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.     

Structural features and methylation patterns associated with paramutation at the r1 locus of Zea mays.

In paramutation, two alleles of a gene interact and, during the interaction, one of them becomes epigenetically silenced. The various paramutation systems that have been studied to date exhibit intriguing differences in the physical complexity of the loci involved. B and Pl alleles that participate in paramutation are simple, single genes, while the R haplotypes that participate in paramutation contain multiple gene copies and often include rearrangements. The number and arrangement of the sequences in particular complex R haplotypes have been correlated with paramutation behavior. Here, the physical structures of 28 additional haplotypes of R were examined. A specific set of physical features is associated with paramutability (the ability to be silenced). However, no physical features were strongly correlated with paramutagenicity (the ability to cause silencing) or neutrality (the inability to participate in paramutation). Instead, paramutagenic haplotypes were distinguished by high levels of cytosine methylation over certain regions of the genes while neutral haplotypes were distinguished by lack of C-methylation over these regions. These findings suggest that paramutability of r1 is determined by the genetic structure of particular haplotypes, while paramutagenicity is determined by the epigenetic state.     

Organization of Paramutagenicity in R-Stippled Maize

In heterozygotes, R-stippled (R-st) reduces the pigmenting potential of sensitive r alleles heritably (paramutation). R-st is comprised of four r genes arranged in direct orientation. Unequal crossing over within R-st generates deletion products retaining from one to three r genes. Paramutagenic strength decreased in parallel with copy number, both among internal and distal deletions. Single-gene R-st derivatives were nonparamutagenic. This was so whether or not the single gene retained the transposable element (I-R) responsible for seed spotting. Adding back r genes by intragenic recombination increased paramutagenicity in proportion to total gene number. Each member of a set of overlapping deletions retained moderately strong activity, showing that no single r gene or intragenic region is required for paramutagenicity. Proximal and distal loss R-st derivatives, each retaining two r genes, were less paramutagenic in trans than the corresponding four copy cis combination, indicating R-st's paramutagenic determinants function as a cis-interdependent unit in bringing about modification of a sensitive allele.     

The maize b1 paramutation control region causes epigenetic silencing in Drosophila melanogaster

Paramutation is an epigenetic process in which a combination of alleles in a heterozygous organism results in a meiotically stable change in expression of one of the alleles. The mechanisms underlying paramutation are being actively investigated, and examples have been described in both plants and mammals, suggesting that it may utilize epigenetic mechanisms that are widespread and evolutionarily conserved. Paramutation at the well-studied maize b1 locus requires a control region consisting of seven 853 bp tandem repeats. To study the conservation of the epigenetic mechanisms underlying seemingly unique epigenetic processes such as paramutation, we created transgenic Drosophila melanogaster carrying the maize b1 control region adjacent to the Drosophila white reporter gene. We show that the b1 tandem repeats cause silencing of the white reporter in Drosophila. A single copy of the tandem repeat sequence is sufficient to cause silencing, and silencing strength increases as the number of tandem repeats increases. Additionally, transgenic lines with the full seven tandem repeats demonstrate evidence of either pairing-sensitive silencing and silencing in trans, or epigenetic activation in trans. These trans-interactions are dependent on repeat number, similar to maize b1 paramutation. Also, as in maize, the tandem repeats are bidirectionally transcribed in Drosophila. These results indicate that the maize b1 tandem repeats function as an epigenetic silencer and mediate trans-interactions in Drosophila, and support the hypothesis that the mechanisms underlying such epigenetic processes are conserved.     

Maize Unstable factor for orange1 Is Required for Maintaining Silencing Associated with Paramutation at the pericarp color1 and booster1 Loci

To understand the molecular mechanisms underlying paramutation, we examined the role of Unstable factor for orange1 (Ufo1) in maintaining paramutation at the maize pericarp color1 (p1) and booster1 (b1) loci. Genetic tests revealed that the Ufo1-1 mutation disrupted silencing associated with paramutation at both p1 and b1. The level of up regulation achieved at b1 was lower than that at p1, suggesting differences in the role Ufo1-1 plays at these loci. We characterized the interaction of Ufo1-1 with two silenced p1 epialleles, P1-rr′ and P1-pr^TP, that were derived from a common P1-rr ancestor. Both alleles are phenotypically indistinguishable, but differ in their paramutagenic activity; P1-rr′ is paramutagenic to P1-rr, while P1-pr^TP is non-paramutagenic. Analysis of cytosine methylation revealed striking differences within an enhancer fragment that is required for paramutation; P1-rr′ exhibited increased methylation at symmetric (CG and CHG) and asymmetric (CHH) sites, while P1-pr^TP was methylated only at symmetric sites. Both silenced alleles had higher levels of dimethylation of lysine 9 on histone 3 (H3K9me2), an epigenetic mark of silent chromatin, in the enhancer region. Both epialleles were reactivated in the Ufo1-1 background; however, reactivation of P1-rr′ was associated with dramatic loss of symmetric and asymmetric cytosine methylation in the enhancer, while methylation of up-regulated P1-pr^TP was not affected. Interestingly, Ufo1-1–mediated reactivation of both alleles was accompanied with loss of H3K9me2 mark from the enhancer region. Therefore, while earlier studies have shown correlation between H3K9me2 and DNA methylation, our study shows that these two epigenetic marks are uncoupled in the Ufo1-1–reactivated p1 alleles. Furthermore, while CHH methylation at the enhancer region appears to be the major distinguishing mark between paramutagenic and non-paramutagenic p1 alleles, H3K9me2 mark appears to be important for maintaining epigenetic silencing.     

Gene frequency-based estimation of natural outcrossing in opium poppy (<Emphasis Type="Italic">Papaver somniferum</Emphasis> L.)

Mating systems are generally thought to be important factors in determining the amount and nature of genetic variability in a population. Nearly 1,000 individuals at a single location (Lucknow) and over two years were crossed and subsequently scored for selfing versus outcrossing in 9–10 monohybrid populations of opium poppy (Papaver somniferum). Three different alleles of two marker loci (two—R/r and P/p—for anthocyanin locus and B/b for capsule size locus) were used to determine the male gametes that had effected fertilizations in F₂ recessives (rr, pp and bb). The estimates of the gene frequency-based outcrossing parameter (α) were found to vary with year, cross and marker locus used (α range: 7.21–71.03%). Study of the two dihybrid crosses concerning the two marker loci simultaneously, further confirmed that outcrossing at the R/r or P/p locus was significantly greater than that at the B/b locus. The nature of the outcrossing was, in general, nonrandom. In this species, in general, selfing predominated, with one exception in respect of monohybrid crosses involving the purple form of anthocyanin locus, in which outcrossing predominated.     

Genetic and molecular characterization of a-mrh-Mrh, a new mutable system of Zea mays

A new allele of the maize A1 gene, a gene required for anthocyanin pigment biosynthesis, was identified in a genetic stock exhibiting a high frequency of chromosome breakage at the second microspore mitosis. This allele, a-mrh, is unstable in both somatic and germinal tissue when an independent locus, Mrh, is present in the genome. a-mrh was molecularly cloned, and a 246 bp DNA insertion with characteristics of a transposable element was identified within the fourth exon of the gene. Southern blot analysis of germinal derivatives of a-mrh suggests that the DNA insert rMrh is excised from the locus when a wild-type phenotype is restored. Genetic crosses with components of other two-element mutable systems of maize failed to induce mutability. We therefore conclude that rMrh is a member of a new, two-element transposon system of maize. The genetic and molecular characteristics of the elements involved are discussed with respect to stress-activated transposition, response of an element to developmental signals, and a possible new role of plant transposons in gene evolution.     

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.     

The evolutionary potential of paramutation: A population-epigenetic model

Paramutation involves an interaction between homologous alleles resulting in a heritable change in gene expression without altering the DNA sequence. Initially believed to be restricted to plants, paramutation has recently been observed in animal models, and a paramutation-like event has been noted in humans. Despite the accumulating evidence suggesting that trans-acting epigenetic effects can be inherited transgenerationally and therefore generate non-genomic phenotypic variation, these effects have been largely ignored in the context of evolutionary theory. The model presented here incorporates paramutation into the standard model of viability selection at one locus and demonstrates that paramutation can create long-term biological diversity in the absence of genetic change, and even in the absence of the original paramutagenic allele. Therefore, if paramutation is present, attributing evolution to only a traditional genetic model may fail to encompass the broad scope of phenotypic differences observed in nature. Moreover, we show also that an unusual mathematical behaviour, analogous to “Ewens’ gap” of the two-locus two-allele symmetric-selection model, occurs: when the rate of one parameter–for example, the rate of paramutation–is increased, a pair of equilibria may disappear only to reappear as this parameter increases further. In summary, by incorporating even the simplest epigenetic parameters into the standard population-genetic model of selection, we show how this type of inheritance system can profoundly alter the course of evolution.     

玉米副突变及其分子机制

副突变是一种表观遗传现象,通过同源基因间染色质状态信息的转移建立新的基因表达状态,这种表达状态能够通过减数分裂而传递到后代。玉米是研究副突变及其机制的模式植物,目前已经发现有5个基因位点能够发生副突变。对玉米b1副突变系统的广泛研究发现DNA重复序列、siRNA途径、DNA结合蛋白等在副突变状态的建立和维持过程中可能起着重要的作用。