We hypothesize that some epigenetic signals in sperm from males reared under nutritional stress are common across vertebrate species, and constitute essential mediators of the preconceptional influence of nutritional factors on body weight and metabolism for the next generation. By using advances in nutritional biology (the Nutritional Geometry Framework, NGF) applied to a variety of animal model systems, and then taking a comparative biology approach across vertebrate species spanning taxa and nutritional ecologies, we will gain mechanistic and evolutionary understanding of the essential mediators of epigenetic inheritance of obesity and

metabolic disease.  Comparative analyses of the responses to nutritional stress will help us in unlocking critical information about the specificiteis of epigenetic inheritance in humans, and allow the identification of core pathways controlling epigenetic response to nutritional stress.

Delivering nutritional interventions to males of reproductive age, followed by collection of viable sperm samples from research subjects, allows us to draw a clear picture of how nutritional stresses lead to reshaping of the sperm epigenome.  We are conducting several of such studies, including in mice, pigs and humans, to determine how diet influences male reproduction, in terms of reproductive health and epigenetic signature of the spermatozoa. We then conduct in-depth characterisation of the epigenome of sperm, including smallRNA expression, DNA methylation, and histone retention. In some cases, we are breeding dietary-perturbed fathers and further characterising the epigenetic signature of metabolic tissues within their offspring. The aim of these projects is to precisely define the effect of certain diets on the gametic epigenome of fathers, identifying Genomic Hotspots of Epigenetic Variation (GHEVs), along with the downstream phenotypic effects on offspring. These studies will be a pivotal step in defining optimised male diet for improved epigenetic signature and developmental health of offspring.

Thus far, understandings of epigenetic inheritance have been limited to correlation between gametic epigenome and offspring phenotype, as tools to address causal mechanism were lacking. Fortunately, we can now take advantage of the CRISPR-Cas9 system to modify the epigenome of multipotent cells at genomic regions related to gametic epigenetic features. We selectively methylate genomic regions of interest in neuronal stem cells, and determine the role of this engineered epigenome at GHEVs on neuronal and metabolic-cell lineage commitment and cellular function. Further, we investigate the mechanistic role of these GHEVs ex vivo by exploring the relationship between GHEV remodelling in spermatozoa of fathers and gene expression in metabolic tissues of offspring. In order to understand the impact of GHEVs on the phenotype and epigenotype of the next generation offspring, we integrate chromatin conformation and transcriptomic data to identify genes regulated by these GHEVs. We have developed integrated genomic platforms to comprehensively annotate regulatory networks in specific tissues, identifying regulatory elements and characterise the downstream target genes.