Epigenetic memory and control in plants pdf

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epigenetic memory and control in plants pdf

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Epigenetic memory for stress response and adaptation in plants.

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. Epigenetic modification of plant genomes resembles that of mammals in that there is a similar profile of histone marks and the DNA can be methylated at cytosine residues.

However, plant epigenomes are more susceptible to environmental influence than those in animals. In this article we review environmentally mediated epigenetic regulation in plants using two case histories. One of these involves a repressor of flowering, FLC.

The basal level of expression of FLC is set by opposing processes that either activate or repress its level of expression. FLC expression is then epigenetically silenced following exposure to prolonged cold through a process known as vernalization.

Subsequent spreading of this complex then leads to high levels of H3K27 methylation over the whole locus. The quantitative nature of vernalization is the result of cell-autonomous switching of FLC expression off in an increasing proportion of cells. Variation in this epigenetic silencing mechanism underpins the adaptation of plants to climates with different winters. The vernalization requirement is reset during gametogenesis or embryogenesis so that flowering is dependent on exposure to cold in each generation.

The second case history involves virus-induced silencing and epigenetic marks associated with methylation of DNA. The mechanism of virus-induced epigenetic modification is likely to involve a pathway that has also been implicated in transposon silencing in which Dicer generates small interfering RNAs siRNAs that are targeted to a chromatin-bound scaffold RNA in association with an Argonaute protein.

These DNA methylation marks may result in silencing of gene expression if they are in or close to promoter sequences and, in some instances, they are inherited across generations. If there is heritable phenotypic variation due to the gene silencing effect, there also can be an effect on fitness that is subject to natural selection.

However, unlike genetic inheritance, the epigenetic modifications are unstable and are influenced by the environment. These two case histories illustrate mechanisms that are likely to explain phenomena in plant biology in which stresses of various kinds can trigger responses that persist for longer than the inducing stimulus.

In some instances, the persistence extends across generations indicating the potential role of epigenetic mechanisms in evolution. Epigenetic mechanisms, by definition, allow changed states to persist through cell divisions, even in the absence of the inducing stimulus, and they provide a molecular memory that underpins the maintenance phase of these responses. Many of the environmentally induced epigenetic changes in plants are reset during gametogenesis, as are most epigenetic marks in animals.

However, some persist through gametogenesis and can be stable through many generations. There is, therefore, the definite potential for transgenerational epigenetic change in plants whereas, in animals, this possibility is more controversial. There are two factors that account for the greater potential for heritable epigenetic regulation in plants versus animals. First, there is the late differentiation of the germline.

It is not laid down in embryogenesis as in animals, but it arises from somatic tissue after flowering in the male and female reproductive organs illustrated in Fig. The plant germline cells are, therefore, descended from somatic cells and they carry epigenetic marks as persistent remnants of earlier environmental stimuli.

The second factor to differentiate transgenerational inheritance in plants and animals is related to epigenetic erasure during embryogenesis, which is more complete in animals than in plants Gutierrez-Marcos and Dickinson The first sections of this article describe plant case histories in which induced epigenetic changes are well-understood and can be used as a general framework for further analysis of the role of the environment as a trigger for epigenetic changes.

Later, in Sections 4—8 of this article, we discuss various examples in plant biology that are likely to represent epigenetic responses to environmental stimuli. Plants are sessile and they have to continually adjust their growth and physiology to changing environmental conditions. This adjustment is particularly important in developmental timing: Plants need to align their seed production to periods with favorable environmental conditions to maximize reproductive success.

Environmental cues are therefore monitored and can act to regulate the timing of different developmental switches. One of the earliest characterized processes involving epigenetic regulation in plants is vernalization. This vernalization memory even persists through tissue culture. Single cells of a vernalized plant can be cultured and regenerated into new plants that flower without prolonged cold Burn et al. Each sexual generation of plants, however, needs re-vernalizing because the vernalized state is effectively reset during meiosis or embryo formation Fig.

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.

The biological function of vernalization is to align flowering with spring and the return of more favorable environmental conditions. This ensures effective flower formation, pollination, and fruit set. Breeding for vernalization has increased the production range of most of our major crops although the process has malign association from the Soviet era.

The Soviet scientist and politician, Lysenko, claimed falsely that a vernalized state could be inherited into subsequent generations and increase wheat yields.

His anti-Mendelian doctrine gained him power and influence in the political establishment and influenced practice in wheat production. However, when crops failed, it led to mass starvation and the persecution of Vavilov and other geneticists. Vernalization involves the epigenetic silencing of a floral repressor in response to cold periods. Prolonged cold progressively silences expression of FLC and this is epigenetically maintained during subsequent development in the warm Fig.

Vernalization thus provides a clear example of the separation of the establishment and maintenance phases of epigenetic gene silencing. In the absence of cold, FLC acts as a brake to flowering. The restraint is removed following prolonged cold so that, once plants have detected inductive photoperiods and warm ambient temperatures, the switch to flowering is activated.

The repression of FLC is epigenetically stable and is maintained for many months after the cold exposure until embryogenesis in the next generation.

Many pathways regulate FLC and variation in their activity determines the reproductive habit of the plant. High FLC levels cause plants to overwinter before flowering, thereby limiting flowering to once a year. Low FLC levels enable plants to flower without the need for cold, opening up the possibility of reproducing more than once a year.

The level of expression of FLC is set very early in development: in the early multicellular embryo for maternally derived FLC, and in the sporogenous pollen mother cells or single-celled zygote for the paternal copy Sheldon et al. Many regulators determine this expression level summarized by pathway in Fig. Its function requires the conserved RNA polymerase-associated factor 1 complex He et al. Functioning antagonistically to these activators is the autonomous pathway, which reduces H3K4 and H3K36 methylation and increases H3K27 methylation.

The balance of these antagonistic FRIGIDA and autonomous pathways determines levels of FLC expression in the young seedlings and establishes whether or not they require vernalization for flowering i. 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.

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. FLC expression is progressively silenced by vernalization as plants are exposed to increasing periods of cold. This epigenetic process translates the prolonged exposure to cold into a stable silencing of FLC expression. This is maintained throughout the rest of development until it is reset in the embryo Fig.

Early molecular work investigated whether the mitotic memory of vernalization involved changes in DNA methylation, a well-characterized epigenetic mark in plants reviewed in Finnegan et al. This is unlike the situation in Drosophila in which PRC2 generally associates with targets after repression of transcription by other factors for more detail, see Grossniklaus and Paro These very high levels of H3K27me3 are required for the epigenetic maintenance of the silencing De Lucia et al.

An unusual characteristic of the epigenetic silencing during vernalization is its quantitative nature: The degree of silencing is dependent on how much cold the plant perceives. This feature ensures the plant can distinguish a cold snap in autumn from a whole winter.

Detailed analysis on whole tissue showed a quantitative cold-induced accumulation of H3K27me3 at the FLC intronic nucleation site Fig. The quantitative nature is also reflected in the level of H3K27me3 over the body of the gene after transfer to warm.

Mathematical modeling, constrained by the H3K27me3 data, predicted that the quantitative nature of vernalization was generated by a cell-autonomous switch, in which the FLC locus flipped into a fully epigenetically silenced state, marked by high levels of H3K27me3 over the whole locus Fig.

Lengthening cold would increase the proportion of cells that have undergone this switch Fig. The prediction that vernalization is quantitative because of the degree of cells that flip was confirmed in transgenic plants carrying an FLC fusion that could be visualized at the cellular level: A bistable expression pattern was indeed verified in partially vernalized plants see middle panel of Fig. The quantitative increase is thus a reflection of an increasing proportion of cells with a fully epigenetically silenced FLC locus, rather than all cells carrying an increasingly silenced FLC.

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. The cold-induced nucleation of the PHD-PRC2 complex is a key regulatory step in the environmental induction of this process.

However, the establishment of silencing still occurs in plants deficient for the PHD proteins Swiezewski et al. These antisense transcripts encompass the whole length of the sense transcript, are alternatively polyadenylated and alternatively spliced Fig. Increased use of the proximal poly A site in the antisense transcript is linked to reduction in transcription of FLC in the warm and cold Swiezewski et al.

Epigenetic Memory and Control in Plants

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Epigenetics commonly acts at the chromatin level modulating its structure and consequently its function in gene expression and as such plays a critical role in plant response to internal and external cues. This book highlights recent advances in our understanding of epigenetic mechanisms as a major determinant through which internal and external signals, such as those occurring during hybridization, flowering time, reproduction and response to stress, communicate with plant cells to bring about activation of multiple nuclear processes and consequently plant growth and development. The outcome of these processes may persist for generations long after the initial cues have expired and may contribute to plant evolution. Skip to main content Skip to table of contents. Advertisement Hide. This service is more advanced with JavaScript available. Epigenetic Memory and Control in Plants.


Epigenetics commonly acts at the chromatin level modulating its structure and PDF · Epigenetic Control of Plant Immunity. Yusuke Saijo, Eva-Maria Reimer-.


Epigenetic Regulation in Plant Responses to the Environment

In biology , epigenetics is the study of heritable phenotype changes that do not involve alterations in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors, or be part of normal development. The standard definition of epigenetics requires these alterations to be heritable [3] [4] in the progeny of either cells or organisms.

Epigenetic memory in plants

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