@article{20404, abstract = {Collagens are fundamental components of extracellular matrices, requiring precise intracellular post-translational modifications for proper function. Among the modifications, prolyl 4-hydroxylation is critical to stabilise the collagen triple helix. In humans, this reaction is mediated by collagen prolyl 4-hydroxylases (P4Hs). While humans possess three genes encoding these enzymes (P4H⍺s), Drosophila melanogaster harbour at least 26 candidates for collagen P4H⍺s despite its simple genome, and it is poorly understood which of them are actually working on collagen in the fly. In this study, we addressed this question by carrying out thorough bioinformatic and biochemical analyses. We demonstrate that among the 26 potential collagen P4H⍺s, PH4⍺EFB shares the highest homology with vertebrate collagen P4H⍺s. Furthermore, while collagen P4Hs and their substrates must exist in the same cells, our transcriptomic analyses at the tissue and single cell levels showed a global co-expression of PH4⍺EFB but not the other P4H⍺-related genes with the collagen IV genes. Moreover, expression of PH4⍺EFB during embryogenesis was found to precede that of collagen IV, presumably enabling efficient collagen modification by PH4⍺EFB. Finally, biochemical assays confirm that PH4⍺EFB binds collagen, supporting its direct role in collagen IV modification. Collectively, we identify PH4⍺EFB as the primary and potentially constitutive prolyl 4-hydroxylase responsible for collagen IV biosynthesis in Drosophila. Our findings highlight the remarkably simple nature of Drosophila collagen IV biosynthesis, which may serve as a blueprint for defining the minimal requirements for collagen engineering.}, author = {Ishikawa, Yoshihiro and Toups, Melissa A and Elkrewi, Marwan N and Zajac, Allison L. and Horne-Badovinac, Sally and Matsubayashi, Yutaka}, issn = {1569-1802}, journal = {Matrix Biology}, number = {11}, pages = {101--113}, publisher = {Springer Nature}, title = {{Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV}}, doi = {10.1016/j.matbio.2025.09.002}, volume = {141}, year = {2025}, } @article{20796, abstract = {Rapid prophase chromosome movements ensure faithful alignment of the parental homologous chromosomes and successful synapsis formation during meiosis. These movements are driven by cytoplasmic forces transmitted to the nuclear periphery, where chromosome ends are attached through transmembrane proteins. During many developmental stages a specific genome architecture with chromatin nuclear periphery contacts mediates specific gene expression. Whether chromatin is removed from the nuclear periphery as a consequence of chromosome motions or by a specific mechanism is not fully understood. Here, we identify a mechanism to remove chromatin from the nuclear periphery through vaccinia related kinase (VRK-1)–dependent phosphorylation of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early prophase of meiosis. Interfering with chromatin removal delays chromosome pairing, impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis. Long read sequencing reveals deletions and duplications in offspring lacking VRK-1 underscoring the importance of the BAF-1–VRK-1 module in preserving genome stability in gametes during rapid chromosome movements.}, author = {Paouneskou, Dimitra and Baudrimont, Antoine and Kelemen, Réka K and Elkrewi, Marwan N and Graf, Angela and Moukbel Ali Aldawla, Shehab and Kölbl, Claudia and Tiemann-Boege, Irene and Vicoso, Beatriz and Jantsch, Verena}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity}}, doi = {10.1038/s41467-025-65420-9}, volume = {16}, year = {2025}, } @article{19735, abstract = {The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome.}, author = {Bett, Vincent K and Trejo Arellano, Minerva S and Vicoso, Beatriz}, issn = {1537-1719}, journal = {Molecular Biology and Evolution}, number = {5}, publisher = {Oxford University Press}, title = {{Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana}}, doi = {10.1093/molbev/msaf085}, volume = {42}, year = {2025}, } @phdthesis{20449, author = {Bett, Vincent K}, issn = {2663-337X}, pages = {114}, publisher = {Institute of Science and Technology Austria}, title = {{Evolution and regulation of the Z chromosome}}, doi = {10.15479/AT-ISTA-20449}, year = {2025}, } @phdthesis{19386, abstract = {Crustaceans are a large group of arthropods with a great diversity of species and different types of sex determination systems and reproductive modes (Subramoniam, 2017). This makes them a great model for exploring the evolution of sex chromosomes and sexual dimorphism and investigating the evolutionary mechanisms driving and maintaining the diversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a branchiopod crustacean, are well suited for such explorations, as they have both highly dimorphic traits and closely related sexual and asexual species. Although brine shrimp are known to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex chromosomes are still not well characterized at the genomic level, the sex-determination gene is unknown, and it is still unclear whether the same sex chromosomes as shared by the different species. The first part of this thesis was to characterize the Z and W chromosomes in Artemia using an array of methods, from generating multiple chromosome and contig level genome assemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer based approaches. The second part tackles the conservation of the cell type specific regulatory pathways in the female reproductive system between Artemia and Drosophila, and the expression of the Z-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show that germline cells lack dosage compensation, with a subset of cells showing evidence of extreme repression of the Z chromosome. With multiple sexual species and several asexual lineages of parthenogenetic females that produce rare males at low frequencies, Brine shrimp present the perfect opportunity to explore the transition to asexuality and shed light on the prerequisites and repercussions of the form of modified meiosis maintaining the asexual lineages. The last chapter is an investigation of the molecular pathways involved in asexual reproduction in Artemia using newly generated single nucleus RNAseq and WGS data and previously published data. }, author = {Elkrewi, Marwan N}, isbn = {9783990780534}, issn = {2663-337X}, pages = {170}, publisher = {Institute of Science and Technology Austria}, title = {{Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp}}, doi = {10.15479/AT-ISTA-19386}, year = {2025}, } @misc{14705, abstract = {Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.}, author = {Elkrewi, Marwan N}, keywords = {sex chromosome evolution, genome assembly, dosage compensation}, publisher = {Institute of Science and Technology Austria}, title = {{Data from "Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation"}}, doi = {10.15479/AT:ISTA:14705}, year = {2024}, } @misc{17362, abstract = {This is the supplementary data for the paper titled "Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome.}, author = {Elkrewi, Marwan N and Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Data for: "Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome"}}, doi = {10.15479/AT:ISTA:17362}, year = {2024}, } @phdthesis{17119, abstract = {Genomes are shaped by natural selection at the level of the organism, as genomic variants that have a beneficial effect on the viability or fecundity of their carriers are on average expected to be passed on to more offspring than less beneficial alleles. However, selection also favors genomic variants that drive their own transmission to the next generation above the mendelian expectation of 50 percent in heterozygotes, even if these self-promoting variants are less beneficial to the organism than other variants at the same locus. Such variants, called meiotic drivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As meiotic drivers often require multiple genes and sequences for transmission ratio distortion, they are often found in regions of low recombination, such as inversions, which prevent their recombination with the non-driving homologous regions. Reduced recombination rates are expected to lead to the accumulation of deleterious mutations, which may affect hundreds of genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of self-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has systematically investigated the level of degeneration on a meiotic driver. Further, the low rates of recombination between driving and non-driving haplotypes have limited the power of traditional genetic studies in uncovering the gene content of meiotic drivers, and made the the identification of the genes causing transmission ratio distortion difficult. After an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that make use of next generation sequencing data to characterize the sequence and expression evolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is transmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents a comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of sequence degeneration counteracted by occasional recombination with the non-driving homolog over large parts of the meiotic driver, proposing an explanation for its long-term survival. Chapter 3 investigates the sequence and expression evolution of genes on the t-haplotype, and finds widespread expression and copy number changes and signs of less efficient purifying selection compared to the genes on the non-driving homolog. Further, this chapter finds candidates for involvment in drive: two positively selected genes on the t-haplotype, and the discovery of a t-specific gene duplicate, which was gained from another chromosome, and which acquired novel sequence and testis-specific expression on the t-haplotype. Finally, Chapter 4 provides unprecedented insights into the gene expression landscape in testes of t-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the comparison of expression in spermatids carrying or not carrying the t-haplotype as well as the timing of t-haplotype-induced expression changes along spermatogenesis. This study shows the timing of previously found drive-associated genes, and uncovers novel candidate genes and biological processes that may underlie the complex biology of transmission ratio distortion of the t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in the context of the current state of meiotic drive research.}, author = {Kelemen, Réka K}, isbn = {978-3-99078-039-8}, issn = {2663-337X}, keywords = {meiotic driver, neofunctionalization, single nucleus sequencing}, pages = {105}, publisher = {Institute of Science and Technology Austria}, title = {{Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver}}, doi = {10.15479/at:ista:17119}, year = {2024}, } @article{17890, abstract = {Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group.}, author = {Elkrewi, Marwan N and Vicoso, Beatriz}, issn = {1553-7404}, journal = {PLoS Genetics}, number = {8}, publisher = {Public Library of Science}, title = {{Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome}}, doi = {10.1371/journal.pgen.1011376}, volume = {20}, year = {2024}, } @article{14613, abstract = {Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.}, author = {Lasne, Clementine and Elkrewi, Marwan N and Toups, Melissa A and Layana Franco, Lorena Alexandra and Macon, Ariana and Vicoso, Beatriz}, issn = {1537-1719}, journal = {Molecular Biology and Evolution}, keywords = {Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics}, number = {12}, publisher = {Oxford University Press}, title = {{The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome}}, doi = {10.1093/molbev/msad245}, volume = {40}, year = {2023}, } @article{12248, abstract = {Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.}, author = {Elkrewi, Marwan N and Khauratovich, Uladzislava and Toups, Melissa A and Bett, Vincent K and Mrnjavac, Andrea and Macon, Ariana and Fraisse, Christelle and Sax, Luca and Huylmans, Ann K and Hontoria, Francisco and Vicoso, Beatriz}, issn = {1943-2631}, journal = {Genetics}, keywords = {Genetics}, number = {2}, publisher = {Oxford University Press}, title = {{ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp}}, doi = {10.1093/genetics/iyac123}, volume = {222}, year = {2022}, }