Paramutation: just a curiosity or fine tuning of gene expression in the next generation?

Preliminary Evidence of a Horizontal Transfer of Paramutation Phenomenon at the pl1 Gene in Maize (Zea mays L.)

Paramutation, a specific epigenetic phenomenon first identified in Zea mays by Alexander Brink in the 1950s, has since been observed in different plant and animal species. What sets paramutation apart from other gene silencing processes is its ability for one silenced allele (referred to as paramutagenic) to silence another allele (paramutable) in trans. The resultant silenced allele (paramutated) remains stable across generations, even after separating from the paramutagenic allele, and acquires paramutagenic properties itself. This hereditary behavior facilitates the rapid dissemination of specific gene expression patterns or phenotypes within populations, disrupting the Hardy-Weinberg equilibrium even without other evolutionary pressures. Despite extensive research, the molecular mechanisms underlying paramutation are still not fully understood, although numerous studies suggest the involvement of RNA-mediated changes in DNA methylation and in the chromatin structure of silenced genes. In this paper, we report preliminary evidence regarding horizontal paramutation transfer at the pl1 (purple plant1) regulatory gene involved in the accumulation of anthocyanin in several plant tissues such as tassel, kernel, and cob. A paramutated pl1' allele arose spontaneously in a pl1 population, and in this study, we found evidence of silencing events spatially associated in the field, suggesting a possible horizontal transfer of silencing among nearby plants.

Backcrossing Modulates the Metabolic Profiles of Anthocyanin-Pigmented 'Vitamaize' Lines Derived from Elite Maize Lines

Vitamaize lines (VMLs) were created by backcrossing the pigmented aleurone trait into Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT) maize lines (CMLs). This study evaluates metabolic differences between the VMLs and their original CMLs. Direct infusion mass spectrometry (DIMS) analyses, carotenoid profiling, total anthocyanins content (TAC) determination, and biochemical evaluation of the quality protein maize (QPM) endosperm trait allowed a comprehensive chemical characterization of the maize lines. DIMS data indicate higher hexoses and trigonelline content for most VMLs; the carotenoid profile revealed a decrease in β-cryptoxanthin to less than half of the original parent content for two VMLs but an augmentation for one VML. The pigmented aleurone VMLs did not inherit the complex QPM endosperm trait of the QPM CMLs. Except for anthocyanin accumulation, no other metabolites were consistently modified across all the backcross-generated maize lines with a pigmented aleurone trait. These findings suggest using genetic or metabolic markers rather than morphological or visual traits for future breeding programs.

Epimutations and mutations, nurturing phenotypic diversity

Epimutations and mutations are two dissimilar mechanisms that have contributed to the phenotypic diversities in organisms. Though dissimilar, many previous studies have revealed that the consequences of epimutations and mutations are not mutually exclusive. DNA rich in epigenetic modifications can be prone to mutations and vice versa. In order to get a better insight into the molecular evolution in organisms, it is important to consider the information of both genetic and epigenetic changes in their genomes. Understanding the similarities and differences between the consequences of epimutations and mutations is required for a better interpretation of phenotypic diversities in organisms. Factors contributing to epigenetic changes such as paramutations and mutation hotspots and, the correlation of the interdependence of mutations and epigenetic changes in DNA are important aspects that need to be considered for molecular evolutionary studies. Thus, this review explains what epimutations are, their causes, how they are similar/different from mutations, and the influence of epigenetic changes and mutations on each other, further emphasizing how molecular evolution involving both mutations and epimutations can lead to speciation. Considering this approach will aid in reorganizing taxonomic classifications, importantly, solving disparities in species identification.

The Pea (Pisum sativum L.) Rogue Paramutation is Accompanied by Alterations in the Methylation Pattern of Specific Genomic Sequences

The spontaneous emergence among common pea (Pisum sativum L.) cultivars of off-type rogue plants exhibiting leaves with narrower and pointed leaflets and stipules and the non-Mendelian inheritance of this new phenotype were first described in the early 20th century. However, so far, no studies at the molecular level of this first identified case of paramutation have been carried out. In this study, we show for the first time that the pea rogue paramutation is accompanied by alterations in the methylation status of specific genomic sequences. Although, no significant differences were observed in the genome-wide DNA methylation in leaves of non-rogue cv. Onward in comparison to its rogue paramutant line JI2723, 22 DNA sequences were identified by methylation-sensitive amplified fragment length polymorphisms (MS-AFLP) analysis as differentially methylated in the two epigenomes. Mitotically inherited through all leaf tissues, the differential methylation patterns were also found to be meiotically inherited and conserved in pollen grains for 12 out of the 22 sequences. Fourteen of the sequences were successfully amplified in cDNA but none of them exhibited significant differential expression in the two contrasting epigenotypes. The further exploitation of the present research results on the way towards the elucidation of the molecular mechanisms behind this interesting epigenetic phenomenon is discussed.

Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila

Transgenerational Epigenetic Inheritance (TEI) studies the transmission of alternative functional states through multiple generations in the presence of the same genomic DNA sequence. Very little is known on the principles and the molecular mechanisms governing this type of inheritance. Here, by transiently enhancing 3D chromatin interactions, we established stable and isogenic Drosophila epilines that carry alternative epialleles, defined by differential levels of the Polycomb-dependent H3K27me3 mark. Once established, epialleles can be dominantly transmitted to naïve flies and induce paramutation. Importantly, epilines can be reset to a naïve state by disrupting chromatin interactions. Finally, we show that environmental changes can modulate the expressivity of the epialleles and we extend our paradigm to naturally occurring phenotypes. Our work sheds light on how nuclear organization and Polycomb group proteins contribute to epigenetically inheritable phenotypic variability.

From epigenetic landscape to phenotypic fitness landscape: Evolutionary effect of pathogens on host traits

The epigenetic landscape illustrates how cells differentiate through the control of gene regulatory networks. Numerous studies have investigated epigenetic gene regulation but there are limited studies on how the epigenetic landscape and the presence of pathogens influence the evolution of host traits. Here, we formulate a multistable decision-switch model involving several phenotypes with the antagonistic influence of parasitism. As expected, pathogens can drive dominant (common) phenotypes to become inferior through negative frequency-dependent selection. Furthermore, novel predictions of our model show that parasitism can steer the dynamics of phenotype specification from multistable equilibrium convergence to oscillations. This oscillatory behavior could explain pathogen-mediated epimutations and excessive phenotypic plasticity. The Red Queen dynamics also occur in certain parameter space of the model, which demonstrates winnerless cyclic phenotype-switching in hosts and in pathogens. The results of our simulations elucidate the association between the epigenetic and phenotypic fitness landscapes and how parasitism facilitates non-genetic phenotypic diversity.

Epigenetic Changes in Hybrids

Genome-wide approaches to the study of hybrid vigor have identified epigenetic changes in the hybrid nucleus in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). DNA methylation associated with 24-nucleotide small interfering RNAs exhibits transallelic effects in hybrids of Arabidopsis and other species. Some of the transmethylation changes are inherited and some affect gene expression. Hybrids have larger leaves than those of the parents and have increases in cell size and number. The increased leaf size results in a greater photosynthetic capacity, which may support the increased vegetative and reproductive yields of the F1 hybrids. Genes and metabolic pathways that have altered expression relative to the parents include loci involved in responses to hormones and to biotic and abiotic stress. Whereas epigenetically induced changes in gene expression may contribute to hybrid vigor, the link between the transcriptional changes and the hybrid phenotype is not confirmed. Recurrent selection of high yielding F1 lines from the F2/F3 of a number of crops has fixed heterosis yields in pure breeding lines. These hybrid-like lines may have valuable applications in crop systems.

Anthocyanins in corn: a wealth of genes for human health

Different epidemiological and preclinical studies have demonstrated that regular consumption of anthocyanin-rich foods is associated to a reduced risk of chronic diseases, such as cardiovascular diseases, cancer and obesity. However, assigning a health property to anthocyanins or other classes of flavonoids may be limited by the influence of other metabolites of plant-based food consumed in the diet, acting as possible confounding factors. The development of model foods essentially isogenic and nutritionally identical except that in the type and quantity of plant bioactives to be studied represents an important tool in nutritional studies. The extensive knowledge of the regulation of flavonoid pathway in maize can be exploited to obtain 'near-isogenic' model foods, which differ only in the content of specific classes of flavonoids. Being obtainable by breeding strategies, maize model foods can provide functional foods that can be used for both animal feeding studies and human intervention trials for assessing the role of flavonoids or other bioactives in preventing chronic diseases. This review will be focused on recent advances regarding the anthocyanin biosynthesis in maize, the role of anthocyanins from corn in preventing chronic diseases and finally on the breeding activities to produce maize functional foods with increased anthocyanin content.

Anthocyanins in corn: a wealth of genes for human health

Different epidemiological and preclinical studies have demonstrated that regular consumption of anthocyanin-rich foods is associated to a reduced risk of chronic diseases, such as cardiovascular diseases, cancer and obesity. However, assigning a health property to anthocyanins or other classes of flavonoids may be limited by the influence of other metabolites of plant-based food consumed in the diet, acting as possible confounding factors. The development of model foods essentially isogenic and nutritionally identical except that in the type and quantity of plant bioactives to be studied represents an important tool in nutritional studies. The extensive knowledge of the regulation of flavonoid pathway in maize can be exploited to obtain 'near-isogenic' model foods, which differ only in the content of specific classes of flavonoids. Being obtainable by breeding strategies, maize model foods can provide functional foods that can be used for both animal feeding studies and human intervention trials for assessing the role of flavonoids or other bioactives in preventing chronic diseases. This review will be focused on recent advances regarding the anthocyanin biosynthesis in maize, the role of anthocyanins from corn in preventing chronic diseases and finally on the breeding activities to produce maize functional foods with increased anthocyanin content.

Inheritance of Trans Chromosomal Methylation patterns from Arabidopsis F1 hybrids

Hybridization in plants leads to transinteractions between the parental genomes and epigenomes that can result in changes to both 24 nt siRNA and cytosine methylation ((m)C) levels in the hybrid. In Arabidopsis the principle processes altering the hybrid methylome are Trans Chromosomal Methylation (TCM) and Trans Chromosomal deMethylation (TCdM) in which the (m)C pattern of a genomic segment attains the same (m)C pattern of the corresponding segment on the other parental chromosome. We examined two loci that undergo TCM/TCdM in the Arabidopsis C24/Landsberg erecta (Ler) F1 hybrids, which show patterns of inheritance dependent on the properties of the particular donor and recipient chromosomal segments. At At1g64790 the TCM- and TCdM-derived (m)C patterns are maintained in the F2 generation but are transmitted in outcrosses or backcrosses only by the C24 genomic segment. At a region between and adjacent to At3g43340 and At3g43350, the originally unmethylated Ler genomic segment receives the C24 (m)C pattern in the F1, which is then maintained in backcross plants independent of the presence of the parental C24 segment. In backcrosses to an unmethylated Ler allele, the newly methylated F1 Ler segment may act as a TCM source in a process comparable to paramutation in maize. TCM-derived (m)C patterns are associated with reduced expression of both At3g43340 and At3g43350 in F1 and F2 plants, providing support for such events influencing the transcriptome. The inheritance of the F1 (m)C patterns and the segregation of other genetic and epigenetic determinants may contribute to the reduced hybrid vigor in the F2 and subsequent generations.

PIWI-interacting RNAs: from generation to transgenerational epigenetics

Small-RNA-guided gene regulation is a recurring theme in biology. Animal germ cells are characterized by an intriguing small-RNA-mediated gene-silencing mechanism known as the PIWI pathway. For a long time, both the biogenesis of PIWI-interacting RNAs (piRNAs) as well as their mode of gene silencing has remained elusive. A recent body of work is shedding more light on both aspects and implicates PIWI in the establishment of transgenerational epigenetic states. In fact, the epigenetic states imposed by PIWI on targets may actually drive piRNA production itself. These findings start to couple small RNA biogenesis with small-RNA-mediated epigenetics.

Extremely stable Piwi-induced gene silencing in Caenorhabditis elegans

In recent years, the Piwi pathway has been shown to regulate the silencing of mobile genetic elements. However, we know little about how Piwi pathways impose silencing and even less about trans-generational stability of Piwi-induced silencing. We demonstrate that the Caenorhabditis elegans Piwi protein PRG-1 can initiate an extremely stable form of gene silencing on a transgenic, single-copy target. This type of silencing is faithfully maintained over tens of generations in the absence of a functional Piwi pathway. Interestingly, RNAi can also trigger permanent gene silencing of a single-copy transgene and the phenomenon will be collectively referred to as RNA-induced epigenetic silencing (RNAe). RNAe can act in trans and is dependent on endogenous RNAi factors. The involvement of factors known to act in nuclear RNAi and the fact that RNAe is accompanied by repressive chromatin marks indicate that RNAe includes a transcriptional silencing component. Our results demonstrate that, at least in C. elegans, the Piwi pathway can impose a state of gene silencing that borders on 'permanently silent'. Such a property may be more widely conserved among Piwi pathways in different animals.

Trans-chromosomal methylation

The epigenome plays a vital role in helping to maintain and regulate cell functions in all organisms. Alleles with differing epigenetic marks in the same nucleus do not function in isolation but can interact in trans to modify the epigenetic state of one or both alleles. This is particularly evident when two divergent epigenomes come together in a hybrid resulting in thousands of alterations to the methylome. These changes mainly involve the methylation patterns at one allele being changed to resemble the methylation patterns of the other allele, in processes we have termed trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM). These processes are primarily modulated by siRNAs and the RNA directed DNA methylation pathway. Drawing from other examples of trans-allelic interactions, we describe the process of TCM and TCdM and the effect such changes can have on genome activity. Trans-allelic epigenetic interactions may be a common occurrence in many biological systems.