Paramutation



In epigenetics, a paramutation is an interaction between two alleles at a single locus, whereby one allele induces a heritable change in the other allele. The change may be in the pattern of DNA methylation, for example. The allele inducing the change is said to be paramutagenic, whilst the allele that has been epigenetically altered is termed paramutant (or paramutated). This change is meiotically inheritable, and therefore paramutation violates Mendel’s first law.

A paramutant allele may have altered levels of gene expression, which may continue in offspring which inherit that allele, even though the paramutagenic allele may no longer be present. Through proper breeding, paramutation can result in sibling plants that have the same genetic sequence, but with drastically different phenotypes.

Paramutation can result in a single allele of a gene controlling a spectrum of phenotypes. At r1 in maize, for example, the weaker expression state adopted by a paramutant allele can range from completely colorless to nearly fully colored kernels. This is an exception to the general observation that traits that vary along a continuum are usually controlled by multiple genes.

History
Paramutation was first discovered and studied in maize (Zea mays) by R.A. Brink at the University of Wisconsin–Madison in the 1950s. Brink noticed that specific weakly expressed alleles of the red1 (r1) locus in maize, which encodes a transcription factor that confers red pigment to corn kernels, can heritably change specific strongly expressed alleles to a weaker expression state. The weaker expression state adopted by the changed allele is heritable and can, in turn, change the expression state of other active alleles in a process termed secondary paramutation. Brink showed that the influence of the paramutagenic allele could persist for many generations.

Mechanism
The molecular basis of paramutation is being unravelled almost exclusively in maize. Paramutation may share common mechanisms with other epigenetic phenomena, such as gene silencing and genomic imprinting. In maize, paramutation seems to share many traits with the well understood RNA-directed DNA-methylation pathway in Arabidopsis thaliana, even though it has never been observed in that species. In maize: "'paramutation is RNA-directed. Stability of the chromatin states associated with paramutation and transposon silencing requires the mop1 gene, which encodes an RNA-dependent RNA polymerase.'" Exactly how the RNA produced by this polymerase causes paramutation in maize is not yet understood, but like other epigenetic changes, it involves the covalent modification of DNA and/or the DNA-bound histone proteins without changing the DNA sequence itself.

Occurrence
Allelic interactions similar to paramutation have since been reported in other organisms, including tomatos, peas, and mice.