Biology subjects

Galli, S.

Publications and source records attributed to Galli, S..

4 recordsLinked to original sources

bioRxiv2026

Application of eDNA metabarcoding for high-resolution reconstruction of the trophic web of an Arctic fjord

In the face of a rapidly changing Arctic, the ecosystem of Kongsfjorden was put under the spotlight to explore its community composition and structural dynamics. An eDNA metabarcoding approach was implemented to carry out a Food Web Analysis. eDNA samples were collected using metaprobes, innovative passive samplers, deployed under two different sampling configurations: in association with set fish traps in the coastal area and a towed sampling along a central transect, an offshore domain of the fjord. Amplification of the mithocondrial COI and ribosomal 18S genes was conducted in order to obtain a comprehensive view of metazoans and protists communities, respectively. The output taxa from the metabarcoding process constituted trophic webs nodes while producers-consumers and prey-predators relationships were identified through a literature review. Qualitative food networks were successfully obtained for each sampled site and for the two domains identified in the ecosystem, the coastal and offshore areas. Moreover, these networks were characterized by using four food web indicators: Species Richness (N), Number of links (L), Direct Connectance (C) and Generality (G). Differences in the apical part of the webs instantly emerged, as well as a clear separation between the coastal and offshore domain. Analyzing the values of the trophic indicators allowed for a deeper consideration regarding the nets structure and relative stability. Overall, eDNA proved sensitive and precise in capturing differences between the two domains and in providing insights into ecosystem structure. Moreover, eDNA-based Food Web Analysis could set the basis for long term monitoring studies in the same area, being cost-effective, rapid and easy to implement when compared to traditional methods.

ecology↗

bioRxiv2025

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions

G-quadruplexes (G4s) are non-canonical DNA structures formed in guanine-rich sequences that are proposed to act as regulatory elements in trypanosomatid parasites, including Trypanosoma brucei, the causative agent of African sleeping sickness. However, their functional roles remain poorly understood, largely due to limited knowledge of their genomic distribution. Herein, we performed computational analyses across 63 trypanosomatid species uncovering high degree of variability in G4-prevalence and species-specific patterns. We generated the first genome-wide map of G4s in T. brucei using G4 chromatin immunoprecipitation followed by sequencing (G4 ChIP-Seq), which revealed a striking enrichment of G4s within coding DNA sequences (CDSs). This pattern diverges markedly from in silico predictions and previous genome-wide G4 mapping studies in humans, suggesting that G4s may play unique roles exclusive to trypanosome biology. To investigate their functional relevance, we profiled the transcriptome of T. brucei upon treatment with the G4-stabilising ligand PhenDC3. We observed that PhenDC3 exerts targeted gene expression perturbation of genes bearing G4s, particularly those located within coding CDSs, where G4s are mostly enriched. Altogether, our findings highlight a distinctive role for G4s in the regulation of gene expression in T. brucei and support their potential as therapeutic targets in the treatment of African sleeping sickness. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/666098v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1a2e0b5org.highwire.dtl.DTLVardef@4eba13org.highwire.dtl.DTLVardef@9a46fdorg.highwire.dtl.DTLVardef@aabc90_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Individual G-quadruplex targeting with ligand-functionalized CRISPR-Cas9 uncovers transcriptional-dependent functional responses

The development of selective ligands to target DNA G-quadruplexes (G4s) and i-motifs (iMs) has revealed their relevance in transcriptional regulation. However, most of these ligands are unable to target individual G4s or iMs in the genome, severely limiting their scope. Herein, we describe a new Approach to Target Exact Nucleic Acid alternative structures (ATENA) that relies on the chemical conjugation of established G4 and iM ligands to a catalytically inactive Cas9 protein (dCas9), enabling their individual targeting in living cells. ATENA demonstrated that the selective targeting of the G4 present in the oncogene c-MYC leads to the suppression of transcripts regulated exclusively by one of its promoters (P1). Conversely, targeting the c-MYC iMs on the opposite strand leads to the selective increase of P1-driven transcripts. ATENA revealed that G4-mediated transcriptional responses are highly ligand-specific, with different ligands eliciting markedly different effects at the same G4-site. We further demonstrated that the basal expression levels of the gene targeted can be used to predict the transcriptional impact associated with G4-stabilization. Our study provides an innovative platform to investigate G4- and iM-biology with high precision and unveils the therapeutic relevance of individual DNA structures with unprecedented selectivity.

cell biology↗

bioRxiv2024

G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer

Epigenetic evolution is a common mechanism used by cancer cells to evade the therapeutic effects of drug treatment. In ovarian cancers, epigenetically-driven resistance may be responsible for a large number of late-stage patient deaths. Here, we describe the first investigation into the role of G-quadruplex (G4) DNA secondary structures in mediating epigenetic regulation in drug-resistant ovarian cancer cells. Through genome-wide mapping of G4s in paired drug-sensitive and drug-resistant cell lines, we find that increased G4 formation is associated with significant increase in gene expression, with high enrichment in signalling pathways previously established to promote drug-resistant states. However, in contrast to previous studies, the expression-enhancing effects of G4s were not found at gene promoters, but intergenic and intronic regions, indicating that G4s promote long-range transcriptional regulation in drug-resistant cells. Furthermore, we discovered that clusters of G4s (super-G4s) are associated with particularly high levels of transcriptional enhancement that surpass the effects of super-enhancers, which act as well established regulatory sites in many cancers. Finally, we demonstrate that targeting G4s with small molecules results in significant down-regulation of pathways associated with drug-resistance, which results in resensitisation of resistant cells to chemotherapy agents. These findings indicate that G4 structures are critical for the epigenetic regulatory networks of drug-resistant cells and may represent a promising target to treat drug-tolerant ovarian cancer.

cancer biology↗