Read The Epigenetics Revolution Online
Authors: Nessa Carey
Tags: #Science/Life Sciences/Genetics and Genomics
The Epigenetics Revolution (22 page)
Figure 8.3
Diagram showing how the somatic cells arising from a fertilised zygote all carry the same DNA methylation patterns as each other at imprinted genes, but the imprinting methylation is removed and then reestablished in the germ cells. This ensures that females only pass on maternal marks to their offspring, and males only pass on paternal ones.
Diagram showing how the somatic cells arising from a fertilised zygote all carry the same DNA methylation patterns as each other at imprinted genes, but the imprinting methylation is removed and then reestablished in the germ cells. This ensures that females only pass on maternal marks to their offspring, and males only pass on paternal ones.
The tiny population of cells that carry out this process are know as the primordial germ cells. It’s these cells that will ultimately settle in the developing gonads (testicles or ovaries) and act as the stem cells that produce all the gametes (sperm or eggs respectively). In the stage described in the previous paragraph, the primordial germ cells are reverting to a state more like that of the cells of the inner cell mass (ICM). Essentially, they are becoming pluripotent, and potentially able to code for most of the tissue types in the body. This phase is fleeting. The primordial germ cells quickly get diverted into a new developmental pathway where they differentiate to form stem cells that will give rise to eggs or sperm. To do so, they gain a new set of epigenetic modifications. Some of these modifications are ones that define cellular identity, i.e. switch on the genes that make an egg an egg. But a small number are the ones that serve as parent-of-origin marks, so that in the next generation the imprinted regions of the genome can be recognised with respect to their parent-of-origin.
This seems horribly complicated. If we follow the path from the sperm that fertilised the egg to a new sperm being formed in male offspring, the sequence goes like this:
1. The sperm that enters the egg has epigenetic modifications on it;
2. The epigenetic modifications get taken off, except at the imprinted regions (in the immediate post-fertilisation zygote);
3. Epigenetic modifications get put on (as the cells of the ICM begin to specialise);
4. The epigenetic modifications get taken off, including at the imprinted regions (as the primordial germ cells break away from the somatic differentiation pathway);
5. Epigenetic modifications get put on (as the sperm develops).
This could seem like an unnecessarily complicated way to get back to where we started from, but it’s essential.
The modifications that make a sperm a sperm, or an egg an egg, have to come off at stage 2 or the zygote wouldn’t be totipotent. Instead it would have a genome that was half-programmed to be an egg and half-programmed to be a sperm. Development wouldn’t be possible if the inherited modifications stayed on. But to create primordial germ cells, some of the cells from the differentiating ICM have to lose their epigenetic modifications. This is so they can become temporarily more pluripotent, lose their imprinting marks and transfer across into the germ cell lineage.
Once the primordial germ cells have been diverted, epigenetic modifications again get attached to the genome. This is partly because pluripotent cells are potentially extremely dangerous as a multicellular organism develops. It might seem like a great idea to have cells in our body that can divide repeatedly and give rise to lots of other cell types, but it’s not. Those sorts of cells are the type that we find in cancer. Evolution has favoured a mechanism where the primordial germ cells can regain pluripotency for a period, but then this pluripotency is re-suppressed by epigenetic modifications. Coupled with this, the wiping out of the imprints means that chromosomes can be marked afresh with their parent-of-origin.
Occasionally this process of setting up the new imprints on the progenitors of egg or sperm can go wrong. There are cases of Angelman syndrome and Prader-Willi syndrome where the imprint has not been properly erased during the primordial germ cell stage
24
. For example, a woman may generate eggs where chromosome 15 still has the paternal mark on it that she inherited from her father, rather than the correct maternal mark. When this egg is fertilised by a sperm, both copies of chromosome 15 will function like paternal chromosomes, and create a phenotype just like uniparental disomy.
24
. For example, a woman may generate eggs where chromosome 15 still has the paternal mark on it that she inherited from her father, rather than the correct maternal mark. When this egg is fertilised by a sperm, both copies of chromosome 15 will function like paternal chromosomes, and create a phenotype just like uniparental disomy.
Research is ongoing into how all these processes are controlled. We don’t fully understand how imprints are protected from reprogramming following fusion of the egg and the sperm, nor how they lose this protection during the primordial germ cell stage. We’re also not entirely sure how imprints get put back on in the right place. The picture is still quite foggy, although details are starting to emerge from the haze.
Part of this may involve the small percentage of histones that are present in the sperm genome. Many of these are located at the imprinting control regions, and may protect these regions from reprogramming when the sperm and the egg fuse
25
. Histone modifications also play a role in establishing ‘new’ imprints during gamete production. It seems to be important that the imprinting control regions lose any histone modifications that are associated with switching genes on. Only then can the permanent DNA methylation be added
26
. It’s this permanent DNA methylation that marks a gene with a repressive imprint.
25
. Histone modifications also play a role in establishing ‘new’ imprints during gamete production. It seems to be important that the imprinting control regions lose any histone modifications that are associated with switching genes on. Only then can the permanent DNA methylation be added
26
. It’s this permanent DNA methylation that marks a gene with a repressive imprint.
Dolly and her daughters
The reprogramming events in the zygote and in primordial germ cells impact on a surprising number of epigenetic phenomena. When somatic cells are reprogrammed in the laboratory using the Yamanaka factors, only a tiny percentage of them form iPS cells. Hardly any seem to be exactly the same as ES cells, the genuinely pluripotent cells from the inner cell mass of the blastocyst. A group in Boston, based at Massachusetts General Hospital and Harvard University, assessed genetically identical iPS and ES cells from mice. They looked for genes that varied in expression between the two types of cells. The only major differences in expression were in a chromosomal region known as
Dlk1-Dio3
27
. A few iPS cells expressed the genes in this region in a way that was very similar to how the ES cell did this. These were the best iPS cells for forming all the different tissues of the body.
Dlk1-Dio3
27
. A few iPS cells expressed the genes in this region in a way that was very similar to how the ES cell did this. These were the best iPS cells for forming all the different tissues of the body.
Dlk1-Dio3
is an imprinted region on chromosome 12 of the mouse. It’s perhaps not surprising that an imprinted region turned out to be so important. The Yamanaka technique triggers the reprogramming process that normally occurs when a sperm fuses with an egg. Imprinted regions of the genome are resistant to reprogramming in normal development. It is likely that they present too high a barrier to reprogramming in the very artificial environment of the Yamanaka method.
is an imprinted region on chromosome 12 of the mouse. It’s perhaps not surprising that an imprinted region turned out to be so important. The Yamanaka technique triggers the reprogramming process that normally occurs when a sperm fuses with an egg. Imprinted regions of the genome are resistant to reprogramming in normal development. It is likely that they present too high a barrier to reprogramming in the very artificial environment of the Yamanaka method.
The
Dlk1-Dio3
region has been of interest to researchers for quite some time. In humans, uniparental disomy in this region is associated with growth and developmental defects, amongst other symptoms
28
. This region has also been shown to be critical for the prevention of parthenogenesis, at least in mice. Researchers from Japan and South Korea genetically manipulated just this region of the genome in mice. They reconstructed a fertilised egg with two female pronuclei. The
Dlk1-Dio3
region in one of the pronuclei had been altered so that it carried the equivalent of a paternal rather than maternal imprint. The live mice that were born were the first example of a placental mammal with two maternal genomes
29
.
Dlk1-Dio3
region has been of interest to researchers for quite some time. In humans, uniparental disomy in this region is associated with growth and developmental defects, amongst other symptoms
28
. This region has also been shown to be critical for the prevention of parthenogenesis, at least in mice. Researchers from Japan and South Korea genetically manipulated just this region of the genome in mice. They reconstructed a fertilised egg with two female pronuclei. The
Dlk1-Dio3
region in one of the pronuclei had been altered so that it carried the equivalent of a paternal rather than maternal imprint. The live mice that were born were the first example of a placental mammal with two maternal genomes
29
.
The reprogramming that occurs in the primordial germ cells isn’t completely comprehensive. It leaves the methylation on some IAP retrotransposons more or less intact. The DNA methylation level of the
Axin
Fu
retrotransposon in sperm is the same as it is in the body cells of this strain of mice. This shows that the DNA methylation was not removed when the PGCs were reprogrammed, even though most other areas of the genome did lose this modification. This resistance of the
Axin
Fu
retrotransposon to both rounds of epigenetic reprogramming (in the zygote and in the primordial germ cells) provides a mechanism for the transgenerational inheritance of the kinked tail trait that we met in earlier chapters.
Axin
Fu
retrotransposon in sperm is the same as it is in the body cells of this strain of mice. This shows that the DNA methylation was not removed when the PGCs were reprogrammed, even though most other areas of the genome did lose this modification. This resistance of the
Axin
Fu
retrotransposon to both rounds of epigenetic reprogramming (in the zygote and in the primordial germ cells) provides a mechanism for the transgenerational inheritance of the kinked tail trait that we met in earlier chapters.
We know that not all transgenerational inheritance happens in the same way. In the
agouti
mouse the phenotype is transmitted via the mother, but not via the father. In this case, the DNA methylation on the IAP retrotransposon is removed in both males and females during normal primordial germ cell reprogramming. However, mothers whose retrotransposon originally carried DNA methylation pass on a specific histone mark to their offspring.
agouti
mouse the phenotype is transmitted via the mother, but not via the father. In this case, the DNA methylation on the IAP retrotransposon is removed in both males and females during normal primordial germ cell reprogramming. However, mothers whose retrotransposon originally carried DNA methylation pass on a specific histone mark to their offspring.
This is a repressive histone modification and it acts as a signal to the DNA methylation machinery. This signal attracts the enzymes that put the repressive DNA methylation onto a specific region on a chromosome. The final outcome is the same – the DNA methylation in the mother is restored in the offspring. Male
agouti
mice don’t pass on either DNA methylation or repressive histone modifications on their retrotransposon, which is why transmission of the phenotype only occurs through the maternal line
30
.
agouti
mice don’t pass on either DNA methylation or repressive histone modifications on their retrotransposon, which is why transmission of the phenotype only occurs through the maternal line
30
.
This is a slightly more indirect method of transmitting epigenetic information. Instead of direct carry-over of DNA methylation, an intermediate surrogate (a repressive histone modification) is used instead. This is probably why the maternal transmission of the
agouti
phenotype is a bit ‘fuzzy’. Not all offspring are exactly the same as the mother, because there is a bit of ‘wriggle-room’ in how DNA methylation gets re-established in the offspring.
agouti
phenotype is a bit ‘fuzzy’. Not all offspring are exactly the same as the mother, because there is a bit of ‘wriggle-room’ in how DNA methylation gets re-established in the offspring.
In the summer of 2010, there were reports in the British press about cloned farm animals. Meat that had come from the offspring of a cloned cow had entered the human food chain
31
. Not the cloned cow itself, just its offspring, created by conventional animal breeding. Although there were a few alarmist stories about people unwittingly eating ‘Frankenfoods’, the coverage in the mainstream media was pretty balanced.
31
. Not the cloned cow itself, just its offspring, created by conventional animal breeding. Although there were a few alarmist stories about people unwittingly eating ‘Frankenfoods’, the coverage in the mainstream media was pretty balanced.
To some extent, this was probably because of a quite intriguing phenomenon, which has allayed certain fears originally held by scientists about the consequences of cloning. When cloned animals breed, the offspring tend to be healthier than the original clones. This is almost certainly because of primordial germ cell reprogramming. The initial clone was formed by transfer of a somatic nucleus into an egg. This nucleus only went through the first round of reprogramming, the one that normally happens when a sperm fertilises an egg. The likelihood is that this epigenetic reprogramming wasn’t entirely effective – it’s a big ask to get an egg to reprogram a ‘wrong’ nucleus. This is likely to be the reason why clones tend to be unhealthy.
When the cloned animals breed, they pass on either an egg or a sperm. Before the clone produced these gametes, its primordial cells underwent the second round of reprogramming, as part of the normal primordial germ cell pathway. This second reprogramming stage seems to reset the epigenome properly. The gametes lose the abnormal epigenetic modifications of their cloned parent. Epigenetics explains why cloned animals have health issues, but also explains why their offspring don’t. In fact, the offspring are essentially indistinguishable from animals produced naturally.
Assisted reproductive technologies in humans (such as in vitro fertilisation) share certain technical aspects with some of the methods used in cloning. In particular, pluripotent nuclei may be transferred between cells, and cells are cultured in the laboratory before being implanted in the uterus. There is a substantial amount of controversy in the scientific journals about the abnormality rates from these procedures
32
. Some authors claim there is an increased rate of imprinting disorders in pregnancies from assisted reproductive technologies. This would imply that procedures such as culturing fertilised eggs outside the body may disrupt the delicately poised pathways that control reprogramming, especially of imprinted regions. It’s important to note, however, that there is no consensus yet on whether this really is a clinically relevant issue.
32
. Some authors claim there is an increased rate of imprinting disorders in pregnancies from assisted reproductive technologies. This would imply that procedures such as culturing fertilised eggs outside the body may disrupt the delicately poised pathways that control reprogramming, especially of imprinted regions. It’s important to note, however, that there is no consensus yet on whether this really is a clinically relevant issue.
All the reprogramming of the genome in early development has multiple effects. It allows two highly differentiated cell types to fuse and form one pluripotent cell. It balances out the competing demands of the maternal and paternal genomes, and ensures that this balancing act can be re-established in every generation. Reprogramming also prevents inappropriate epigenetic modifications being passed from parent to offspring. This means that even if cells have accumulated potentially dangerous epigenetic changes, these will be removed before they are passed on.
This is why we don’t normally inherit acquired characteristics. But there are certain regions of the genome, such as IAP retrotransposons, that are relatively resistant to reprogramming. If we want to work out how certain acquired characteristics – responses to vinclozolin or responses to paternal nutrition, for example – get transmitted from parent to offspring, these IAP retrotransposons might be a good place to start looking.
The sound of a kiss is not so loud as that of a cannon, but its echo lasts a great deal longer.
Oliver Wendell Holmes
At a purely biological, and especially an anatomical level, men and women are different. There are ongoing debates about whether or not certain behaviours, ranging from aggression to spatial processing, have a biological gender bias. But there are certain physical characteristics that are linked unequivocally to gender. One of the most fundamental differences is in the reproductive organs. Women have ovaries, men have testicles. Women have a vagina and a uterus, men have a penis.
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