AP Syllabus focus:
‘Epigenetic changes, such as reversible modifications of DNA or histone proteins, can alter chromatin structure and influence gene expression patterns.’
Epigenetic regulation explains how cells with the same DNA can maintain different, stable gene-expression programs. By modifying DNA and histone proteins, cells change chromatin packing and tune transcription on or off without altering base sequence.
Core idea: epigenetics links chromatin structure to transcription
Epigenetic modifications act like molecular “tags” that influence whether transcription machinery can access a gene. More open chromatin generally increases transcriptional potential; more compact chromatin generally reduces it.
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Epigenetics: Heritable (through cell division) changes in gene expression that occur without a change in DNA nucleotide sequence.
These changes are central to how a genome produces different expression patterns across cell types while keeping the same genetic information.
Chromatin as the physical target
Genes are packaged into chromatin, and packing level influences access to promoters and regulatory DNA.
Chromatin: A DNA–protein complex (DNA wrapped around histone proteins) whose structure can be altered to regulate gene accessibility and transcription.
Chromatin exists on a spectrum from relatively open (transcription more likely) to highly compact (transcription less likely).
This diagram summarizes chromatin packaging from the nucleosome upward and contrasts euchromatin (more open, transcription-permissive) with heterochromatin (more compact, transcription-restrictive). It reinforces the core idea that chromatin structure controls how easily regulatory proteins and RNA polymerase can access DNA. Source
Major epigenetic mechanisms emphasized in AP Biology
The syllabus highlights reversible modifications of DNA or histone proteins that change chromatin structure and thereby influence gene expression patterns.
DNA methylation (a DNA modification)
A common epigenetic mark is addition of a methyl group (–CH₃) to DNA bases (often cytosine in certain contexts).
DNA methylation: Addition of methyl groups to DNA that typically reduces transcription by decreasing DNA accessibility or recruiting proteins that compact chromatin.
Mechanistic outcomes that connect methylation to gene expression patterns include:
Blocking binding of some transcription factors at or near regulatory sequences
Recruiting “reader” proteins that attract chromatin-compacting complexes
Supporting long-term gene silencing across many cell divisions
Histone modifications (protein modifications)
Histone “tails” can be chemically modified, changing how tightly DNA associates with histones and which regulatory proteins bind chromatin.
Histone acetylation: Addition of acetyl groups to histone tails that usually loosens DNA–histone interactions, increasing chromatin openness and promoting transcription.
Key principles linking histone modifications to expression patterns:
Acetylation often correlates with active chromatin (greater accessibility)
Deacetylation often correlates with repressed chromatin (reduced accessibility)
Other histone marks can create binding sites for proteins that either open or compact chromatin, shifting transcriptional potential
How epigenetic marks create stable, cell-specific expression patterns
Epigenetic control helps cells maintain identity by preserving expression states after DNA replication.
During DNA replication and chromatin reassembly, existing epigenetic marks can help guide placement of similar marks on newly assembled chromatin
This supports cell memory, so daughter cells often retain similar expression patterns as the parent cell
Because marks are reversible, cells can also remodel expression patterns in response to signals, developmental cues, or environmental conditions
What “reversible” means in practice
Epigenetic marks can be added or removed by enzymes, enabling dynamic regulation:
This schematic shows a nucleosome with histone tails bearing different post-translational modifications and classifies the main epigenetic regulators as writers (add marks), erasers (remove marks), and readers (bind marks to recruit additional factors). It provides a concrete visual for how reversible chemical tags on chromatin can be interpreted to shift transcriptional potential. Source
“Writers” add marks (e.g., methyl or acetyl groups)
“Erasers” remove marks
“Readers” bind marks and recruit other factors that alter chromatin structure and transcriptional activity
The result is coordinated control of chromatin accessibility, explaining how the same genome can produce different gene expression patterns in different contexts.
FAQ
Some marks are reset during gamete formation and early development, but a subset may escape reprogramming.
Evidence varies by species and trait, so “transgenerational epigenetic inheritance” is context-dependent.
A common approach is bisulphite-based methods that convert unmethylated cytosines while leaving methylated cytosines unchanged.
Sequencing then reveals methylation patterns at single-base resolution.
It’s the idea that combinations of histone tail modifications can be “read” by proteins to recruit complexes that activate or repress chromatin.
Different combinations can have different regulatory outcomes.
No. The effect depends on the specific modification, its location, and which reader proteins bind.
Some marks correlate with activation, others with repression, and context matters.
Yes. Some therapies target enzymes that add/remove marks (e.g., inhibitors of histone deacetylases).
These can shift expression programmes, especially in certain cancers, but effects can be broad and require careful targeting.
Practice Questions
Explain how DNA methylation can affect gene expression. (2 marks)
States that methylation typically reduces/silences transcription (1)
Links reduced expression to decreased DNA accessibility or recruitment of chromatin-compacting proteins (1)
A researcher increases histone acetylation at a gene locus in cultured cells. Predict the effect on chromatin structure and transcription, and justify your answer. (5 marks)
Predicts chromatin becomes more open/less condensed (1)
Predicts transcription increases (1)
Justifies: acetylation reduces positive charge on histones/weakens DNA–histone interaction (1)
Links openness to increased access for transcription machinery/transcription factors (1)
Notes reversibility/dynamic nature of histone marks in regulating expression patterns (1)
