Biology subjects

Turco, A.

Publications and source records attributed to Turco, A..

4 recordsLinked to original sources

bioRxiv2026

Epigenome-informed Polymer Modeling Reveals Chromosome Folding Landscapes across Distinct Genetic and Epigenetic Contexts

Three-dimensional (3D) genome organization is critical for gene regulation, enabling long-range interactions between genes and distal regulatory elements. Genomic structural variations and epigenetic differences can perturb this organization, contributing to phenotypic variation and tissue-specific gene regulation. Prior studies have assessed the impact of these genetic and epigenetic changes on 3D genome folding, primarily using population-averaged features such as topologically associating domains and loops. However, growing evidence from single-cell and live-imaging studies indicates that chromosomes are highly dynamic and exist as heterogeneous ensembles of conformations. Here, we applied an epigenetic-state-informed polymer modeling framework to generate chromosomal conformational ensembles directly from cell- and tissue-specific epigenomic data. The resulting ensembles reproduced experimental Hi-C maps across cell lines and tissue types. Comparison of these conformational ensembles revealed that, although polymer dynamics were conserved across cell lines, their folding landscapes diverged. These differences arose primarily from cell-line-specific chromatin-state interaction networks and were concentrated in rare, long-lived contacts. Furthermore, modeling a TAD-boundary-disrupting deletion without re-optimizing the model parameters indicated a shift in the chromatin conformational ensemble from predominantly insulated to predominantly fused states. The modeled deletion also selectively strengthened active chromatin contacts and differentially disrupted enhancer contacts involving neighboring genes. Finally, comparison of two tissue types from the same donor revealed epigenetically driven rewiring of chromatin-state interaction networks. These findings establish chromosomal conformational ensembles as a sensitive readout of genome reorganization across distinct genetic and epigenetic contexts.

genomics↗

bioRxiv2026

Diversity and Genomic Organization of Non-B DNA Motifs in Haplotype-Resolved Human Genome Assemblies

Long-read sequencing and telomere-to-telomere genome assemblies now enable the exploration of previously inaccessible repetitive and structurally complex regions of the human genome. Using 130 haplotype-resolved genome assemblies from 65 individuals across diverse populations, we systematically analyzed six major classes of non-B DNA motifs. By evaluating their biophysical stability, we distinguished structurally stable motifs from those forming unstable secondary structures and mapped their distribution across individuals and genomic contexts. Our work revealed significant variation at the population level in both motif abundance and predicted structural stability, uncovering previously unrecognized diversity in non-B DNA landscapes. Non-B DNA motifs exhibit notable, structure-specific enrichment in highly repetitive and evolutionarily dynamic regions that remain largely unresolved in short-read-based genomes, including centromeres, segmental duplications, structural variant breakpoints, and mobile element insertions. Our findings provide a refined view of the potential secondary-structure organization within repetitive regions of the human genome and highlight structural stability as a key factor shaping the distribution of non-B DNA motifs in regions linked to genome instability, evolution, and human variation.

genomics↗

bioRxiv2025

JNK signaling regulates reproductive trade-offs after Plasmodium infection in the malaria mosquito

Environmental stress can limit mammalian reproduction by affecting production of sexual steroid hormones. Here we reveal a similar mechanism in the malarial mosquito Anopheles gambiae: activation of the stress-sensitive c-Jun N-terminal kinase, JNK, constrains reproductive investment by suppressing production of ecdysteroids that orchestrate egg development in this species. We show that infection with Plasmodium berghei parasites increases JNK signalling in the reproductive tract causing a JNK-dependent reduction in both egg development and mosquito survival. Moreover, JNK signaling supresses expression of Cyp315a1 (AGAP000284), a rate-limiting enzyme in ecdysteroid synthesis, a transcriptional change reflected in reduced ecdysteroid production following an infected blood meal. A similar mechanism limits egg production under other stressors (heat stress, or ectopic activation of JNK signaling). Together, these data reveal a regulatory circuit whereby Plasmodium infection curtails reproductive investment in an important vector of human malaria, one that may be applicable to environmental stressors more generally.

zoology↗

bioRxiv2021

The influence of sponge-dwelling gobies (Elacatinus horsti) on the feeding efficiency of their Caribbean tube sponge ( Aplysina sp.) hosts

Mutualistic associations between benthic marine invertebrates and reef taxa are common. Sponge-dwelling gobies benefit from protection within sponge tubes and greater food availability. Sponge-dwelling gobies are hypothesized to increase sponge pump rates by consuming polychaete parasites, but such increases have not yet been demonstrated. We investigated the association between sponge-dwelling gobies (Elacatinus horsti) and two species of tube sponge (Aplysina lacunosa and Aplysina archeri) in Bonaire, Caribbean Netherlands. We visually assessed goby presence in sponges and used in situ methods with fluorescein dye to estimate feeding rates via pump rates. Aplysina archeri were more likely to host a goby than A. lacunosa. For both sponge species, pump rates of tubes with gobies were higher on average than those of tubes without gobies. Our observations, therefore, suggest that E. horsti associations with Aplysina are likely mutualistic relationships in which sponges benefit from higher feeding rates when gobies are present.

ecology↗