Genetic factors required to maintain repression of a paramutagenic maize pl1 allele

A genetic screen identified two novel gene functions required to maintain mitotically and meiotically heritable gene silencing associated with paramutation of the maize purple plant 1 (pl1) locus. Paramutation at pl1 leads to heritable alterations of pl1 gene regulation; the Pl-Rhoades (Pl-Rh) allele, which typically confers strong pigmentation to juvenile and adult plant structures, changes to a lower expression state termed Pl'-mahogany (Pl'). Paramutation spontaneously occurs at low frequencies in Pl-Rh homozygotes but always occurs when Pl-Rh is heterozygous with Pl'. We identified four mutations that caused increased Pl' pigment levels. Allelism tests revealed that three mutations identified two new maize loci, required to maintain repression 1 (rmr1) and rmr2 and that the other mutation represents a new allele of the previously described mediator of paramutation 1 (mop1) locus. RNA levels from Pl' are elevated in rmr mutants and genetic tests demonstrate that Pl' can heritably change back to Pl-Rh in rmr mutant individuals at variable frequencies. Pigment levels controlled by two pl1 alleles that do not participate in paramutation are unaffected in rmr mutants. These results suggest that RMR functions are intimately involved in maintaining the repressed expression state of paramutant Pl' alleles. Despite strong effects on Pl' repression, rmr mutant plants have no gross developmental abnormalities even after several generations of inbreeding, implying that RMR1 and RMR2 functions are not generally required for developmental homeostasis.     

Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function

Paramutations represent directed and meiotically-heritable changes in gene regulation leading to apparent violations of Mendelian inheritance. Although the mechanism and evolutionary importance of paramutation behaviors remain largely unknown, genetic screens in maize (Zea mays) identify five components affecting 24 nucleotide RNA biogenesis as required to maintain repression of a paramutant purple plant1 (pl1) allele. Currently, the RNA polymerase IV largest subunit represents the only component also specifying proper development. Here we identify a chromodomain helicase DNA-binding 3 (CHD3) protein orthologous to Arabidopsis (Arabidopsis thaliana) PICKLE as another component maintaining both pl1 paramutation and normal somatic development but without affecting overall small RNA biogenesis. In addition, genetic tests show this protein contributes to proper male gametophyte function. The similar mutant phenotypes documented in Arabidopsis and maize implicate some evolutionarily-conserved gene regulation while developmental defects associated with the two paramutation mutants are largely distinct. Our results show that a CHD3 protein responsible for normal plant ontogeny and sperm transmission also helps maintain meiotically-heritable epigenetic regulatory variation for specific alleles. This finding implicates an intersection of RNA polymerase IV function and nucleosome positioning in the paramutation process.     

Hérédité et épigénétique: un rôle inattendu pour l’ARN

Although Mendel’s first laws explain the transmission of most characteristics, there has recently been a renewed interest in the notion that DNA is not the sole determinant of our inherited phenotype. Human epidemiology studies and animal and plant genetic studies have provided evidence that epigenetic information (“epigenetic” describes an inherited effect on chromosome or gene function that is not accompanied by any alteration of the nucleotide sequence) can be inherited from parents to offspring. Most of the mechanisms involved in epigenetic “memory” are paramutation events, which are heritable epigenetic changes in the phenotype of a “paramutable” allele. Initially demonstrated in plants, paramutation is defined as an interaction between two alleles of a single locus that results in heritable changes of one allele that is induced by the other. The authors describe an unexpected example of paramutation in the mouse revealed by a recent analysis of an epigenetic variation modulating expression of theKit locus. The progeny of hétérozygote intercrosses (carrying one mutant and one wild-type allele) showed persistence of the white patches (characteristic of hétérozygotes) in the homozygous Kit^+/+ progeny. The DNA sequences of the two wild-type alleles were structurally normal, revealing an epigenetic modification. Further investigations showed that RNA and microRNA, released by sperm, mediate this epigenetic inheritance. The molecular mechanisms involved in this unexpected mode of inheritance and the role of RNA molecules in the spermatozoon head as possible vectors for the hereditary transfer of such modifications — implying that paternal inheritance is not limited to just one haploid copy of the genome — are still a matter of debate. Paramutations may be considered to be one possibility of epigenetic modification in the case of familial disease predispositions not fully explained by Mendelian analysis.     

Paramutation in maize

Paramutation is a heritable change in gene expression induced by allele interactions. This review summarizes key experiments on three maize loci, which undergo paramutation. Similarities and differences between the phenomenology at the three loci are described. In spite of many differences with respect to the stability of the reduced expression states at each locus or whether paramutation correlates with DNA methylation and repeated sequences within the loci, recent experiments are consistent with a common mechanism underlying paramutation at all three loci. Most strikingly, trans-acting mutants have been isolated that prevent paramutation at all three loci and lead to the activation of silenced Mutator transposable elements. Models consistent with the hypothesis that paramutation involves heritable changes in chromatin structure are presented. Several potential roles for paramutation are discussed. These include localizing recombination to low-copy sequences within the genome, establishing and maintaining chromatin domain boundaries, and providing a mechanism for plants to transmit an environmentally influenced expression state to progeny.