Genetic Rearrangements Can Modify Chromatin Features at Epialleles

Abstract

Analogous to genetically distinct alleles, epialleles represent heritable states of different gene expression from sequence-identical genes. Alleles and epialleles both contribute to phenotypic heterogeneity. While alleles originate from mutation and recombination, the source of epialleles is less well understood. We analyze active and inactive epialleles that were found at a transgenic insert with a selectable marker gene in Arabidopsis. Both converse expression states are stably transmitted to progeny. The silent epiallele was previously shown to change its state upon loss-of-function of trans-acting regulators and drug treatments. We analyzed the composition of the epialleles, their chromatin features, their nuclear localization, transcripts, and homologous small RNA. After mutagenesis by T-DNA transformation of plants carrying the silent epiallele, we found new active alleles. These switches were associated with different, larger or smaller, and non-overlapping deletions or rearrangements in the 3′ regions of the epiallele. These cis-mutations caused different degrees of gene expression stability depending on the nature of the sequence alteration, the consequences for transcription and transcripts, and the resulting chromatin organization upstream. This illustrates a tight dependence of epigenetic regulation on local structures and indicates that sequence alterations can cause epigenetic changes at some distance in regions not directly affected by the mutation. Similar effects may also be involved in gene expression and chromatin changes in the vicinity of transposon insertions or excisions, recombination events, or DNA repair processes and could contribute to the origin of new epialleles.

Epigenetic and epigenomic variation in Arabidopsis thaliana

“…However, several examples of phenotypic variation that can arise through epigenetic variation are known, including the peloric ( Linaria vulgaris ) [17], colorless non-ripening (cnr – Solanum lycopersicum ) [18] and B′ ( Zea mays ) [19] epialleles. Studies in Arabidopsis thaliana have provided the richest source of known epialleles [20–32]. Many of the Arabidopsis epialleles require the activities of the RNA-directed DNA methylation (RdDM) machinery [33] for their formation and stability.…”

DNA methylation maintenance consolidates RNA‐directed DNA methylation and transcriptional gene silencing over generations in Arabidopsis thaliana

“…This is unlikely to be cytosine methylation itself, as DNA methylation has already reached its final level in F 1 K /– ;H /– plants, and little methylation inheritance is seen in F 2 K/K * plants derived from them. Dimethylation at lysine 9 of histone H3 (H3K9me2) may be associated with transcriptionally silenced transgenes in plants (Foerster et al ., ), and thus represents an obvious candidate for such a mark. Chromatin immunoprecipitation combined with quantitative PCR was performed to quantify H3K9me2 relative to total H3 at various regions of the TARGET ProNOS sequence in 1‐week‐old F 4 K/K and F 4 K/K ; H/H seedlings (Figure ).…”

Epigenetic switches of tobacco transgenes associate with transient redistribution of histone marks in callus culture

“…Two independently established calli were analyzed as biological replicates at the promoter (~349 bp, ~212 bp in locus 271) and at the 3? end of the npt II transcribed region (~174 bp) that appear to be critical for epiallele formation 49 (Fig. 1, 5A).…”