Here is the idea that surprises most students: your surroundings can change which of your genes are read, without changing a single letter of your DNA. Chemical tags get added on top of the code, and they decide what the cell is allowed to see. That is epigenetics.
📚 What you need to know
Epigenesis is the way patterns of differentiation develop in a multicellular organism as it grows from a zygote.
Epigenetics is control of gene expression by factors other than the DNA sequence — heritable changes in how genes work, with no change to the bases.
In eukaryotes, DNA is wrapped around proteins called histones to form chromatin.
Chromatin can be chemically modified, for example by methylation (adding a –CH3 group). These modifications are epigenetic tags; all of them together are the epigenome.
Because the sequence is untouched, the genotype stays the same while the phenotype changes.
The genome is all the DNA, the transcriptome is all the mRNA in a cell, the proteome is all the proteins made.
Tags that survive mitosis and meiosis are passed on — this is epigenetic inheritance.
Epigenesis: how one cell becomes many kinds of cell
You started as a single zygote. Every cell in your body came from that one cell by mitosis, so they all carry the same genome. And yet you ended up with muscle, bone, blood and brain.
Epigenesis is the name for that whole process of differentiation patterns appearing as the organism develops. What drives it is not different DNA in different cells but different patterns of gene expression in different cells.
Epigenetics: changing how the code is read
Epigenetics is genetic control by something other than the base sequence itself. The changes are heritable — they get passed to daughter cells — but the DNA sequence is left completely alone.
Think of the DNA as a book and the epigenetic tags as sticky notes on certain pages saying “skip this one”. The words in the book never change. What changes is which pages get read.
The line examiners want to see
same genotype + different epigenetic tags = different phenotype
This is the cleanest way to separate epigenetics from mutation. A mutation changes the code itself. An epigenetic change only changes how the code is read. Both alter the characteristics you end up with.
Chromatin: DNA plus histones
Nuclear DNA does not float around loose. It is wound around proteins called histones, and the DNA-plus-histone package is called chromatin. That packaging matters, because how tightly the DNA is wound decides whether transcription factors and RNA polymerase can physically reach a gene.
So the cell has two places to add a tag: on the DNA itself, or on the histones it is wrapped around. Both are used.
Genome, transcriptome and proteome
Three words that sound similar and mean quite different things. The proteome is every protein a cell makes, and it is ultimately determined by the genome — but not every gene is switched on, so the proteome is only a selection from what the genome offers.
The transcriptome sits in between: it is the full range of mRNA transcripts present in a particular cell or tissue. Since mRNA is what gets translated, the transcriptome decides which proteins appear.
Ask yourself which of the three a question is really about — the wrong one will cost you the mark even if the biology is right.
Term
What it includes
Same in every body cell?
Genome
All of the DNA, coding and non-coding
Yes
Transcriptome
All the mRNA transcripts in that cell or tissue
No, it varies
Proteome
All the proteins synthesised in that cell
No, it varies
Epigenetic tags: methylation
Methylation of DNA
Methylation means adding a methyl (–CH3) group. On DNA it is usually added to cytosine bases in the promoter region of a gene.
Now follow the chain. The methyl groups sit right where transcription factors need to bind. Their binding is inhibited, so RNA polymerase cannot be recruited, so transcription is suppressed. The cell uses this to lock a gene firmly in the off position. And crucially, how much methylation occurs can be affected by environment, lifestyle and age.
The tags sit on the control region, not on the gene. That is why the genotype is unaffected while the phenotype changes.
Methylation of histones
The tails of histone proteins can be chemically modified too. Methyl groups added to the amino acids of a histone can either activate or deactivate a gene, by making the DNA more or less accessible to transcription factors.
Do not over-generalise. Methylation of DNA at a promoter switches a gene off. Methylation of histones can go either way depending on where it lands. If a question is about histones, keep your answer to “more or less accessible”.
Epigenetic inheritance
Epigenetic tags are copied along with the DNA. If they stay in place through cell division, they get passed on.
Through mitosis, the daughter cells end up with the same tags as the parent cell — which is exactly why a liver cell divides to make more liver cells rather than something random. Through meiosis, gametes can carry tags, which are then passed to the offspring that develop after fertilisation. That is epigenetic inheritance: a phenotypic change inherited with no change at all to the base sequence.
The reverse is just as important. If the tags are stripped off during mitosis or meiosis, epigenetic inheritance cannot happen. Evidence is building that changes to the epigenome in one generation can be passed on at cell level and at whole-organism level.
Worked examples
WORKED EXAMPLE
Distinguish between a mutation and an epigenetic change. [2]
Point 1 — the mutation
A mutation changes the genetic code itself, for example by altering the nucleotide sequence of a gene.
Point 2 — the epigenetic change
An epigenetic change leaves the sequence intact and instead alters how the code is read, by adding tags such as methyl groups.
2 marksBoth change the characteristics expressed — the difference is whether the DNA sequence itself is altered.
WORKED EXAMPLE
Explain how methylation of the promoter region reduces the expression of a gene. [3]
Step 1 — what is added and where
Methyl groups are added to cytosine bases in the promoter region of the gene.
Step 2 — the immediate effect
This inhibits the binding of transcription factors, so RNA polymerase cannot attach to the promoter.
Step 3 — the outcome
Transcription is suppressed, so less mRNA and therefore less protein is produced — the gene is effectively locked off.
3 marksAdding “the base sequence is unchanged” often picks up a further mark on longer questions.
💡 Exam tip
Learn one sentence you can always fall back on: epigenetic tags change gene expression, which changes which proteins are made, which changes the phenotype.
Say genotype unchanged, phenotype changed whenever epigenetics comes up. It is a frequent mark.
Be specific: methyl groups go onto cytosine bases in the promoter.
Use “suppresses transcription” or “inhibits transcription factor binding” rather than vague phrases like “stops the gene working”.
For inheritance questions, the deciding factor is whether the tags survive mitosis or meiosis.
Remember the three -omes. Genome is fixed; transcriptome and proteome vary between cells.
⚠ Common mix-up
Epigenetic changes are not mutations. No base is added, removed or swapped.
Methylation of DNA and methylation of histones are not the same thing. One silences; the other can go either way.
The epigenome is not the genome. It is the full set of tags sitting on top of it.
Epigenesis and epigenetics are different words. Epigenesis is the development of differentiation patterns; epigenetics is control of expression by non-sequence factors.
Chromatin is DNA plus histones, not a type of DNA on its own.
Tags are not permanent. They can be added and removed, which is exactly why the environment can influence them.
Up next: Environment & Gene Expression: Examples — air pollution, imprinting in ligers and tigons, twin studies and the lac operon, all of it built on what you have just learned.
Want this explained one-to-one?
Book a free session with an experienced IB Biology tutor and get your trickiest topics made simple.
