Epigenetic history of an Arabidopsis trans-silencer locus and a test for relay of trans-silencing activity

Paramutation: a heritable change in gene expression by allelic interactions in trans

Epigenetic gene regulation involves the stable propagation of gene activity states through mitotic, and sometimes even meiotic, cell divisions without changes in DNA sequence. Paramutation is an epigenetic phenomenon involving changes in gene expression that are stably transmitted through mitosis as well as meiosis. These heritable changes are mediated by in trans interactions between homologous DNA sequences on different chromosomes. During these in trans interactions, epigenetic information is transferred from one allele of a gene to another allele of the same gene, resulting in a change in gene expression. Although paramutation was initially discovered in plants, it has recently been observed in mammals as well, suggesting that the mechanisms underlying paramutation might be evolutionarily conserved. Recent findings point to a crucial role for small RNAs in the paramutation process. In mice, small RNAs appear sufficient to induce paramutation, whereas in maize, it seems not to be the only player in the process. In this review, potential mechanisms are discussed in relation to the various paramutation phenomena.

Transgene-induced silencing of Arabidopsis phytochrome A gene via exonic methylation

Transgene-induced promoter or enhancer methylation clearly retards gene activity. While exonic methylation of genes is frequently observed in the RNAi process, only sporadic evidence has demonstrated its definitive role in gene suppression. Here, we report the isolation of a transcriptionally suppressed epi-allele of the Arabidopsis thaliana phytochrome A gene (PHYA) termed phyA' that shows methylation only in symmetric CG sites resident in exonic regions. These exonic modifications confer a strong phyA mutant phenotype, characterized by elongated hypocotyls in seedlings grown under continuous far-red light. De-methylation of phyA' in the DNA methyl transferase I (met1) mutant background increased PHYA expression and restored the wild-type phenotype, confirming the pivotal role of exonic CG methylation in maintaining the altered epigenetic state. PHYA epimutation was apparently induced by a transgene locus; however, it is stably maintained following segregation. Chromatin immunoprecipitation assays revealed association with dimethyl histone H3 lysine 9 (H3K9me2), a heterochromatic marker, within the phyA' coding region. Therefore, transgene-induced exonic methylation can lead to chromatin alteration that affects gene expression, most likely through reduction in the transcription rate.

The trans-silencing capacity of invertedly repeated transgenes depends on their epigenetic state in tobacco

We studied the in trans-silencing capacities of a transgene locus that carried the neomycin phosphotransferase II reporter gene linked to the 35S promoter in an inverted repeat (IR). This transgene locus was originally posttranscriptionally silenced but switched to a transcriptionally silenced epiallele after in vitro tissue culture. Here, we show that both epialleles were strongly methylated in the coding region and IR center. However, by genomic sequencing, we found that the 1.0 kb region around the transcription start site was heavily methylated in symmetrical and non-symmetrical contexts in transcriptionally but not in posttranscriptionally silenced epilallele. Also, the posttranscriptionally silenced epiallele could trans-silence and trans-methylate homologous transgene loci irrespective of their genomic organization. We demonstrate that this in trans-silencing was accompanied by the production of small RNA molecules. On the other hand, the transcriptionally silenced variant could neither trans-silence nor trans-methylate homologous sequences, even after being in the same genetic background for generations and meiotic cycles. Interestingly, 5-aza-2-deoxy-cytidine-induced hypomethylation could partially restore signaling from the transcriptionally silenced epiallele. These results are consistent with the hypothesis that non-transcribed highly methylated IRs are poor silencers of homologous loci at non-allelic positions even across two generations and that transcription of the inverted sequences is essential for their trans-silencing potential.

Paramutation: an encounter leaving a lasting impression

Paramutation is the result of heritable changes in gene expression that occur upon interaction between alleles. Whereas Mendelian rules, together with the concept of genetic transmission via the DNA sequence, can account for most inheritance in sexually propagating organisms, paramutation-like phenomena challenge the exclusiveness of Mendelian inheritance. Most paramutation-like phenomena have been observed in plants but there is increasing evidence for its occurrence in other organisms, including mammals. Our knowledge of the underlying mechanisms, which might involve RNA silencing, physical pairing of homologous chromosomal regions or both, is still limited. Here, we discuss the characteristics of different paramutation-like interactions in the light of arguments supporting each of these alternative mechanisms.

Epigenetic interactions between Arabidopsis transgenes: characterization in light of transgene integration sites

The stochastic variability of expression that is a characteristic of eukaryotic nuclear transgenes is often attributed to epigenetic mechanisms that are triggered by repetitive transgene locus structures and influenced by chromosomal position effects. In order to address the contribution of chromosomal position effects in the context of a fully sequenced genome, a novel set of transgene loci was established in the compact genome of Arabidopsis thaliana. Transgenes expressing GFP-tagged or GUS-tagged fusion proteins of Arabidopsis COP1 collectively displayed three types of gene silencing, which are distinguished by their developmental timing, gene dosage dependence, (post)transcriptional control, and extent of endogene co-suppression. Subsequently, the heritability of epistatic interactions between allelic and non-allelic transgene loci was investigated in light of both intrinsic transgene features, in particular T-DNA copy number per locus, and chromosomal insertion sites. The notion that chromosomal flanking sequences underlie the ability of transgenes to function as masters or targets of epigenetically heritable trans-silencing interactions was generally not favored by our data. Moreover, among single T-DNA loci at different chromosomal locations the great majority showed homozygosity-dependent posttranscriptional silencing. However, spontaneous silencing (in cis) may be promoted by a pericentromeric location. Instead, intrinsic transgene features correlated with all major aspects of silencing behavior tested.