publications

2026

1. The deacetylase Sir2 is the primary sensor driving transcriptional changes in response to low NAD+ in the yeast Kluyveromyces lactis

   Mahasweta Acharjee^*, Kristen Humphrey^*, Vincent Lactaoen, Charikleia Karageorgiou, and 3 more authors

   Genetics, Jan 2026

   Abs DOI

   The coenzyme NAD+ (nicotinamide adenine dinucleotide) is a critical electron carrier in central metabolism and is required for cellular health. Cells are proposed to monitor and respond to fluctuating intracellular NAD+ levels using sirtuin deacetylases as sensors because these enzymes require NAD+ for activity. We tested this hypothesis by examining how intracellular NAD+ levels affect Sir2-mediated repression of transcription in the yeast Kluyveromyces lactis. Because K. lactis cannot synthesize NAD+, we could create a gradient of intracellular NAD+ levels by growing cells in varying concentrations of the precursor nicotinic acid. We found that as NAD+ levels decreased, acetylation of histones at target promoters increased, as did expression of these genes. RNA sequencing analysis revealed that genes induced in low nicotinic acid include some that would restore NAD+ levels, such as the high-affinity nicotinic acid transporter TNA1, and some that would enable long-term survival by promoting sporulation. Most genes induced in low nicotinic acid (99/112 or 88%) were also induced by the deletion of SIR2. Moreover, in sir2Δ cells, few transcriptional changes occurred in response to low nicotinic acid. Thus, Sir2 is the primary sensor driving the transcriptional response to low NAD+ in K. lactis. Finally, the degree of transcriptional induction varied with NAD+ levels, suggesting that Sir2 behaves as a rheostat that tunes gene expression to NAD+ availability.

2. Structural variation in context: mechanisms, functions and selection regimes across the tree of life

   Charikleia Karageorgiou, Ellen M Leffler, Megan Y Dennis, and Omer Gokcumen

   Heredity, Mar 2026

   Abs DOI

   Genomic structural variants (SVs) are central to modern genetics. However, they do not fit easily into the simple classifications and analytical frameworks that work well for single‑nucleotide polymorphisms (SNPs). The papers in this special issue underscore that SVs cannot be treated as a homogeneous class, nor can their evolutionary consequences be inferred directly from their structural category alone. Instead, they compel us to engage explicitly with mutational mechanism, genomic context, and selection regime, and to recognize that the structural category only weakly predicts their functional and evolutionary impact.

3. Rapid adaptive increase of amylase gene copy number in Indigenous Andeans

   Kendra Scheer^*, Luane J B Landau^*, Kelsey Jorgensen, Charikleia Karageorgiou, and 13 more authors

   Nature Communications, May 2026

   Abs DOI

   The salivary amylase gene AMY1 exhibits remarkable copy number variation linked to dietary shifts in human evolution. While global studies highlight its structural complexity and association with starch-rich diets, localized selection patterns remain underexplored. Here, we analyze AMY1 copy number in 3,723 individuals from 85 populations, revealing that Indigenous Peruvian Andean populations possess the highest AMY1 copy number globally. A genome-wide analysis shows significantly higher amylase copy numbers in Peruvian Andean genomes compared to closely related populations. Further, we identify positive selection (selection coefficient of 0.0124, log likelihood ratio of 11.1543) at the nucleotide level on a haplotype harboring at least five haploid AMY1 copies, with a Peruvian Andean-specific expansion dated to around 10,000 years ago, coinciding with potato domestication in the region. Using ultra-long-read sequencing, we demonstrate that previously described recombination-based mutational mechanisms drive the formation of high-copy AMY1 haplotypes observed in Andean population. Our study provides a framework for investigating structurally complex loci and their role in human dietary adaptation.

4. Convergent evolution through independent rearrangements in the primate amylase locus

   Charikleia Karageorgiou, Petar Pajic, Stefan Ruhl, and Omer Gokcumen

   Cell Reports, Jun 2026

   Abs DOI

   Structurally complex genomic regions can foster evolutionary convergence by repeatedly generating gene duplications that yield similar expression patterns and traits across lineages. Focusing on the primate amylase locus, we leveraged high-quality genome assemblies from 53 primate species and multi-tissue transcriptomes from Old World monkeys to reconstruct the evolutionary history of recurrent duplications. We show that lineage-specific long terminal repeat retrotransposon insertions may be associated with initial structural instability, while subsequent duplications are primarily driven by non-allelic homologous recombination. Independent duplications in rhesus macaques, olive baboons, and great apes produced distinct amylase copies with convergent expression in pancreas and salivary glands, and it signals episodic diversifying selection, consistent with emerging functional divergence. Our analyses indicate that an ancestral gene with dual pancreas and salivary expression in Catarrhini duplicated in great apes, facilitating subfunctionalization and regulatory rewiring. These findings illuminate how modular structural and regulatory variation drives evolutionary innovation and molecular convergence.

2024

1. Deciphering the role of structural variation in human evolution: a functional perspective

   Charikleia Karageorgiou, Omer Gokcumen, and Megan Y Dennis

   Curr. Opin. Genet. Dev., Oct 2024

   Abs DOI

   Advances in sequencing technologies have enabled the comparison of high-quality genomes of diverse primate species, revealing vast amounts of divergence due to structural variation. Given their large size, structural variants (SVs) can simultaneously alter the function and regulation of multiple genes. Studies estimate that collectively more than 3.5% of the genome is divergent in humans versus other great apes, impacting thousands of genes. Functional genomics and gene-editing tools in various model systems recently emerged as an exciting frontier - investigating the wide-ranging impacts of SVs on molecular, cellular, and systems-level phenotypes. This review examines existing research and identifies future directions to broaden our understanding of the functional roles of SVs on phenotypic innovations and diversity impacting uniquely human features, ranging from cognition to metabolic adaptations.

2. Evolution of gene regulatory networks by means of selection and random genetic drift

   Stefanos Papadadonakis, Antonios Kioukis, Charikleia Karageorgiou, and Pavlos Pavlidis

   PeerJ, Aug 2024

   DOI
3. Investigating the mechanism of neurotoxic effects of PFAS in differentiated neuronal cells through transcriptomics and lipidomics analysis

   Logan Running^*, Judith R Cristobal^*, Charikleia Karageorgiou, Michelle Camdzic, and 4 more authors

   ACS Chem. Neurosci., Dec 2024

   Abs DOI

   Per- and polyfluorinated alkyl substances (PFAS) are pervasive environmental contaminants that bioaccumulate in tissues and pose risks to human health. Increasing evidence links PFAS to neurodegenerative and behavioral disorders, yet the underlying mechanisms of their effects on neuronal function remain largely unexplored. In this study, we utilized SH-SY5Y neuroblastoma cells, differentiated into neuronal-like cells, to investigate the impact of six PFAS compounds─perfluorooctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), perfluorodecanoic acid (PFDA), perfluorodecanesulfonic acid (PFDS), 8:2 fluorotelomer sulfonate (8:2 FTS), and 8:2 fluorotelomer alcohol (8:2 FTOH)─on neuronal health. Following a 30 \muM exposure for 24 h, PFAS accumulation ranged from 40-6500 ng/mg of protein. Transcriptomic analysis revealed 721 differentially expressed genes (DEGs) across treatments (padj < 0.05), with 11 DEGs shared among all PFAS exposures, indicating potential biomarkers for neuronal PFAS toxicity. PFOA-treated cells showed downregulation of genes involved in synaptic growth and neural function, while PFOS, PFDS, 8:2 FTS, and 8:2 FTOH exposures resulted in the upregulation of genes related to hypoxia response and amino acid metabolism. Lipidomic profiling further demonstrated significant increases in fatty acid levels with PFDA, PFDS, and 8:2 FTS and depletion of triacylglycerols with 8:2 FTOH treatments. These findings suggest that the neurotoxic effects of PFAS are structurally dependent, offering insights into the molecular processes that may drive PFAS-induced neuronal dysfunction.

4. Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation

   Feyza Yilmaz^*, Charikleia Karageorgiou^*, Kwondo Kim^*, Petar Pajic, and 6 more authors

   Science, Nov 2024

   Abs DOI

   Previous studies suggested that the copy number of the human salivary amylase gene, AMY1, correlates with starch-rich diets. However, evolutionary analyses are hampered by the absence of accurate, sequence-resolved haplotype variation maps. We identified 30 structurally distinct haplotypes at nucleotide resolution among 98 present-day humans, revealing that the coding sequences of AMY1 copies are evolving under negative selection. Genomic analyses of these haplotypes in archaic hominins and ancient human genomes suggest that a common three-copy haplotype, dating as far back as 800,000 years ago, has seeded rapidly evolving rearrangements through recurrent nonallelic homologous recombination. Additionally, haplotypes with more than three AMY1 copies have significantly increased in frequency among European farmers over the past 4000 years, potentially as an adaptive response to increased starch digestion.

2023

1. Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World

   Frédéric Labbé, Maha Abdeladhim, Jenica Abrudan, Alejandra Saori Araki, and 79 more authors

   PLoS Negl. Trop. Dis., Apr 2023

   Abs DOI

   Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.

2020

1. The cyclically seasonal Drosophila subobscura inversion O7 originated from fragile genomic sites and relocated immunity and metabolic genes

   Charikleia Karageorgiou, Rosa Tarrı́o, and Francisco Rodrı́guez-Trelles

   Front. Genet., Oct 2020

   Abs DOI

   Chromosome inversions are important contributors to standing genetic variation in Drosophila subobscura. Presently, the species is experiencing a rapid replacement of high-latitude by low-latitude inversions associated with global warming. Yet not all low-latitude inversions are correlated with the ongoing warming trend. This is particularly unexpected in the case of O7 because it shows a regular seasonal cycle that peaks in summer and rose with a heatwave. The inconsistent behavior of O7 across components of the ambient temperature suggests that is causally more complex than simply due to temperature alone. In order to understand the dynamics of O7, high-quality genomic data are needed to determine both the breakpoints and the genetic content. To fill this gap, here we generated a PacBio long read-based chromosome-scale genome assembly, from a highly homozygous line made isogenic for an O3 + 4 + 7 chromosome. Then we isolated the complete continuous sequence of O7 by conserved synteny analysis with the available reference genome. Main findings include the following: (i) the assembled O7 inversion stretches 9.936 Mb, containing > 1,000 annotated genes; (ii) O7 had a complex origin, involving multiple breaks associated with non-B DNA-forming motifs, formation of a microinversion, and ectopic repair in trans with the two homologous chromosomes; (iii) the O7 breakpoints carry a pre-inversion record of fragility, including a sequence insertion, and transposition with later inverted duplication of an Attacin immunity gene; and (iv) the O7 inversion relocated the major insulin signaling forkhead box subgroup O (foxo) gene in tight linkage with its antagonistic regulatory partner serine/threonine-protein kinase B (Akt1) and disrupted concerted evolution of the two inverted Attacin duplicates, reattaching them to dFOXO metabolic enhancers. Our findings suggest that O7 exerts antagonistic pleiotropic effects on reproduction and immunity, setting a framework to understand its relationship with climate change. Furthermore, they are relevant for fragility in genome rearrangement evolution and for current views on the contribution of breakage versus repair in shaping inversion-breakpoint junctions.

2019

1. Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

   Charikleia Karageorgiou, Vı́ctor Gámez-Visairas, Rosa Tarrı́o, and Francisco Rodrı́guez-Trelles

   BMC Genomics, Mar 2019

   Abs DOI

   BACKGROUND: Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, together with the available wealth of genetic marker information, to assemble and annotate a high-quality nuclear and complete mitochondrial genome for the species. With the obtained assembly, we performed the first synteny analysis of genome structure evolution in the subobscura subgroup. RESULTS: We generated a highly-contiguous   129 Mb-long nuclear genome, consisting of six pseudochromosomes corresponding to the six chromosomes of a female haploid set, and a complete 15,764 bp-long mitogenome, and provide an account of their numbers and distributions of codifying and repetitive content. All 12 identified paracentric inversion differences in the subobscura subgroup would have originated by chromosomal breakage and repair, with some associated duplications, but no evidence of direct gene disruptions by the breakpoints. Between lineages, inversion fixation rates were 10 times higher in continental D. subobscura than in the two small oceanic-island endemics D. guanche and D. madeirensis. Within D. subobscura, we found contrasting ratios of chromosomal divergence to polymorphism between the A sex chromosome and the autosomes. CONCLUSIONS: We present the first high-quality, long-read sequencing of a D. subobscura genome. Our findings generally support genome structure evolution in this species being driven indirectly, through the inversions’ recombination-suppression effects in maintaining sets of adaptive alleles together in the face of gene flow. The resources developed will serve to further establish the subobscura subgroup as model for comparative genomics and evolutionary indicator of global change.