epigenetics at the very beginning of life – my explorations

So let me see if I can understand epigenetics through other sources, and through what I’ve read so far. First, it’s essential for the very first cell divisions in human – or shall we say mammalian – life, at least for placental mammals. Their lives begin with a fertilised egg, a sperm cell and an egg cell (both known as gametes), each with its complement of DNA (but the egg cell contains much more, and there’s a difference between an ovum and an oocyte, which I won’t go into, as if I could). This cell, also known as a zygote, is the ultimate totipotent stem cell, potentially able to form every type of somatic (diploid) cell. So what causes this cell to divide and multiply, and become, in a few days, a blastocyst?

A blastocyst is already quite a complex collection of cells, with an outer layer, the trophectoderm, an inner cell mass, and a blastocoel, which is a fluid-filled cavity. So, already quite a jump from a zygote, so I need to know how that happens. But even before that, I need to know how a zygote comes into being. Wikipedia puts it this way:

The formation of a totipotent zygote with the potential to produce a whole organism depends on epigenetic reprogramming. DNA demethylation of the paternal genome in the zygote appears to be an important part of epigenetic reprogramming.

That doesn’t help too much, but I’m guessing that this ‘epigenetic reprogramming’ thing is what creates cell diversity – but this description tells us that the formation of the zygote is itself an epigenetic product. Here’s another description of the first steps:

The four stages of embryonic development include fertilization (zygote formation), cleavage (rapid cell division), blastocyst formation, and finally, implantation into the uterine lining.

Cleavage? The website I filched this from (ferty9.com, listed below) fails to elaborate, and looking up the word an sich just takes me to female breasts, which is pleasant but distracting. AI (never lies) gives more detail, claiming four cleavage stages, 1. the zygote stage, 2. the 2 to 8 cell stage, 3. the morula stage, and 4. blastocyst formation. And presumably epigenetics plays a role in the move from one stage to the next?

So, I’ve tracked down a most sciencey article, from ScienceDirect, entitled ‘Epigenetic regulation of early human embryo development’, which I hope to make sense of. Its opening paragraph is a bit daunting though:

Epigenomes undergo profound change during the first few days of embryonic development. The resetting and establishment of epigenomes are coordinated within and contribute to the wider processes of embryogenesis. As a consequence, faithful epigenetic regulation is required to safeguard development and to establish long-lived epigenetic states that have effects on genome function throughout the life course.

So now we have epigenomes, and here’s a definition:

Epigenome: The epigenome consists of all the chemical modifications of DNA and histones of a cell/organism that contribute to regulate gene expression independently of DNA sequence.

I actually understand this, I think. And clearly, problems with epigenetic regulation at this most early stage of growth, the embryonic stage, can have serious or catastrophic, life-denying effects. But what are these profound changes? I’ll try to explain them to myself. There are many types of epigenomic modifications, such as methylation of DNA, chromatin remodeling, and histone modifications. So, methylation is when a chemical methyl (CH3) group is added to the DNA, ‘repressing gene transcription’ without altering its sequence. Chromatin remodelling involves changing the structure of chromatin, a complex mixture of genetic material and proteins, to reposition it on the histone octamers, two by four protein structures, essential to nucleosomes. And nucleosomes? They are the packages of chromatin around histones. DNA is wrapped around these octamers, the fundamental DNA packaging system in eukaryotic cells. And here’s a summary of the histone thing:

Histone modification involves the post-translational modification of specific amino acids that influence the overall structure of histone proteins. Changes in histone structure may then influence their function, resulting in incomplete DNA unwinding that may also effect transcription activity. Major histone modifications include acetylation, methylation, phosphorylation, ubiquitylation, and, less frequently, ribosylation, sumoylation, and citrullination

Don’t thank me, just send money. But ok – post-translational? Gene transcription and translation are the two sequential processes for the production of proteins. Transcription happens in the nucleus to create messenger RNA, and translation occurs via that ticker-tape machine, the ribosome, to create proteins – chains of amino acids. DNA unwinding involves ‘the separation of double-stranded helical nucleic acids into single-stranded coils’.

So let’s look at the -ations mentioned above. Are they all epigenetic modifications? Methinks yes. Here’s my take from AI (never lies). These are of course very brief summaries of complex processes.

Epigenetic acetylation is the addition of an acetyl group to histone proteins with their DNA wrappings. This loosens the histones’ grip on their DNA, allowing certain genes to be switched on.

Methylation is a primary epigenetic process, attaching methyl groups to genes, typically turning them off by blocking transcription machinery from accessing them.

Phosphorylation adds phosphate groups to the histone proteins via enzymes called kinases, changing chromatin structure.

Ubiquitylation is, apparently, the attachment of a ubiquitin protein to a histone target, thus modifying it and affecting gene expression. It’s a major approach to cancer therapies.

So I’m getting the picture, and clearly, research is ongoing in this fascinating field.

Anyway, this has taken me a little away from the very early cell differentiation process, so I’ll return to that next time.

References

https://pmc.ncbi.nlm.nih.gov/articles/PMC4783933/

https://www.sciencedirect.com/science/article/pii/S153458072101042

https://embryology.med.unsw.edu.au/embryology/index.php/Blastocyst_Development#Introduction

https://www.ferty9.com/blog/the-four-stages-of-embryonic-development#:~:text=The%20four%20stages%20of%20embryonic%20development%20include%20fertilization%20(zygote%20formation,implantation%20into%20the%20uterine%20lining.

https://www.sciencedirect.com/science/article/pii/S1934590923003314

Written by stewart henderson

July 15, 2026 at 7:46 pm

Posted in epigenetics, genetics

Tagged with chromatin, early life, epigenetics, genetics, histones, proteins

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