Biology subjects

Slack, C.

Publications and source records attributed to Slack, C..

3 recordsLinked to original sources

bioRxiv2025

DNA-binding-independent mechanisms of metabolic regulation by the Drosophila FOXO transcription factor

Forkhead box-O (FOXO) transcription factors are evolutionarily conserved regulators of several biological processes, including development, stress responses, metabolism and ageing. As downstream effectors of nutrient-dependent cell signalling pathways, including insulin/IGF signalling, they integrate signals from multiple stimuli to orchestrate appropriate transcriptional responses to changes in the nutritional environment. Traditionally, FOXO-dependent responses have been attributed to target gene regulation through direct interactions with regulatory regions by DNA-binding via the conserved Forkhead (FH) domain. However, emerging evidence suggests that FOXO proteins may also influence gene expression through DNA-binding-independent mechanisms. However, differences in transcriptional outputs between DNA-binding dependent and independent FOXO functions have yet to be explored. Here, we have used genomic engineering of the endogenous Drosophila foxo locus to disrupt the DNA-binding activity of the single fly FOXO orthologue, allowing us to dissect the in vivo contributions of canonical and non-canonical dFOXO functions. We show that while DNA-binding is essential for several dFOXO-mediated phenotypes including female fecundity, lifespan, and resistance to oxidative and xenobiotic stress, other traits such as adult body size and survival during starvation remain intact. Notably, DNA-binding-deficient dFOXO flies exhibit defective lipid mobilisation under starvation, implicating a DNA-binding-independent role for dFOXO in metabolic regulation. Differential gene expression analysis during starvation in these mutants revealed key transcriptional changes in genes encoding metabolic regulators as well as regulators of transcription and chromatin structure. Together, these findings reveal distinct modes of dFOXO transcriptional regulation that depend on its direct association with DNA.

genetics↗

bioRxiv2021

The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip

BackgroundDNA methylation (DNAm) is commonly assayed using the Illumina Infinium MethylationEPIC BeadChip, but there is currently little published evidence to define the lower limits of the amount of DNA that can be used whilst preserving data quality. Such evidence is valuable for analyses utilising precious or limited DNA sources. Materials and methodsWe use a single pooled sample of DNA in quadruplicate at three dilutions to define replicability and noise, and an independent population dataset of 328 individuals (from a community-based study including US-born non-Hispanic Black and white persons) to assess the impact of total DNA input on the quality of data generated using the Illumina Infinium MethylationEPIC BeadChip. ResultsData are less reliable and more noisy as DNA input decreases to 40ng, with clear reductions in data quality; however samples with a total input as low as 40ng pass standard quality control tests, and we observe little evidence that low input DNA obscures the associations between DNAm and two phenotypes, age and smoking status. ConclusionsDNA input as low as 40ng can be used with the Illumina Infinium MethylationEPIC BeadChip, provided quality checks and sensitivity analyses are undertaken.

bioinformatics↗

bioRxiv2020

Zoledronate extends healthspan and survival via the mevalonate pathway in a FOXO-dependent manner

Increased longevity has not been paralleled by extended healthspan, resulting in more years spent with multiple diseases in older age. As such, interventions to improve healthspan are urgently required. Zoledronate is a nitrogen containing bisphosphonate, which inhibits the farnesyl pyrophosphate synthase (FPPS) enzyme, central to the mevalonate pathway. It is already used clinically to prevent fractures in osteoporotic patients, who have been reported to derive unexpected and unexplained survival benefits. In this study we show that zoledronate has beneficial effects on both lifespan and healthspan using Drosophila as a model. We found that zoledronate extended lifespan, improved climbing activity and reduced intestinal epithelial dysplasia and permeability in aged flies. Mechanistic studies showed that zoledronate conferred resistance to oxidative stress and reduced accumulation of X-ray-induced DNA damage via inhibition of FPPS. Moreover, zoledronate inhibited pAKT in the mTOR pathway and functioned via dFOXO, a molecule associated with increased longevity, downstream of the mevalonate pathway. Taken together, our work indicates that zoledronate, a drug already widely used and dosed only once a year to prevent osteoporosis, modulates important mechanisms of ageing. Its repurposing holds great promise as a treatment to improve healthspan.

pharmacology and toxicology↗