The Cytoplasm Affects the Epigenome in Drosophila melanogaster

Abstract

Cytoplasmic components and their interactions with the nuclear genome may mediate patterns of phenotypic expression to form a joint inheritance system. However, proximate mechanisms underpinning these interactions remain elusive. To independently assess nuclear genetic and epigenetic cytoplasmic effects, we created a full-factorial design in which representative cytoplasms and nuclear backgrounds from each of two geographically disjunct populations of Drosophila melanogaster were matched together in all four possible combinations. To capture slowly-accumulating epimutations in addition to immediately occurring ones, these constructed populations were examined one year later. We found the K4 methylation of histone H3, H3K4me3, an epigenetic marker associated with transcription start-sites had diverged across different cytoplasms. The loci concerned mainly related to metabolism, mitochondrial function, and reproduction. We found little overlap (<8%) in sites that varied genetically and epigenetically, suggesting that epigenetic changes have diverged independently from any cis-regulatory sequence changes. These results are the first to show cytoplasm-specific effects on patterns of nuclear histone methylation. Our results highlight that experimental nuclear-cytoplasm mismatch may be used to provide a platform to identify epigenetic candidate loci to study the molecular mechanisms of cyto-nuclear interactions.

Diet’s impact dictated by synonymous mitochondrial SNP interacting with nucleotype

“…Furthermore, the finding of mito-nuclear variation in the response to EAAs enrichment demonstrates that certain individuals may bear particularly strong costs of eating such diets. At present, we do not know the mechanistic basis of the diet-mito-nuclear interactions that we have uncovered, but the transgenerational effects hint at epigenetics, consistent with preceding findings that epigenetic marks respond to genetic variation in the cytoplasm (Bellizzi et al, 2012; Grunau et al, 2018; Vivian et al, 2017; Yan et al, 2011).…”

“…It is The copyright holder for this preprint this version posted March 8, 2021. ; https://doi.org/10.1101/2021.03.07.434274 doi: bioRxiv preprint buffered or augmented by variants in the other. In animals, this has been observed for fecundity (Mossman et al, 2016a), fertility (Camus et al, 2015), lifespan (Camus et al, 2015;Vaught et al, 2020), gene expression (Camus et al, 2015;Mossman et al, 2019Mossman et al, , 2016b, and epigenomic modifications (Grunau et al, 2018). Novel mitonuclear pairings can even change the course of nuclear genomic evolution (Healy and Burton, 2020), and lead to reproductive isolation (Hill, 2019;Ma et al, 2016).…”

Interactions between cytoplasmic and nuclear genomes confer sex‐specific effects on lifespan in Drosophila melanogaster

“…A set of fully-crossed cyto-nuclear populations of D. melanogaster was created (described also in Grunau et al, (2018) and Dong et al, (2019)) using three distinct laboratory populations.…”

Interactions between cytoplasmic and nuclear genomes confer sex-specific effects on lifespan inDrosophila melanogaster

“…Construction of cyto-nuclear populations 205 A set of fully-crossed cyto-nuclear populations of D. melanogaster was created (described also 206 in Grunau et al, (2018) and Dong et al, (2019)) using three distinct laboratory populations. 207 Each of these derived laboratory populations had originally been sourced from one of three 208 separate continents.…”

“…Wolbachia screening 329 A screen for Wolbachia infection was performed across each of the cyto-nuclear population 330 replicates using the approach described in Richardson et al, (2012) and Grunau et al, (2018), 331 involving diagnostic PCR, on DNA extracted from pools of 15 adult flies, using Wolbachia-332 specific wsp primer-sets (Richardson et al, 2012). This screen revealed that all populations 333 harbouring Australian cytoplasms were infected with Wolbachia, while those possessing 334 cytoplasms originating from Benin or Canada were uninfected.…”