Paramutation
Encyclopedia
In epigenetics
, paramutation is an interaction between two alleles of a single locus
, resulting in a heritable change of one allele that is induced by the other allele. Paramutation violates Mendel’s first law, which states that in the process of the formation of the gametes (egg or sperm) the allelic pairs separate, one going to each gamete, and that each allele remains completely uninfluenced by the other. In paramutation an allele in one generation heritably affects the other allele in future generations, even if the allele causing the change is itself not transmitted. What may be transmitted are patterns of DNA methylation
or RNAs such as piRNA
s, siRNA
s, miRNA
s or other regulatory RNA
s. Through proper breeding, paramutation can result in isogenic
sibling plants with drastically different phenotype
s.
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.
Interestingly, 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 an allele following paramutation can range from completely colorless to nearly fully colored kernels. This is an exception to the general observation that continuous variation is controlled by many genes.
Allelic interactions similar to paramutation have since been reported in other organisms, including tomato
, pea
, and mice
.
The molecular basis of paramutation is being unraveled, 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 the famous model plant. Alleman (2006) reported that, 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.
Epigenetics
In biology, and specifically genetics, epigenetics is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence – hence the name epi- -genetics...
, paramutation is an interaction between two alleles of a single locus
Locus (genetics)
In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...
, resulting in a heritable change of one allele that is induced by the other allele. Paramutation violates Mendel’s first law, which states that in the process of the formation of the gametes (egg or sperm) the allelic pairs separate, one going to each gamete, and that each allele remains completely uninfluenced by the other. In paramutation an allele in one generation heritably affects the other allele in future generations, even if the allele causing the change is itself not transmitted. What may be transmitted are patterns of DNA methylation
DNA methylation
DNA methylation is a biochemical process that is important for normal development in higher organisms. It involves the addition of a methyl group to the 5 position of the cytosine pyrimidine ring or the number 6 nitrogen of the adenine purine ring...
or RNAs such as piRNA
Pirna
Pirna is a town in the Free State of Saxony, Germany, capital of the administrative district Sächsische Schweiz-Osterzgebirge. The town's population is over 40,000. Pirna is located near Dresden and is an important district town as well as a Große Kreisstadt...
s, siRNA
Sírna
Sírna Sáeglach , son of Dian mac Demal, son of Demal mac Rothechtaid, son of Rothechtaid mac Main, was, according to medieval Irish legend and historical tradition, a High King of Ireland...
s, miRNA
Mirna
Mirna may refer to:geographical entities* Mirna , a river in Istria, Croatia* Mirna , a river in Slovenia, tributary of the river Sava* Mirna , a settlement in the municipality of Mirna in Southeastern Sloveniapeople...
s or other regulatory RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
s. Through proper breeding, paramutation can result in isogenic
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
sibling plants with drastically different phenotype
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
s.
Paramutation was first discovered and studied in maize
Maize
Maize known in many English-speaking countries as corn or mielie/mealie, is a grain domesticated by indigenous peoples in Mesoamerica in prehistoric times. The leafy stalk produces ears which contain seeds called kernels. Though technically a grain, maize kernels are used in cooking as a vegetable...
(Zea mays) by R.A. Brink
Royal Alexander Brink
Royal Alexander Brink , also known as R. A. Brink, was a Canadian-born plant geneticist and plant breeder at the University of Wisconsin–Madison.- Professional background :...
at the University of Wisconsin–Madison
University of Wisconsin–Madison
The University of Wisconsin–Madison is a public research university located in Madison, Wisconsin, United States. Founded in 1848, UW–Madison is the flagship campus of the University of Wisconsin System. It became a land-grant institution in 1866...
in the 1950s. Brink noticed that specific weakly expressed alleles of the red1 (r1) locus in maize, which encodes a transcription factor
Transcription factor
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
that confers red pigment to corn kernels
Corn kernels
Corn kernels are the seeds of maize.Corn kernels are used as pelletized fuel for pellet stoves and furnaces. Corn kernels are a natural pellet, which gives them a huge economic advantage over other man-made biomass pellets and wood pellets....
, 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.
Interestingly, 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 an allele following paramutation can range from completely colorless to nearly fully colored kernels. This is an exception to the general observation that continuous variation is controlled by many genes.
Allelic interactions similar to paramutation have since been reported in other organisms, including tomato
Tomato
The word "tomato" may refer to the plant or the edible, typically red, fruit which it bears. Originating in South America, the tomato was spread around the world following the Spanish colonization of the Americas, and its many varieties are now widely grown, often in greenhouses in cooler...
, pea
Pea
A pea is most commonly the small spherical seed or the seed-pod of the pod fruit Pisum sativum. Each pod contains several peas. Peapods are botanically a fruit, since they contain seeds developed from the ovary of a flower. However, peas are considered to be a vegetable in cooking...
, and mice
Mouse
A mouse is a small mammal belonging to the order of rodents. The best known mouse species is the common house mouse . It is also a popular pet. In some places, certain kinds of field mice are also common. This rodent is eaten by large birds such as hawks and eagles...
.
The molecular basis of paramutation is being unraveled, almost exclusively in maize
Maize
Maize known in many English-speaking countries as corn or mielie/mealie, is a grain domesticated by indigenous peoples in Mesoamerica in prehistoric times. The leafy stalk produces ears which contain seeds called kernels. Though technically a grain, maize kernels are used in cooking as a vegetable...
. Paramutation may share common mechanisms with other epigenetic phenomena, such as gene silencing
Gene silencing
Gene silencing is a general term describing epigenetic processes of gene regulation. The term gene silencing is generally used to describe the "switching off" of a gene by a mechanism other than genetic modification...
and genomic imprinting. In maize, paramutation seems to share many traits with the well understood RNA-directed DNA-methylation pathway in Arabidopsis thaliana
Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...
, even though it has never been observed in the famous model plant. Alleman (2006) reported that, 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.