompassing NECTIN4. These findings reveal how neoantigen-generating mutational processes can be coupled to structural genome evolution to enable tumor-intrinsic immune cloaking through a therapeutically targetable NECTIN4-DDR1-SHP2 axis.

cancer biology↗

bioRxiv2026

Prefoldin function links meiotic chromosome segregation with cellular remodeling and reveals tubulin sensitivity of the meiotic spindle

Faithful chromosome segregation is essential for producing viable gametes during meiosis, a specialized type of cell division compared to mitosis. Unlike mitosis, meiosis involves two consecutive chromosome segregation events without an intervening round of DNA replication. Here we identify Gim3, a subunit of the ubiquitously expressed and conserved prefoldin complex, as a critical regulator of meiotic but not mitotic chromosome segregation in budding yeast. Loss of Gim3 causes profound defects in chromosome segregation and gamete viability through reduced tubulin protein levels, which are also associated with reduced spindle length. In mitosis, however, GIM3 deletion minimally affects spindle length and chromosome segregation, despite similarly reduced tubulin levels in both contexts, highlighting a previously unrecognized difference between the sensitivity of meiotic and mitotic spindles to tubulin abundance. In addition to chromosome segregation defects, gim3{Delta} cells exhibit aberrant meiotic cellular remodeling, including defects in exclusion of age-associated protein aggregates from newly forming gametes. Importantly, experimentally induced meiotic chromosome mis-segregation similarly disturbs cellular remodeling. Together, our findings identify Gim3 as a key factor required for maintaining chromosome segregation integrity during meiosis and reveal a previously unrecognized link between chromosome segregation and meiotic cellular remodeling.

cell biology↗

bioRxiv2026

T cell-specific loss of IRF1 results in defective CD8 T cell activation and antitumor immunity

Interferon regulatory factor 1 (IRF1) has long been recognized as a tumor suppressor; however, recent studies have revealed context-specific and sometimes opposing roles in cancer progression. Here, we describe a T cell-specific mechanism underlying the antitumor activity of IRF1. Unlike germline Irf1-deficient mice, T cell-specific loss of IRF1 does not lead to a deficiency in cytotoxic CD8 T cells. Nevertheless, tumor burden remains elevated in these mice, associated with reduced CD8 T cell infiltration driven by impaired activation and proliferation in the absence of IRF1. Transcriptomic analysis of activated Irf1-deficient T cells identified NFATc1 as a key gene significantly downregulated upon IRF1 loss. Analysis of human melanoma datasets further corroborated this finding, highlighting a previously unappreciated role for IRF1 in regulating T cell activation and antitumor immunity.

immunology↗

bioRxiv2026

Glutamine codon-driven translational readthrough reveals context-dependent stop codon decoding fidelity

Deviations from the canonical genetic code include reassignment of UAA/UAG stop codons to glutamine in divergent eukaryotes, and tRNAGln has been shown to mediate near-cognate stop codon readthrough in canonical-code organisms. However, the sequence determinants and mechanistic basis of this decoding event remain poorly understood. Using ribosome profiling, quantitative immunoblotting, and mass spectrometry in Saccharomyces cerevisiae, we demonstrate that premature stop codon readthrough efficiency is governed by both local glutamine codon context and the global glutamine codon content of the mRNA. A QXQ motif flanking the stop codon promotes baseline readthrough, which is amplified in proportion to total transcript glutamine codon abundance. Mass spectrometry confirms that glutamine is specifically inserted at the premature stop, with no flanking miscoding, implicating tRNAGln competition with the release factor as the mechanistic basis of readthrough. Consistent with this model, yeast proteins terminating in short C-terminal glutamine repeats are evolutionarily enriched for strong stop codon contexts, suggesting selective pressure to reinforce termination fidelity at readthrough-prone loci.

molecular biology↗

bioRxiv2026

Non-canonical sex chromosome evolution revealed by extreme heterogeneity in homomorphic Y chromosome differentiation in the common frog

Sex chromosome evolution is often viewed as a unidirectional process in which recombination suppression expands around a sex-determining locus, leading eventually to Y-chromosome degeneration. Yet many vertebrates, including frogs, retain homomorphic sex chromosomes and polymorphic differentiation despite long-term recombination suppression, which is quite puzzling. Here, we combine pooled whole-genome resequencing, doubled-haploid YY genomes, and RNA-seq to understand the dynamics of homomorphic sex chromosome evolution in a Swiss Alpine population of the common frog, Rana temporaria, where multiple Y haplotypes coexist. We show that two fully differentiated Y haplotypes carry exceptionally large nonrecombining regions spanning [~]90% of the sex chromosome ([~]618-625 Mb), whereas semi-differentiated Y haplotype retains only a 4.64 Mb Dmrt1-linked sex-determining region, and XX males are genetically indistinguishable from XX females. The large NRRs show limited degeneration, with no evidence of gene loss, Y-linked copy decay, faster-X evolution or enrichment of sex-biased genes, and only modest repeat accumulation. Surprisingly, the coexisting Y haplotypes are neither independent sex-determining systems nor successive stages of a single degeneration trajectory. Instead, they share an ancestral Dmrt1-linked region whose X-Y divergence dates to [~]3.47-5.70 Mya, while present-day Y copies of this region remain nearly identical and the large NRRs have accumulated private mutations independently. We thus propose that the Y chromosome undergoes cyclic dynamics of differentiation: extreme heterochiasmy promotes rapid large NRRs formation, sex-reversed XY females recurrently restore X-Y recombination, gene conversion and/or rare Y-Y recombination may homogenize Y copies at the Dmrt1-linked region, and renewed male transmission drives subsequent Y-specific differentiation. The findings provide a genome-wide resolution to a central paradox in sex chromosome evolution: how sex chromosomes can experience extensive recombination suppression yet remain homomorphic and only weakly degenerated. By showing that heterochiasmy and sex reversal uncouple the physical extent, age, and degeneration of sex-linked regions, our study reframes homomorphic sex chromosomes as dynamic, repeatedly regenerated systems shaped by alternating phases of recombination suppression, restored X-Y recombination and renewed Y differentiation. Significance statementWhy many vertebrate sex chromosomes remain homomorphic despite long-term recombination suppression remains unresolved. Using whole-genome population genomics, doubled-haploid YY genomes, and transcriptomics in the common frog, we show that multiple coexisting Y haplotypes in a single pond share an old Dmrt1-linked sex-determining region but carry younger, independently differentiated Y chromosomes. This genome-wide resolution reveals that extreme heterochiasmy, where recombination is largely restricted to chromosome ends in males, can rapidly generate very large nonrecombining regions, while sex-reversed XY females can restore X-Y recombination and reduce divergence outside the Dmrt1-linked region. These opposing processes generate cyclic dynamics of Y differentiation rather than a directional path towards degeneration. Our study provides a mechanistic explanation for the persistence of co-existing multiple Y haplotypes in one population, maintenance of homomorphic sex chromosomes, and a broadly relevant framework for sex chromosome evolution in lineages with heterochiasmy and sex reversal.

evolutionary biology↗

bioRxiv2025

A microfluidics-based platform enables discovery of gametogenicrejuvenation factors in Saccharomyces cerevisiae

During mitotic growth, Saccharomyces cerevisiae cells age by dividing asymmetrically producing young daughter cells while retaining age-associated damage in the mother cell, which will eventually become senescent. Gametogenesis naturally and fully resets precursor cell lifespan, even for replicatively aged cells. However, the mechanisms responsible for gametogenic rejuvenation remain elusive. This is, in part, due to the existing methods to quantify replicative lifespan resetting in this context, which are limited to low-throughput and labor-intensive approaches. Here, we introduce a high-throughput microfluidic-based assay that allows systematic characterization of factors required for gametogenic rejuvenation in S. cerevisiae. With this technique, we show that we can sensitively measure a wide range of gamete replicative lifespans that are consistent with known short and long-lived mutants. Excitingly, using this technique, we report Atg39 and Atg40, receptors involved in selective autophagy of the ER, as the first identified molecular determinants of gametogenic rejuvenation. We anticipate that this novel technique will enable systematic identification of additional molecular factors that drive gametogenic rejuvenation.

molecular biology↗

bioRxiv2025

Development and characterisation of pNarsenic: a naringenin-inducible biosensor for arsenic in Escherichia coli

Whole-cell biosensors detecting the heavy metal arsenic have been widely studied for their potential in environmental monitoring. And while inducible biosensors have been shown to be an effective tool to tune the operational range, a thoroughly characterised inducible biosensor is currently lacking. Here, we present an Escherichia coli biosensor for arsenic in which the transcription factor gene arsR is inducible by naringenin, a plant-derived secondary metabolite. Increasing naringenin concentrations reduced the basal output while increasing both the dynamic range and sensing threshold of the biosensor dose-response curves, but the operational ranges appeared constrained by a fixed upper limit. Comparison with a previously published phenomenological model revealed good overall agreement between experimental data and model predictions, except for the behaviour of the maximum output and threshold. This work expands the biosensor toolbox with a profoundly characterised arsenic biosensor and raises a potential practical limit to dose-response curve engineering by tuning transcription factor expression alone. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/678503v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@c15051org.highwire.dtl.DTLVardef@180214forg.highwire.dtl.DTLVardef@10afa84org.highwire.dtl.DTLVardef@1c51bba_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2023

Multi-signal regulation of the GSK-3β homolog Rim11 governs meiosis entry in yeast

Starvation of budding yeast diploid cells induces the cell-fate program that drives meiosis and spore formation. Transcription activation of early meiotic genes (EMGs) requires the transcription activator Ime1, its DNA-binding partner Ume6, and GSK-3{beta} kinase Rim11. Phosphorylation of Ume6 by Rim11 is key for EMG activation. We report that Rim11 integrates multiple input signals to control Ume6 phosphorylation and EMG transcription. Under nutrient-rich conditions PKA represses Rim11 to low levels while TORC1 keeps Rim11 localized to the cytoplasm. Inhibiting PKA and TORC1 induces Rim11 expression and nuclear localization. Remarkably, nuclear Rim11 is required, but not sufficient, for Rim11-dependent Ume6 phosphorylation. Additionally, Ime1 is an essential anchor protein for phosphorylating Ume6. Subsequently, Ume6-Ime1 coactivator complexes form that drive EMG transcription. Our results demonstrate how varied signalling inputs (PKA/TORC1/Ime1) integrated by Rim11 determine EMG expression and entry into meiosis. We propose that the signalling-regulatory network described here generates robustness in cell-fate control.

molecular biology↗

bioRxiv2023

Swi/Snf Chromatin Remodeling Regulates Transcriptional Interference and Gene Repression

Alternative transcription start sites can affect transcript isoform diversity and translation levels. In a recently described form of gene regulation, coordinated transcriptional and translational interference results in transcript isoform-dependent changes in protein expression. Specifically, a long undecoded transcript isoform (LUTI) is transcribed from a gene-distal promoter, interfering with expression of the gene-proximal promoter. While transcriptional and chromatin features associated with LUTI expression have been described, the mechanism underlying LUTI-based transcriptional interference is not well understood. Using an unbiased genetic approach followed by integrated genomic analysis, we uncovered that the Swi/Snf chromatin remodeling complex is required for co-transcriptional nucleosome remodeling that leads to LUTI-based repression. We identified genes with tandem promoters that rely on Swi/Snf function for transcriptional interference during protein folding stress, including LUTI-regulated genes. To our knowledge, this study is the first to observe Swi/Snfs direct involvement in gene repression via a cis transcriptional interference mechanism.

molecular biology↗

bioRxiv2022

Meiotic Nuclear Pore Complex Remodeling Provides Key Insights into Nuclear Basket Organization

Nuclear pore complexes (NPCs) are large proteinaceous assemblies that mediate nuclear compartmentalization. NPCs undergo largescale structural rearrangements during mitosis in metazoans and some fungi. However, our understanding of NPC remodeling beyond mitosis remains limited. Using time-lapse fluorescence microscopy, we discovered that NPCs undergo two mechanistically-separable remodeling events during budding yeast meiosis whereby parts or all of the nuclear basket transiently dissociate from the NPC core during meiosis I and II, respectively. Meiosis I detachment, observed for Nup60 and Nup2, is driven by Polo kinase-mediated phosphorylation of Nup60 at its interface with the Y-complex. Subsequent reattachment of Nup60-Nup2 to the NPC core is mediated by a lipid-binding amphipathic helix in Nup60. Preventing Nup60-Nup2 reattachment causes misorganization of the entire nuclear basket in gametes. Strikingly, meiotic nuclear basket remodeling also occurs in the distantly related fission yeast, Schizosaccharomyces pombe. Our study reveals a conserved and developmentally programmed aspect of NPC plasticity, providing key mechanistic insights into nuclear basket organization. SUMMARYKing and Wettstein et al. reveal that nuclear pore complexes undergo two distinct remodeling events during budding yeast meiosis: partial and full nuclear basket detachment. By dissecting the regulation of these events, the study provides mechanistic insights into NPC organization.

cell biology↗

bioRxiv2019

Integrated Genomic Analysis Reveals Key Features of Long Undecoded Transcript Isoform (LUTI)-based Gene Repression

Long Undecoded Transcript Isoforms (LUTIs) represent a class of non-canonical mRNAs that downregulate gene expression through the combined act of transcriptional and translational repression. While single gene studies revealed some important aspects of LUTI-based repression, how these features impact gene regulation at a global scale is unknown. By using transcript leader and direct RNA sequencing, here we identify 74 LUTI candidates that are expressed specifically during meiotic prophase. Translational repression of these candidates is ubiquitous and dependent on upstream open reading frames. However, LUTI-based transcriptional repression is highly variable. In only 50% of the cases, LUTI transcription causes downregulation of the protein-coding transcript isoform. Higher LUTI expression, enrichment of histone 3 lysine 36 trimethylation, and changes in nucleosome position are the strongest predictors of LUTI-based transcriptional repression. We conclude that LUTIs downregulate gene expression in a manner that integrates translational repression, chromatin state changes, and the magnitude of LUTI expression.

molecular biology↗

bioRxiv2019

Aurora B-dependent Ndc80 Degradation Regulates Kinetochore Composition in Meiosis

The kinetochore complex is a conserved machinery that connects chromosomes to spindle microtubules. During meiosis, the kinetochore is restructured to accommodate a specialized chromosome segregation pattern. In budding yeast, meiotic kinetochore remodeling is mediated by the temporal changes in the abundance of a single subunit called Ndc80. We have previously described the regulatory events that control the timely synthesis of Ndc80. Here, we report that Ndc80 turnover is also tightly regulated in meiosis: Ndc80 degradation is active in meiotic prophase, but not in metaphase I. Ndc80 degradation depends on the ubiquitin ligase APCAma1 and is mediated by the proteasome. Importantly, Aurora B-dependent Ndc80 phosphorylation, a mark that has been previously implicated in correcting erroneous microtubule-kinetochore attachments, is essential for Ndc80 degradation in a microtubule-independent manner. The N-terminus of Ndc80, including a 27-residue sequence and Aurora B phosphorylation sites, is both necessary and sufficient for kinetochore protein degradation. Finally, defects in Ndc80 turnover predispose meiotic cells to chromosome mis-segregation. Our study elucidates the mechanism by which meiotic cells modulate their kinetochore composition through regulated Ndc80 degradation, and demonstrates that Aurora B-dependent regulation of kinetochores extends beyond altering microtubule attachments.

genetics↗

bioRxiv2018

Developmental Regulation of an Organelle Tether Coordinates Mitochondrial Remodeling in Meiosis

Cellular differentiation involves remodeling cellular architecture to transform one cell type to another. By investigating mitochondrial dynamics during meiotic differentiation in budding yeast, we sought to understand how organelle morphogenesis is developmentally controlled in a system where regulators of differentiation as well as organelle architecture are known, but the interface between them remains unexplored. We found that mitochondria abruptly detach from the cell cortex shortly before segregating into gametes. Mitochondrial detachment is enabled by the programmed destruction of the mitochondria-endoplasmic reticulum-cortex anchor (MECA), an organelle tether that forms contact sites between mitochondria and the plasma membrane. MECA regulation is governed by a meiotic transcription factor, Ndt80, which promotes the activation of a conserved kinase, Ime2. We found that MECA undergoes Ime2-dependent phosphorylation. Furthermore, Ime2 promotes MECA degradation in a temporally controlled manner. Our study defines a key mechanism that coordinates mitochondrial morphogenesis with the landmark events of meiosis and demonstrates that cells can developmentally regulate tethering to induce organelle remodeling.

cell biology↗