Epigenetic regulation in plant responses to the environment

Abstract

In this article, we review environmentally mediated epigenetic regulation in plants using two case histories. One of these, vernalization, mediates adaptation of plants to different environments and it exemplifies processes that are reset in each generation. The other, virus-induced silencing, involves transgenerationally inherited epigenetic modifications. Heritable epigenetic marks may result in heritable phenotypic variation, influencing fitness, and so be subject to natural selection. However, unlike genetic inheritance, the epigenetic modifications show instability and are influenced by the environment. These two case histories are then compared with other phenomena in plant biology that are likely to represent epigenetic regulation in response to the environment.

Figure 1.

FLC expression is epigenetically silenced by cold and reset during embryo development. (A) The floral repressor gene, FLC, is highly expressed in young seedlings. As plants perceive cold, the expression is quantitatively repressed, dependent on the length of cold experienced. As temperatures warm in spring, the repression is epigenetically maintained until seed development when it is reset. This ensures that each generation of seedlings requires vernalization. (B) Epigenetic and transcriptional pathways activate or inhibit FLC expression and, hence, contribute to flowering time control. Chromatin modifications and noncoding RNAs contribute in different ways to each pathway.

Figure 2.

The Polycomb complex composition and localization changes dynamically at FLC during different phases of vernalization. (A) Before the onset of cold, which triggers vernalization, the PRC2 core complex is already associated with chromatin over the length of the active FLC locus. The exon–intron structure is indicated beneath the chromatin fiber as black bars for each exon. (B) Prolonged cold leads to the accumulation and nucleation of an alternative Polycomb complex containing plant homeodomain (PHD) proteins (VIN3, VRN5) at a specific intragenic site near the beginning of the first intron. (C) In plants returned to warm conditions, the cold-induced VIN3 PHD protein is lost. A modified PHD-PRC2 complex associates across the whole locus, inducing high levels of H3K27me3, which blanket the locus and provide repressive epigenetic stability (maintenance).

Figure 3.

Stochastic switching mechanism underlies the quantitative nature of vernalization. (A) During cold, H3K27me3 quantitatively accumulates in the nucleation region of the FLC gene, indicated schematically below each graph, with increasing weeks of cold (top row of figure). (B) After cold, the nucleated H3K27me3 causes some cells to switch to a silenced state with high levels of H3K27me3 blanketing the gene. This epigenetic switch is cell-autonomous. (C) The quantitative nature of the vernalization response is due to an increasing number of cells switching to a silenced state after increasing cold exposure. Each cell is indicated by a square. (Figure courtesy of Dr. Jie Song.)

Figure 4.

Noncoding transcripts at the FLC locus. Many classes of noncoding transcripts have been characterized at the FLC locus. A set of antisense transcripts have collectively been called COOLAIR (red). These are alternatively spliced and alternatively polyadenylated, and encompass the whole length of the sense transcript. They are an integral part of FLC regulation both in the warm and in the cold. An FLC noncoding sense transcript, termed COLDAIR (blue), is transcribed from a cryptic promoter in intron 1. There are also homologous 24- and 30-mer siRNAs (gray) mapping just upstream of the COOLAIR transcription start site.

Figure 5.

Quantitative variation in the epigenetic silencing of FLC in Arabidopsis accessions from different climates. (A) An Arabidopsis accession from Germany (Col, red line) requires only 4 wk of cold to epigenetically silence FLC. Lov-1, from the northern limit of its range in Northern Sweden (latitude 62.5°N), sees reactivation of the FLC gene if the cold period is so short, resulting in an inability to become vernalized and, hence, does not flower. (B) Lov-1 needs a much longer period of cold (12 wk) for full epigenetic silencing. Molecular analysis has shown this difference is the result of a small number of cis polymorphisms near the PHD-PRC2 nucleation region in intron 1.

Figure 6.

Virus- and transgene-induced RNA silencing in plants. (A) The core RNA silencing pathway: dsRNA is processed into 21-nt and 24-nt RNA by Dicer and then bound to the Argonaute slicer protein, to guide the complex to specific target RNA sequences. (B) The p19 viral suppressor of RNA silencing (VSR): The siRNA (stick diagram) is bound to a dimeric form of the p19 viral suppressor and held in place by helical brackets formed by the respective amino termini. (B, Reproduced from Vargason et al. 2003, with permission from Elsevier.)

Figure 7.

Endogenous RNA silencing in plants. The difference between miRNAs and siRNAs: miRNAs are generated by DCL cleavage of a single RNA molecule in which there is a secondary structure. Mismatches in base-paired regions guide the DCL protein so that it releases a single miRNA from the long precursor. In contrast, the siRNAs are derived from a perfectly base-paired precursor molecule that is cleaved at several sites to release multiple siRNAs.

Figure 8.

The Pol IV pathway of siRNA biogenesis. The variant form of RNA polymerase II (Pol II), known as Pol IV, generates single-stranded RNA (ssRNA) from a DNA template. The ssRNA is converted to a ds form by RdRP and then processed into 24-nt siRNAs by a DCL protein. The siRNA then binds to an AGO protein and it targets nascent transcripts in noncoding regions of the genome that are transcribed by a second variant form of Pol II known as Pol V. The AGO protein then recruits DNA methyltransferases to introduce methyl groups at cytosine bases (pink hexagon symbols) of the DNA template as well as other histone-modifying enzymes.

Figure 9.

Virus-induced gene silencing—VIGS. A demonstration of VIGS in Nicotiana benthamiana, a plant related to tobacco, carrying an endogenous copy of a transgene construct (A) containing a 35S promoter (pro) driving GFP coding sequences (cod). (B) The tobacco rattle virus vector constructs are replicating RNA molecules that encode several proteins. The proteins include a viral RNA-dependent RNA polymerase (RDR), a movement protein (M), a suppressor of silencing (SS), and a coat protein (CP). The control virus vector (top) has no insert. The experimental constructs carried an insert corresponding either to “pro” or “cod.” The loss of green fluorescence in the plants infected with the experimental constructs indicated that there was gene silencing using both constructs (center); however, with the pro construct, silencing persisted into the progeny seedlings (right side).

Figure 10.

Separate establishment and maintenance of transcriptional silencing induced by a virus. The red vertical lines represent the interaction between the viral RNA containing the promoter sequence insert (pro) and the cognate DNA. The promoter DNA is assumed to be the target of the RNA silencing pathway to which methyl groups are introduced (Fig. 8). TGS initially occurs through de novo DNA methylation (pink hexagon symbols) of the promoter sequence, catalyzed by DRM2. Maintenance of silencing relies on the maintenance DNA methyltransferase, MET1 propagating methylation patterns through DNA replication and cell division.

Figure 11.

An experiment to show mobile silencing. (A) Plants carrying the target GFP transgene coupled to a promoter with meristem-specific enhancer region (arrow) are denominated TT, and were hybridized to SS plants carrying a silencer construct with a 35S promoter that directed transcription of an inverted repeat of the enhancer (arrows). The TT (B) and TTSS plants (B) were grafted as a shoot scion to the TT roots and the expression of GFP was monitored by GFP fluorescence and RNA gel blotting to track spread of silencing from the shoot into the root. In this analysis the panels shown in B and C are images of the roots under UV (left) or white (right) light. TTSS shoot grafts cause GFP silencing in the roots, indicating the mobile nature of the silencing signal. (Adapted from Melnyk et al. 2011.)