Epigenetic reprogramming: how cells start afresh

Last week I talked about the chromatin, the complex of DNA and proteins that resides inside the nucleus. There were two key points to that post: (1) the topology inside of the chromatin, or, in other words, how the chromosomes are arranged inside the nucleus, is correlated to which genes are active and which aren't; (2) these changes in the chromatin that allow for gene expression and gene silencing can be inherited, though how it's still a mystery.

I admit I left that second point a bit vague last week. So, with the help of a fantastic review I found on PubMed [1], today I'd like to develop the topic further.

The rearrangements of the chromosomes within the chromatin determine what are known as epigenetic marks:

"Epigenetic marks are covalent modifications of the DNA (DNA methylation) or post-translational modifications of the histone proteins (histone modifications) that make up the chromatin into which our DNA is packaged. [1]"

Different cells in the body present different epigenetic marks depending on which genes are expressed and which are silent. Within a specific cell line, epigenetic marks are conserved as cells divide, thus maintaining the differentiated state of the cell. For example, skin cells will divide in skin cells and not change into brain cells, right?

This is true for all cells in the body except one very special set: the germline cells. If you think about it, it makes perfect sense: germ cells give rise to an embryo, and hence have to remain undifferentiated. Therefore, all epigenetic marks must be reset in order to enable a completely new undifferentiated state, a process called epigenetic reprogramming.

"It is almost twenty years since the discovery of the biological importance of germline DNA methylation in the context of imprinted genes, and ten years since the identification of the key enzymes responsible for de novo DNA methylation in mammals. Even so, what specifies why specific DNA sequences become epigenetically distinguished in germ cells is still only partially understood."

During developmental epigenetic reprogramming, primordial germ cells emerge with their own epigenetic marks and, as these cells migrate and proliferate, the marks are gradually lost (DNA methylation is globally erased):



It's interesting to see how the new marks are established in an asymmetric fashion for males and females. In the male embryo, de novo methylation takes place and the new marks are established and completed by birth. In the female embryo, the process is arrested in the oocytes and resumed at puberty. In the event of a fertilized oocyte, the marks are erased again, as illustrated by the blue and red line descending again in the above figure.

Smallwood and Kelsey explain the various phases of the above processes in great detail. Interestingly,

"DNA methylation is distributed throughout the genome, at repetitive elements and single-copy sequences. With the recent development of genome-wide methylation profiling techniques employing next-generation sequencing, the full pattern of DNA methylation in gametes, and how it is laid down during germ-cell development, is beginning to emerge. [...]Despite the advances in the identification of key factors in DNA methylation in the germline, many questions remain over mechanism – in particular, how a select number of imprinted gDMRs and CGIs are specified for DNA methylation. The development of deep-sequencing technologies has opened new horizons, and it is now possi- ble to profile DNA methylation on a genome-wide scale in very small amounts of genomic DNA, providing an unparalleled opportunity to shed new light on mechanisms of de novo DNA methylation in germ cells [13,81]. Because the interaction of DNMT3 proteins with nucleosomes is regulated by several histone modifications (at least in vitro) it is now imperative that such capabilities are matched by the development of chromatin immunoprecipitation sequencing (ChIP-Seq) protocols to profile histone modifications in vivo in limited amounts of starting material; this would undoubtedly represent an important advance in the field of epigenetic reprogramming."

I asked my dad, a developmental biologist from the University of Pisa, what his thoughts were on the matter, and this is what he had to say:

"The conclusion to be drawn from these latest findings is thus as follows. So far we have been looking at single epigenetic changes and asked the question what does each one of them mean in relation to the phenotypic effects envisioned on an organismic scale. Needless to say that we have not gone very far by pursuing this simple-minded approach. The newly emerging evidence is pointing to another direction. Taken together, the epigenetic markers of chromatin imprinting, histone acetylation and base methylation should perhaps be considered as systemic modifications rather than simple one-to-one cause-effects relationships. By this I mean to say that the nuclear context in which such modifications occur is as important as any other macromolecular co-factor sustaining their interaction with the phenotypic counterparts. Perhaps by knowing how epigenetic markers are changed on a genomic scale it would be possible in the future to understand how they relate to one another and how altogether have provided living creatures with an adequate responding repertoire to adapt to ever changing environments during evolution."

[1] Smallwood SA, & Kelsey G (2011). De novo DNA methylation: a germ cell perspective. Trends in genetics : TIG PMID: 22019337