DNA methylation has long been the shining star of transgenerational epigenetic inheritance work, with other mechanisms signing backup. But now, the solo act has now become a trio, with histone modifications and non-coding (ncRNA) stepping into the limelight. For an in utero exposure to be truly transgenerational, and not an intergenerational effect, it must impact the F3 generation which was not directly exposed as a fetus (F1) or as germ cells (F2). Environmentally induced transgenerational epigenetic inheritance has been shown for numerous toxins as well as poor maternal nutrition. Studies have found changes in DNA methylation and non-coding RNA in F3 sperm, though no study has examined histone modifications nor multiple marks in mammals.
The laboratory of Michael Skinner at Washington State University has been a leader in transgenerational research. The group commonly uses DDT as an exposure to model transgenerational epigenetic inheritance. DDT was a common pesticide from the 1940s-70s, but persists in the environment after being banned. It causes endocrine and developmental abnormalities. Previous work from this group found that DDT induces transgenerational inheritance of testis, ovary, kidney and prostate disease up to the F3 generation. The group has examined the epigenetic changes in the sperm of each generation that may underlie these diseases. They exposed gestating female rats to DDT from pregnancy day 8 to 14. Each generation was aged to 90 days for mating, and then sperm collected at 120 up to the F3 generation. They looked for DNA methylation, ncRNA, and histone modification changes in the sperm of each generation.
Here’s what they found:
- Using MeDIP-seq, they discovered that the F1 sperm has the fewest differentially methylated regions (DMRs), while the F2 have the most, and there is little overlap between generation
- On average, the DMRs are associated with CpG deserts with a size range of 1-5kb
- Using RNA-seq on small non-coding RNA (sncRNA) and long non-coding RNA (lncRNA) samples, they found 10 times more lncRNAs are differentially expressed in response to DDT in each generation
- There were many more dysregulated lncRNAs in the F1 vs. F2 & F3, and many more sncRNAs dysregulated in F3 vs. F1 & F2
- From the small number of histones that are known to be retained by sperm, there is differential retention in the F3 generation that is not present in the F1/F2
- H3K27me3 changes were also examined in the F3, and found to not be as abundant as the differential histone retention
- About 20% of the DNA methylation, ncRNA, and histone changes occur near genes that are involved in metabolism, transcription, signaling, and receptor functions
- These functions are similar across generations even though the individual genes are not
These data show for the first time that a broad range of epigenetic changes accompany transgenerational disease inheritance. The transgenerational sperm “epimutations” are present in regions with similar genomic features, but their localization is distinct. The fact that different epimutations are found in directly exposed (F1 & F2) vs. indirectly (F3) generations suggests a complex mechanism of transmission that is not yet clear. So, move over DNA methylation and welcome ncRNA and histone; the solo act is now a trio.
Tune into the transgenerational trio over at Epigenetics & Chromatin, February 2018