Epigenetic inheritance of a phenotypically plastic epimutation

Organisms constantly have to adapt to changing environments in order to survive, thrive and successfully
multiply. Phenotypic changes can be acquired by alterations of the deoxyribonucleic acid (DNA)sequence.
If beneficial under natural selection, the DNA variation can become fixed permanently in a population and
thereby drive its evolution. In addition to DNA sequence changes, a concept emerged that a soft, reversible layer could also potentially contribute to heritable adaptation. Epigenetic changes were shown to affect the development and complex phenotypic traits of almost isogenic organisms. Such changes can be inherited over many generations by strong self-reinforcing feedback loops without the initial trigger.
Evidence for such a ‘soft’ inheritance is only just emerging and whether such phenomena are of physiological relevance in heritable adaptation though remains to be unraveled.
Gene expression is regulated through several mechanisms. DNA does not exist as bare molecule, but is packaged into a highly complex structure called chromatin. Besides serving structural functions, chromatin also impacts gene expression. Chromatin can be broadly divided into transcriptionally active, gene-rich euchromatin and gene-poor, condensed heterochromatin, which serves as repressive structure for repetitive elements, such as transposons, and makes up most of the euchromatic genome. In some organisms, nuclear small ribonucleic acid (RNA) pathways are essential to initiate and maintain constitutive heterochromatin. The centerpiece of such pathways is a small RNA-bound Argonaute protein, which binds by complementary base-pairing to nascent transcripts and subsequently recruits effector
complexes that mediate silencing. Given the appropriate small RNA, this pathway can theoretically target
any expressed locus, thereby making it a versatile silencing strategy. In nematodes, small RNAs were shown to induce stable silencing of some protein coding genes that can be epigenetically maintained over tens of generations.
During my PhD, I studied RNA interference (RNAi)-mediated epigenetic phenomena in the fission yeast
Schizosaccharomyces pombe (S. pombe). In S. pombe, RNAi-mediated silencing is under strong negative
control and can only be initiated in the presence of an enabling mutation, such as in genes encoding
subunits of the RNA polymerase-associated factor 1 complex (Paf1C). On one hand, such mutations can
have a detrimental effect on viability. On the other hand, the silencing phenotype observed in Paf1C mutants cannot be inherited to wild-type cells, suggesting that also all marks of the silencing event were erased. If RNAi-mediated epigenetic phenomena also exist in wild-type cells was not known.
My main achievement during PhD was to discover that wild-type S. pombe cells remember a parental silencing event through acquiring a phenotypically neutral epimutation. I could show that such epimutation does not cause gene silencing when inherited by wild type cells. Yet, upon repeated mutation of Paf1C, the silencing phenotype was reinstated in subsequent generations. I could further show that the phenotypically neutral epimutation entails high levels of small interfering RNA (siRNA) and histone 3 lysine 9 tri-methylation (H3K9me3), and that its transgenerational inheritance depends on RNAi and H3K9 methylation. This finding is astounding, because H3K9me3 has commonly been associated with gene repression. That we have not observed silencing, despite high enrichments of this mark, was therefore highly unexpected. Based on my findings, I conclude that H3K9me3 is not repressive per se, but rather
functions as stable epigenetic mark that can retain information of a previous gene-silencing event. Upon
deposition of H3K9me3, the silencing phenotype is dependent on the modulation of Paf1C function. The
discovery of this distinct form of epigenetic memory lets me speculate that it may have evolved to allow
population adaptation to dynamic environments.