The Epigenetics Revolution

miRNAs play major roles in control of pluripotency and control of cellular differentiation. ES cells can be encouraged to differentiate into other cell types by changing the culture conditions in which they’re grown. When they begin to differentiate, it’s essential that ES cells switch off the gene expression pathways that normally allow them to keep producing additional ES cells (self-renewal). There is a miRNA family called let-7 which is essential for this switch-off process[145].

One of the mechanisms the let-7 family uses is the down-regulation of a protein called Lin28. This implies that Lin28 is a pro-pluripotency protein. It’s therefore not that surprising to discover that Lin28 can act as a Yamanaka factor. Over-expression of Lin28 protein in somatic cells increases the chances of reprogramming them to iPS cells[146].

Conversely, there are other miRNA families that help ES cells to stay pluripotent and self-renewing. Unlike let-7, these miRNAs promote the pluripotent state. In ES cells, the key pluripotency factors such as Oct4 and Sox2 are bound to the promoters of these miRNAs, activating their expression. As the ES cells start to differentiate, these factors fall off the miRNA promoters, and stop driving their expression[147]. Just like the Lin28 protein, these miRNAs also improve reprogramming of somatic cells into iPS cells[148].

When we compare stem cells with their differentiated descendants, we find that they express very different populations of mRNA molecules. This seems reasonable, as the stem and differentiated cells express different proteins. But some mRNAs can take a long time to break down in a cell. This means that when a stem cell starts to differentiate, there will be a period when it still contains many of the stem cell mRNAs. Happily, when the stem cell starts differentiating, it switches on a new set of miRNAs. These target the residual stem cell mRNAs and accelerate their destruction. This rapid degradation of the pre-existing mRNAs ensures that the cell moves into a differentiated state as quickly and irreversibly as possible[149].

This is an important safety feature. It’s not good for cells to retain inappropriate stem cell characteristics – it increases the chance they will move down a cancer cell pathway. This mechanism is used even more dramatically in species where embryonic development is very rapid, such as fruit flies or zebrafish. In these species this process ensures that maternally-inherited mRNA transcripts supplied by the egg are rapidly degraded as the fertilised egg turns into a pluripotent zygote[150].

miRNAs are also vital for that all-important phase in imprinting control, the formation of primordial germ cells. A key stage in creation of primordial germ cells is the activation of the Blimp1 protein that we met in Chapter 8. Blimp1 expression is controlled by a complex interplay between Lin28 and let-7 activity[151]. Blimp1 also regulates an enzyme that methylates histones, and a class of proteins known as PIWI proteins. PIWI proteins in turn bind to another type of small ncRNAs known as PIWI RNAs[152]. PIWI ncRNAs and proteins don’t seem to play much of a role in the somatic cells but are required for generation of the male germline[153]. PIWI actually stands for P element-induced wimpy testis. If the PIWI ncRNAs and PIWI proteins don’t interact properly, the testes in a male foetus don’t form normally.

We are finding more and more instances of cross-talk and interactions between ncRNAs and epigenetic events. Remember that the genetic interlopers, the retrotransposons, are normally methylated in the germline, to prevent their activation. The PIWI pathway is involved in targeting this DNA methylation[154][155]. A substantial number of epigenetic proteins are able to interact with RNA. Binding of non-coding RNAs to the genome may act as the general mechanism by which epigenetic modifications are targeted to the correct chromatin region in a specific cell type[156].

ncRNAs have recently been implicated in Lamarckian transmission of inherited characteristics. In one example, fertilised mouse eggs were injected with a miRNA which targeted a key gene involved in growth of heart tissue. The mice which developed from these eggs had enlarged hearts (cardiac hypertrophy) suggesting that the early injection of the miRNA disturbed the normal developmental processes. Remarkably, the offspring of these mice also had a high frequency of cardiac hypertrophy. This was apparently because the abnormal expression of the miRNA was recreated during generation of sperm in these mice. There was no change in the DNA code of the mice, so this was a clear case of a miRNA driving epigenetic inheritance[157].

Murphy’s Law (if something can go wrong, it usually will)