Epigenetics: How Genes Are Switched On and Off

Identical Twins Share 99.9% of Their DNA — But Their Epigenomes Diverge Dramatically With Age

A landmark 2005 study by Mario Fraga and colleagues, published in the Proceedings of the National Academy of Sciences, compared DNA methylation and histone acetylation patterns in 80 pairs of identical (monozygotic) twins ranging in age from 3 to 74. Young twins were epigenetically nearly identical. By middle age, their epigenomes had diverged substantially — affecting gene expression differences in immune function, cancer susceptibility, and aging. The twins shared identical DNA sequences throughout. What changed was the epigenome: the chemical modifications layered on top of the DNA that determine which genes are expressed, when, and at what level.

DNA Methylation and CpG Islands

DNA methylation is the addition of a methyl group (-CH₃) to the 5-carbon position of cytosine bases, catalyzed by a family of enzymes called DNA methyltransferases (DNMTs: DNMT1, DNMT3A, DNMT3B). In mammals, methylation occurs almost exclusively at CpG dinucleotides — positions in the genome where cytosine is immediately followed by guanine. Approximately 70–80% of all CpG sites in the human genome are methylated.

CpG islands are regions of 200–3,000 base pairs with higher-than-expected CpG density. They occur at the promoters of approximately 60% of human genes. When a CpG island promoter is methylated, it recruits methyl-CpG-binding proteins (MBDs) that condense the chromatin and block transcription factor access, silencing the gene. When unmethylated, the promoter remains accessible and the gene can be expressed.

DNMT1 is the "maintenance" methyltransferase: it preferentially methylates hemi-methylated DNA produced during replication, copying the methylation pattern from parent strand to daughter strand. This is how epigenetic marks are inherited through cell division — the methylation pattern is preserved when cells divide, passing the same gene expression program to daughter cells without changing the underlying DNA sequence.

Histone Modifications: Acetylation and Methylation

DNA in eukaryotic cells is wrapped around protein complexes called nucleosomes, each consisting of eight histone proteins (two copies each of H2A, H2B, H3, and H4). The N-terminal tails of histones project outward from the nucleosome and are subject to dozens of chemical modifications that affect chromatin structure and gene expression:

Chromatin Remodeling

In addition to covalent histone modifications, ATP-dependent chromatin remodeling complexes physically reposition, eject, or restructure nucleosomes to control gene access. Four major families exist:

• SWI/SNF (BAF) complex — repositions nucleosomes to expose or cover regulatory elements; mutated in approximately 20% of human cancers (making it one of the most commonly mutated epigenetic regulators in cancer)
• ISWI complex — spaces nucleosomes evenly along DNA; important for chromatin assembly after replication
• CHD complex — slides and ejects nucleosomes; CHD7 mutations cause CHARGE syndrome
• INO80 complex — exchanges histone variants (e.g., incorporating H2A.Z at enhancers) to fine-tune regulatory element activity

Remodeling complexes work in concert with histone-modifying enzymes and DNA methyltransferases. The integration of these three epigenetic layers — DNA methylation, histone modifications, and chromatin remodeling — creates a complex regulatory code that determines cell identity. A liver cell and a neuron have identical DNA but vastly different epigenomes that maintain their distinct identities through thousands of cell divisions.

Transgenerational Epigenetic Inheritance: The Överkalix Study

One of the most compelling human examples of transgenerational epigenetic inheritance comes from the Överkalix cohort in northern Sweden, studied by Lars Olov Bygren, Gunnar Kaati, and Marcus Pembrey. The isolated parish of Överkalix kept meticulous records of harvests and food availability from the 19th century, enabling researchers to correlate grandparents' nutritional experiences with grandchildren's health outcomes.

Published findings (Pembrey et al., European Journal of Human Genetics, 2006) showed:

• Paternal grandsons of men who experienced a feast (food surplus) during their slow-growth period (ages 9–12) had significantly higher diabetes-related mortality risk
• Paternal granddaughters of women who experienced nutritional excess during their slow-growth period had higher cardiovascular mortality
• The effects were sex-specific and crossed generations — grandparents' nutritional environments predicted grandchildren's health outcomes decades later

The proposed mechanism involves epigenetic marks — particularly DNA methylation patterns in sperm — that escape the global epigenetic reprogramming that normally occurs during gametogenesis and early embryonic development. Specific imprinted genes and transposable element regions are known to partially retain methylation through reprogramming, providing a plausible mechanism for at least some transgenerational effects.

Cancer Epigenetics

Cancer is fundamentally both a genetic and epigenetic disease. Two major epigenetic changes characterize virtually all human cancers:

Global hypomethylation — cancer cells show widespread loss of DNA methylation across the genome, particularly at repetitive elements and transposable elements that are normally silenced by methylation. Hypomethylation causes genomic instability by activating transposable elements and weakening centromeric heterochromatin.

Promoter CpG island hypermethylation — simultaneous with global hypomethylation, specific tumor suppressor gene promoters become hypermethylated and silenced. In colorectal cancer, the mismatch repair gene MLH1 is frequently silenced by promoter methylation rather than by coding mutation — the gene sequence is intact but the gene is turned off. Other commonly silenced tumor suppressors include CDKN2A (p16), BRCA1, VHL, and CDH1.

The reversibility of epigenetic modifications makes them attractive drug targets. HDAC inhibitors (vorinostat, romidepsin) and DNA methyltransferase inhibitors (azacitidine, decitabine) are approved cancer therapies that work by reactivating silenced tumor suppressor genes rather than by cytotoxic mechanisms. EZH2 inhibitors (tazemetostat) target the H3K27me3 methyltransferase and are approved for epithelioid sarcoma. The epigenetic therapy field is one of the most active areas in oncology drug development, with dozens of compounds in clinical trials targeting BET bromodomains, LSD1/KDM1A, and other chromatin regulators.