Beyond Mendel: repeats, mitochondria, imprinting and multifactorial traits

Fragile X syndrome is the most common inherited cause of intellectual disability in boys (about 1 in 4,000 males and 1 in 8,000 females). The FMR1 gene at Xq27.3 begins with a run of CGG repeats in its 5′ untranslated region. Above about 200 repeats the run and the neighboring promoter CpG island become hypermethylated, transcription stops, and the RNA-binding protein FMRP, which restrains translation of many mRNAs at synapses, is absent. Cultured cells in folate-poor medium show a constriction at Xq27.3, the “fragile site” that named the disease.

The repeat expands only when transmitted by a woman. A man with a premutation (a “normal transmitting male”) passes it, unchanged, to all of his daughters; their sons are then at risk because the premutation can jump to a full mutation in the daughters' eggs. So the disease becomes more frequent and severe down the generations (anticipation). Females with a full mutation are variably affected (about half have learning difficulty) because X inactivation leaves a varying fraction of cells with the normal X active.

Each mitochondrion carries a small circular genome (37 genes) that encodes 13 subunits of the respiratory chain plus the tRNAs and rRNAs needed to make them. Children receive their mitochondria from the oocyte; sperm mitochondria are destroyed after fertilization. So an affected woman passes her mtDNA mutation to all of her children, and an affected man to none.

Cells contain hundreds to thousands of mtDNA copies, and a mutation usually affects only some of them: heteroplasmy. During oogenesis only a few copies seed each egg (the bottleneck), so siblings receive very different mutant fractions. Within a person, the fraction drifts between tissues as cells divide. Disease appears when the mutant fraction in a tissue crosses its threshold, which is lowest where energy demand is highest: brain, retina, skeletal and heart muscle, inner ear, β cells. This is why severity varies so much within one family.

On a muscle biopsy stained with modified Gomori trichrome, ragged red fibers are fibers whose rims are packed with red-staining mitochondria: the cell has made more mitochondria to compensate for their poor function. Electron microscopy shows enlarged mitochondria with paracrystalline (“parking lot”) inclusions.

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For most genes both parental copies work. For a few hundred imprinted genes, one parent's copy is silenced by DNA methylation set in the egg or sperm, so only the other parent's copy is expressed. The mark is erased and reset in each generation according to the sex of the transmitting parent. Losing the only expressed copy causes disease even though the other copy is perfectly normal.

Chromosome 15q11–q13 holds two neighboring sets. Genes such as SNRPN and the SNORD116 snoRNA cluster are expressed only from the paternal copy; UBE3A is expressed only from the maternal copy in neurons. The same region can therefore cause two different diseases depending on which parent's contribution is missing.

Uniparental disomy (UPD) means both copies of a chromosome come from one parent. It usually starts as a trisomic conceptus that loses one extra chromosome (trisomy rescue): if the lost one was the single copy from the other parent, the embryo is left with two copies from one parent. The count is 46 and the structure normal, so the karyotype looks normal; methylation studies (or SNP marker analysis) reveal it.

Most common birth defects and adult diseases arise from many genes of small effect plus environment. Think of liability as a bell curve across the population; disease appears in those past a threshold. Relatives share genes, so their curve sits closer to the threshold; environment can push it either way. This model explains the recurrence rules: the risk for first-degree relatives is a few percent (not 25% or 50%), it rises with each affected relative and with severity, falls quickly in more distant relatives, and is higher when the affected person is of the less commonly affected sex (a girl with pyloric stenosis carries more liability than a boy).

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