The UHRF1 protein is a key regulator of retrotransposable elements and innate immune response to viral RNA in human cells.

While epigenetic mechanisms such as DNA methylation and histone modification are known to be important for gene suppression, relatively little is still understood about the interplay between these systems. The UHRF1 protein can interact with both DNA methylation and repressive chromatin marks, but its primary function in humans has been unclear. To determine what that was, we first established stable UHRF1 knockdowns (KD) in normal, immortalized human fibroblasts using targeting shRNA, since CRISPR knockouts (KO) were lethal. Although these showed a loss of DNA methylation across the whole genome, transcriptional changes were dominated by the activation of genes involved in innate immune signalling, consistent with the presence of viral RNA from retrotransposable elements (REs). We confirmed using mechanistic approaches that 1) REs were demethylated and transcriptionally activated; 2) this was accompanied by activation of interferons and interferon-stimulated genes and 3) the pathway was conserved across other adult cell types. Restoring UHRF1 in either transient or stable KD systems could abrogate RE reactivation and the interferon response. Notably, UHRF1 itself could also re-impose RE suppression independent of DNA methylation, but not if the protein contained point mutations affecting histone 3 with trimethylated lysine 9 (H3K9me3) binding. Our results therefore show for the first time that UHRF1 can act as a key regulator of retrotransposon silencing independent of DNA methylation.

Epigenetic effects of folate and related B vitamins on brain health throughout life: Scientific substantiation and translation of the evidence for health improvement strategies.

Suboptimal status of folate and/or interrelated B vitamins (B12 , B6 and riboflavin) can perturb one-carbon metabolism and adversely affect brain development in early life and brain function in later life. Human studies show that maternal folate status during pregnancy is associated with cognitive development in the child, whilst optimal B vitamin status may help to prevent cognitive dysfunction in later life. The biological mechanisms explaining these relationships are not clear but may involve folate-related DNA methylation of epigenetically controlled genes related to brain development and function. A better understanding of the mechanisms linking these B vitamins and the epigenome with brain health at critical stages of the lifecycle is necessary to support evidence-based health improvement strategies. The EpiBrain project, a transnational collaboration involving partners in the United Kingdom, Canada and Spain, is investigating the nutrition-epigenome-brain relationship, particularly focussing on folate-related epigenetic effects in relation to brain health outcomes. We are conducting new epigenetics analysis on bio-banked samples from existing well-characterised cohorts and randomised trials conducted in pregnancy and later life. Dietary, nutrient biomarker and epigenetic data will be linked with brain outcomes in children and older adults. In addition, we will investigate the nutrition-epigenome-brain relationship in B vitamin intervention trial participants using magnetoencephalography, a state-of-the-art neuroimaging modality to assess neuronal functioning. The project outcomes will provide an improved understanding of the role of folate and related B vitamins in brain health, and the epigenetic mechanisms involved. The results are expected to provide scientific substantiation to support nutritional strategies for better brain health across the lifecycle.

Field and allozyme studies investigating optimal mating success in two sympatric spring-ephemeral plants, Trillium erectum and T. grandiflorum.

A combination of field experiments and allozyme studies was used to test whether two spring-ephemeral plants growing in eastern North America, Trillium erectum and T. grandiflorum (Liliaceae), exhibited an optimal outcrossing distance for fruit and seed production. Furthermore, the spatial genetic structure of the Trillium populations was examined in light of the outcrossing results. In field experiments, recipient plants were pollinated with either self pollen or with pollen from donors growing 1 m, 10 m, 100 m, and 1500 m away. These distances represented crosses between individuals growing within the same population (1 m, 10 m, and 100 m crosses) and between individuals growing in different populations (1500 m crosses). Self-pollinated T. erectum and T. grandiflorum produced 71% and 89% fewer seeds, respectively, than all other outcrossing treatments. However, there were no significant differences among outcrossing treatments for fruit or seed production. As neither T. erectum nor T. grandiflorum exhibited an optimal outcrossing distance for fruit or seed production, it was predicted that populations of the two would not demonstrate strong spatial genetic structure or isolation by distance. The allozyme results only partially supported the patterns revealed in the outcrossing treatments. Populations of T. erectum and T. grandiflorum showed moderate spatial genetic differentiation based on F-statistics, and only T. grandiflorum exhibited significant isolation by distance based on spatial autocorrelation analyses. The lack of optimal outcrossing distances and the patterns of allozyme variation in T. erectum and T. grandiflorum populations may be attributed to a number of factors, including active seed dispersal by ants, rare long-distance gene-flow events, post-pollination and post-fertilization selection, and/or the severity of inbreeding depression.

Morphological variation and female reproductive success in two sympatric Trillium species: evidence for phenotypic selection in Trillium erectum and Trillium grandiflorum (Liliaceae).

I investigated the mating systems and phenotypic variation of two sympatric spring ephemerals, Trillium erectum and T. grandiflorum (Liliaceae), and phenotypic selection acting through female reproductive success for 11 morphological characters in five sympatric populations of the two species. I examined the degree of self-compatibility, pollinator-visitation rates, and pollen limitation of fruit and seed production in both species. Both Trillium species were self-compatible, but outcrossed flowers produced more successful fruits and seeds than self-pollinated flowers. Pollinator-visitation rates to the two species were low compared to other insect-pollinated spring ephemerals. In addition, both T. erectum and T. grandiflorum experienced pollen limitation in fruit and/or seed production; however, levels of fecundity in both species may be influenced by resource availability as well. I found significant phenotypic variation in 11 morphological characters within and among the five study populations. The sizes of all morphological characters were positively correlated. In general, larger T. erectum and T. grandiflorum produced more seeds. Phenotypic selection analysis revealed that direct and indirect selection acted on the size of morphological characters for both species. But there was no detectable selection acting on plant shape. This study reveals that variation in plant size exists within and among populations of both species, and this variation is associated with variance in female reproductive success. Spatial and temporal variation in pollinator and/or resource abundance may play a role in the phenotypic variation exhibited by both Trillium species.