Chapter 7: The Generations Game

Why does this require a male and a female parent?

Sperm and egg – gametes --- gametes are produced in the mammalian body, each gamete receives only half the normal umber chromosomes. 23 chromosomes one of each pair.  Haploid genome.

Conrad Waddington’s grandson

Robert Edwards received the Nobel Prize 2010    in vitro fertilization    test tube babies.

Quantity isn’t everything

Just having the right number of copies of each gene, doesn’t fulfil the requirements for normal development and healthy life.

Hydatidiform mole --- 80% of hydatidiform molar pregnancies, and empty egg is fertilized by a single sperm.  And the haploid sperm genome is copied to create a diploid genomes, in about 20% of cases the empty egg is fertilized simultaneously by two sperm.  --- in both cases the fertilized egg has the correct number of chromosomes. But all the DNA came from the father. --- no fetus

DNA alone isn’t carrying all the necessary information for the creation of new life. Something else must be required in addition to the genetic information something epigenetic.

Once sperm and egg fuse, these two highly specialized cells form one cell which is so unspecialized it is totipotent and gives rise to every cell in the human body and the placenta. ---zygote  at the very top of Waddingtons’s landscape.

Pronuclei of sperm and eggs carry large numbers of epigenetic modifications. – this part of what keeps these gametes behaving as gametes and not turning into other cell types.

Re-installing the operating system

Almost immediately after the sperm has penetrated the egg, pretty much all the methylation on the male pronucleus DNA gets stripped off, incredibly quickly. --- the same thing happens to the DNA on the female pronucleus, albeit a lot more slowly. --- this put the zygote at the top of Waddington’s epigenetic landscape. --- blastocyst --- the golf ball inside the tennis ball inner cell mass – pluripotent cells  the ones that give rise to embryonic stem cells in the laboratory.

One specific protein OCT4 switches on another set of genes, which results in a further cascade of gene expression, and so on.  - these cascades of gene expression are associated with epigenetic modification of the genomes, changing the DNA and histone marks so that certain genes stay switched on or get switched off appropriately.

1)     The male and female pronuclei are carrying epigenetic modifications

2)     The epigenetic modifications get taken off in the immediate post fertilization zygote

3)     New epigenetic modifications get put on as the cells being to specialize.

In reality, the epigenome is being reprogrammed.

The egg is a wonderful thing, honed through hundreds of millions of years of evolution to be extraordinarily effective at generating vast quantities of epigentic change, across billions of base-pairs. None of the artificial means of reprogramming cells comes close to the natural process in terms of speed or efficiency. --- these priming chromatin modifications are missing if an adult nucleus reprogrammed by transferring it into a fertilized egg.  That’ also true when an adult nucleus is reprogrammed by treating it with four Yamanaka factors to create iPS cells.  --- it is a real challenge to completely reset the epigenome of the adult nucleus. ----this is probably why so many cloned animals have abnormalities and shortened lifespans.

Making the switch  

Male and female pronuclei aren’t functionally equivalent; we need one of each to create a new mammal. – parent of origin effect. ---- this is not genetic effect, it is an epigenetic one, and so there must be some epigenetic modifications that do get transmitted from one generation to the next.

Father always give their offspring white, unmethylated DNA whereas mothers always give their offspring black, methylated DNA, --- the methylation in the offspring is dependent on the sex of the parent who passed the inserted DNA onto them

The chromosome in sperm carry little flags that say, I’m from Dad and the chromosomes in eggs carry little flags that say, I’m from Mun. DNA methylation is the fabric that these flags are made from. ---- the description that is used for this is imprinting.  

Although the vast majority of the mammalian genome does get reset when the egg and the sperm fuse, a small percentage of it is immune from this reprogramming.

The epigenetics arms race

Only 2 % of our genome codes for proteins.  A massive 42% is composed of retrotransposons. These are very odd sequences of DNA, which probably originated from viruses in our evolutionary past. Some retrotransposons are transcribed to produce RNA and this can affect the expression of neighboring genes. This can have serious consequences for cells. If it drives up expression genes that cause cells to proliferate too aggressively, for example, this may nudge cells towards becoming cancerous.

There’s a constant arms race in evolution and mechanisms have evolved in our cells to control the activity of these types of retrotransposons.  One of the major mechanisms that cells use is epigenetic.  the retrotransposon DNA gets methylated by the cell, turning off retrotransposon RNA expression. This prevents the RNA disrupting expression of neighboring gene.  One particular class, known as IAP retrotransposons, seems to be a particular target of this control mechanism.

During reprogramming in the early zygote, the methylation is removed from most of our DNA. But IAP retrotransposons are an exception to this. The reprogramming machinery has evolved to skip these rogue elements and leave the DNA methylation marks on them. This keeps the retrotransposons on an epigenetically repressed state. This has probably evolved as a mechanism to reduce the risk that potentially dangerous IAP retrotransposons will get accidently re-activated.  

Best studied examples of transgenerational inheritance of non genetic features are agouti mouse and the Axin^fu mouse. The phenotypes in both these models are a consequence of the methylation levels of an IAP retrotransposon upstream of a gene. The DNA methylation levels in the parent get passed on to the offspring, and do does the phenotype caused by the expression levels of the retrotransposon.

Other examples of transgenerational inheritance of acquired characteristics the effects of nutrition on subsequent generation and transgenerational effects of environmental pollutants such as vinclozolin. --- hypothesis that these environmental stimuli create epigenetic changes in the chromatin of the gametes. These alterations are probably in regions that are protected from reprograming during early development after the egg and sperm fuse.

Azim Surani --- how and why eggs and sperm barcode their DNA so that a molecular memory is passed on to the next generation.