Programmed suppression of oxidative phosphorylation and mitochondrial function by gestational alcohol exposure correlate with widespread increases in H3K9me2 that do not suppress transcription

Abstract

Background A critical question emerging in the field of developmental toxicology is whether alterations in chromatin structure induced by toxicant exposure control patterns of gene expression or, instead, are structural changes that are part of a nuclear stress response. Previously, we used a mouse model to conduct a three-way comparison between control offspring, alcohol-exposed but phenotypically normal animals, and alcohol-exposed offspring exhibiting craniofacial and central nervous system structural defects. In the cerebral cortex of animals exhibiting alcohol-induced dysgenesis, we identified a dramatic increase in the enrichment of dimethylated histone H3, lysine 9 (H3K9me2) within the regulatory regions of key developmental factors driving histogenesis in the brain. However, whether this change in chromatin structure is causally involved in the development of structural defects remains unknown. Results Deep-sequencing analysis of the cortex transcriptome reveals that the emergence of alcohol-induced structural defects correlates with disruptions in the genetic pathways controlling oxidative phosphorylation and mitochondrial function. The majority of the affected pathways are downstream targets of the mammalian target of rapamycin complex 2 (mTORC2), indicating that this stress-responsive complex plays a role in propagating the epigenetic memory of alcohol exposure through gestation. Importantly, transcriptional disruptions of the pathways regulating oxidative homeostasis correlate with the emergence of increased H3K9me2 across genic, repetitive, and non-transcribed regions of the genome. However, although associated with gene silencing, none of the candidate genes displaying increased H3K9me2 become transcriptionally repressed, nor do they exhibit increased markers of canonical heterochromatin. Similar to studies in C. elegans, disruptions in oxidative homeostasis induce the chromatin looping factor SATB2, but in mammals, this protein does not appear to drive increased H3K9me2 or altered patterns of gene expression. Conclusions Our studies demonstrate that changes in H3K9me2 associate with alcohol-induced congenital defects, but that this epigenetic change does not correlate with transcriptional suppression. We speculate that the mobilization of SATB2 and increased enrichment of H3K9me2 may be components of a nuclear stress response that preserve chromatin integrity and interactions under prolonged oxidative stress. Further, we postulate that while this response may stabilize chromatin structure, it compromises the nuclear plasticity required for normal differentiation.

Maternal background alters the penetrance of growth phenotypes and sex‐specific placental adaptation of offspring sired by alcohol‐exposed males

“…Gene Enrichment Analysis using IPA identified alterations in the pathways regulating oxidative phosphorylation, mitochondrial function, EIF2, and Sirtuin signaling (Figure 6C). We recently described dysfunction of a similar set of pathways in the brains of mice exposed to alcohol in utero , 50 suggesting maternal and paternal alcohol exposures may program similar outcomes. Consistent with our previous study, we identified altered expression of several mitochondrial‐expressed transcripts and nuclear genes encoding mitochondrial enzymes (Figure 6D).…”

“…Identifying alterations in the expression of genes regulating mitochondrial function and oxidative phosphorylation is intriguing, especially given that we recently identified this same signature in a maternal model of alcohol exposure. 50 Epigenetic influences on mitochondrial function are an emerging area of interest in addiction and cancer biology. 61,62 Importantly, mitochondrial genome enriched small RNAs (mitosRNAs) are present in sperm.…”

“…How the memory of preconception alcohol exposures transmit through sperm and into early life remains an open question. Identifying alterations in the expression of genes regulating mitochondrial function and oxidative phosphorylation is intriguing, especially given that we recently identified this same signature in a maternal model of alcohol exposure 50 . Epigenetic influences on mitochondrial function are an emerging area of interest in addiction and cancer biology 61,62 .…”

Paternal alcohol exposures program intergenerational hormetic effects on offspring fetoplacental growth

“…We did not observe any alterations in these same genes in either male or female placenta derived from High-concentration sires. Finally, our previous studies examining alcohol-induced changes in epigenetic programming have identified altered expression of several mitochondrial-expressed transcripts and nuclear genes regulating oxidative phosphorylation and mammalian target of rapamycin (mTOR) signaling ( Chang et al, 2021 ; Thomas et al, 2021 ). Similar to these previous studies, we identify suppression of these same candidate genes in placentae derived from the male and female offspring of Low-concentration sires but not the offspring of High-concentration males ( Figure 8D ).…”

“…In worms, these changes alter chromatin structure, specifically histone H3, lysine four trimethylation (H3K4me3) in both the soma and the germline, enabling the transgenerational propagation of an adaptive state (Tauffenberger and Parker, 2014;Kishimoto et al, 2017). We have observed suppression of pathways regulating oxidative phosphorylation in a high-dose model of early gestational EtOH exposure and recently identified this same signature in male placentae sired by EtOH-exposed fathers (Chang et al, 2021;Thomas et al, 2021). Further, we have identified alcohol-induced increases in H3K4me3 in alcoholexposed sperm (Bedi et al, 2022).…”