Epigenetics of plant growth and development

Last updated October 28, 2022

Plants depend on epigenetic processes for proper function. Epigenetics is defined as "the study of changes in gene function that are mitotically and/or meiotically heritable and that do not entail a change in DNA sequence" (Wu et al. 2001). The area of study examines protein interactions with DNA and its associated components, including histones and various other modifications such as methylation, which alter the rate or target of transcription. Epi-alleles and epi-mutants, much like their genetic counterparts, describe changes in phenotypes due to epigenetic mechanisms. Epigenetics in plants has attracted scientific enthusiasm because of its importance in agriculture.

Background and history

In the past, macroscopic observations on plants led to basic understandings of how plants respond to their environments and grow. While these investigations could somewhat correlate cause and effect as a plant develops, they could not truly explain the mechanisms at work without inspection at the molecular level.

Certain studies provided simplistic models with the groundwork for further exploration and eventual explanation through epigenetics. In 1918, Gassner published findings that noted the necessity of a cold phase in order for proper plant growth. Meanwhile, Garner and Allard examined the importance of the duration of light exposure to plant growth in 1920. Gassner's work would shape the conceptualization of vernalization which involves epigenetic changes in plants after a period of cold that leads to development of flowering (Heo and Sung et al. 2011). In a similar manner, Garner and Allard's efforts would gather an awareness of photoperiodism which involves epigenetic modifications following the duration of nighttime which enable flowering (Sun et al. 2014). Rudimentary comprehensions set precedent for later molecular evaluation and, eventually, a more complete view of how plants operate.

Modern epigenetic work depends heavily on bioinformatics to gather large quantities of data relating the function of elements such as intensive looks at DNA sequences or patterns in DNA modifications. With improved methods, flowering mechanisms including vernalization and photoperiodism, Flowering Wageningen, and the underlying processes controlling germination, meristematic tissue, and heterosis have been explained through epigenetics.

Research on plants looks at several species. These species are apparently selected on the basis of either conventional model organisms status, such as Arabidopsis with its manageability in lab and a known genome, or relevance in agronomy, such as rice, barley or tomatoes.

Epigenetics

Overview

Epigenetic modifications regulate gene expression. The transcription of DNA into RNA and subsequent translation into proteins determines the form and function of all living things. The level of DNA transcription generally depends on how accessible DNA is to transcription factors. Many epigenetic changes occur either on histones, which are normally associated with DNA in chromatin, or directly on the DNA. For instance, methylation of DNA leads to transcriptional silencing by denying access to transcription factors. Histone methylation can lead to either silencing or activation as determined by the amino acid marked. Meanwhile, histone acetylation typically lessens the hold of histones on DNA by reducing positive charge, resulting in facilitation of transcription (Weinhold et al. 2001).

Polycomb group proteins and trithorax group proteins

Polycomb group (PcG) proteins and trithorax groups (TrxG) proteins act as key regulators of gene expression through histone lysine methylation. PcG proteins repress target genes via Histone 3 lysine 27 trimethylation (H3K27me3), whereas TrxG proteins activate gene expression via histone 3 lysine 4 trimethylation (H3K4me3) (Kleinmanns et al. 2014).

Long non-coding RNA

Long non-coding RNA can associate with DNA in tandem with proteins to alter the rate of gene expression. These RNA are upwards of 200 base pairs. They can be transcribed from a standalone sequence or be part of a promoter, intron or other component of DNA. Long non-coding RNA often complement functional regions of DNA with overlaps or antisense (Kung et al. 2013). To direct transcriptional silencing, a non-coding RNA will associate with a polycomb group protein which to tether it to a specific gene for silencing (Kleinmanns et al. 2014).

Seed dormancy and germination

Germination is the early growth of a plant from a seed. Meanwhile, dormancy precedes germination and serves to preserve a seed until conditions are receptive towards growth. The transition from dormancy to germination seems to depend on the removal of factors inhibiting growth. There are many models for germination which may differ between species. The activity of genes such as Delay of Germination and presence of hormones such as gibberelins have been implicated in dormancy while the exact mechanisms surrounding their action is unknown (Nonogaki et al. 2014).

Deacetylation

There are at least eighteen histone deacetylases in Arabidopsis (Hollender et al. 2008). Genome-wide association mapping has shown that deacetylation of histones by Histone Deacetylase 2B negatively affects dormancy. The remodeling of chromatin by histone deacetylase leads to silencing of genes that control plant hormones such as ethylene, abscisic acid, and gibberelin which maintain dormancy. Additionally, Histone Deacetylase A6 and A19 activity contributes to silencing of Cytochrome P450 707A and activation of NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 4, 9. Both of these actions lead to increased abscisic acid (Nonogaki et al. 2014).

Methylaltion

Methylation by the methyltransferase KRYPTONITE causes histone H3 lysine 9 dimethylation which recruits the DNA methyltransferase CHROMOMETHTLASE3 in tandem with HETEROCHROMATIN PROTEIN1. This association methylates cytosine for a stable silencing of Delay of Germination 1 and ABA Insensitive Genes which both contribute to dormancy (Nonogaki et al. 2014).

Flowering and related mechanisms

Flowering is a pivotal step in plant development. Numerous epigenetic factors contribute to the regulation of flowering genes, known as flowering loci (FL). In Arabidopsis, flowering locus t is responsible for the production of florigen, which induces changes in the shoot apical meristem, a special set of growth tissues, to establish flowering (Turck et al. 2008). Homologs of the flowering genes exist in flowering plants, but the exact nature of how the genes respond to each mechanism might differ between species (Sun et al. 2014).

Vernalization

Vernalization depends on the presence of a long non-coding RNA that is termed COLDAIR. The exposure of plants to a significant period of cold results in COLDAIR accumulation. COLDAIR targets polycomb repressive complex 2 which acts to silence flowering locus C through methylation (Heo and Sung et al. 2011). As flowering locus C is repressed it no longer acts to inhibit the transcription of flowering locus t and SOC1. Flowering locus t and SOC1 activity leads to the development of flowers (Deng et al. 2011).

Photoperiodism

Another set of flowering controls stems from photoperiodism which initiates flowering based on the length of nighttime. Long day plants flower with a short night, while short day plants require uninterrupted darkness. Some plants are restricted to either condition, while others can operate under a combination of the two, and some plants do not operate under photoperiodism. In Arabidopsis, the gene CONSTANS responds to long day conditions and enables flowering when it stops repressing flowering locus t (Shim et al. 2015). In rice, photoperiodic response is slightly more complex and is controlled by the florigen genes Rice Flowering locus T 1 (RFT1) and Heading date 3 a (Hd3a). Hd3a, is a homolog of flowering locus t and, when no longer repressed, activates flowering by directing modification of DNA at the shoot apical meristem with florigen. Heading date 1 (Hd1) is a gene that promotes flowering under short day conditions but represses flowering under long day as it either activates or suppresses Hd3a. Meanwhile, RFT1 can cause flowering under non-inductive long day. Polycomb Repressive Complex 2 can lead to silencing of the genes through histone H3 lysine 27 trimethylation. A variety of chromatin modifications operating in both long and short days or only under one condition can also affect the two florigen genes in rice (Sun et al. 2014).

Flowering wageningen (FWA)

The gene FWA has been identified as responsible for late flowering in epi-mutants. Epi-mutants are individuals with particular epigenetic changes that lead to a distinct phenotype. As such, both wild type and epi-mutant variants contain identical sequences for FWA. Loss of methylation in direct repeats in the 5' region of the gene results in expression of FWA and subsequent prevention of proper flowering. The gene is normally silenced by methylation of DNA in tissues not related to flowering (Soppe et al. 2000).

Meristematic tissue

Meristematic tissues contain cells that continue to grow and differentiate throughout the plant's lifetime. Shoot apical meristem gives rise to flowers and leaves while root apical meristem grows into roots. These components are crucial to general plant growth and are the harbingers of development. Meristematic tissue apparently contains characteristic epigenetic modifications. For example, the boundary between the proximal meristem and elongation zone showed elevated H4K5ac along with a high level of 5mC in barley. Root meristematic tissues have been found to contain patterns for histone H4 lysine 5 acetylation, histone H3 lysine 4 and 9 di methylation and DNA methylation as 5-methyl cytosine. So far, only a causal correlation between epigenetic marks and tissue types has been established and further study is required to understand the exact involvement of the marks (Braszewska et al. 2013).

Heterosis

Heterosis is defined as any advantages seen in hybrids. The effects of heterosis seem to follow a rather simple epigenetic premise in plants. In hybrids, lack of proper regulatory action, such as silencing by methylation, leads to uninhibited genes. If the gene is involved in growth, such as photosynthesis, the plant will experience increased vitality (Ni et al. 2008).

The results heterosis can be seen in traits such as increased fruit yield, earlier ripening, and heat tolerance. Heterosis has been shown to provide increased general growth and fruit yield in tomato plants (Xiaodong).

Related Research Articles

In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene regulation and DNA replication. Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 90 micrometers (0.09 mm) of 30 nm diameter chromatin fibers.

In biology, epigenetics is the study of stable phenotypic changes that do not involve alterations in the DNA sequence. The Greek prefix epi- in epigenetics implies features that are "on top of" or "in addition to" the traditional genetic basis for inheritance. Epigenetics most often involves changes that affect gene activity and expression, but the term can also be used to describe any heritable phenotypic change. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors, or be part of normal development.

Vernalization is the induction of a plant's flowering process by exposure to the prolonged cold of winter, or by an artificial equivalent. After vernalization, plants have acquired the ability to flower, but they may require additional seasonal cues or weeks of growth before they will actually flower. The term is sometimes used to refer to the need of herbal (non-woody) plants for a period of cold dormancy in order to produce new shoots and leaves, but this usage is discouraged.

Antisense RNA (asRNA), also referred to as antisense transcript, natural antisense transcript (NAT) or antisense oligonucleotide, is a single stranded RNA that is complementary to a protein coding messenger RNA (mRNA) with which it hybridizes, and thereby blocks its translation into protein. asRNAs have been found in both prokaryotes and eukaryotes, and can be classified into short and long non-coding RNAs (ncRNAs). The primary function of asRNA is regulating gene expression. asRNAs may also be produced synthetically and have found wide spread use as research tools for gene knockdown. They may also have therapeutic applications.

In epigenetics, a paramutation is an interaction between two alleles at a single locus, whereby one allele induces a heritable change in the other allele. The change may be in the pattern of DNA methylation or histone modifications. The allele inducing the change is said to be paramutagenic, while the allele that has been epigenetically altered is termed paramutable. A paramutable allele may have altered levels of gene expression, which may continue in offspring which inherit that allele, even though the paramutagenic allele may no longer be present. Through proper breeding, paramutation can result in siblings that have the same genetic sequence, but with drastically different phenotypes.

Polycomb-group proteins are a family of protein complexes first discovered in fruit flies that can remodel chromatin such that epigenetic silencing of genes takes place. Polycomb-group proteins are well known for silencing Hox genes through modulation of chromatin structure during embryonic development in fruit flies. They derive their name from the fact that the first sign of a decrease in PcG function is often a homeotic transformation of posterior legs towards anterior legs, which have a characteristic comb-like set of bristles.

Chromatin remodeling is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression. Such remodeling is principally carried out by 1) covalent histone modifications by specific enzymes, e.g., histone acetyltransferases (HATs), deacetylases, methyltransferases, and kinases, and 2) ATP-dependent chromatin remodeling complexes which either move, eject or restructure nucleosomes. Besides actively regulating gene expression, dynamic remodeling of chromatin imparts an epigenetic regulatory role in several key biological processes, egg cells DNA replication and repair; apoptosis; chromosome segregation as well as development and pluripotency. Aberrations in chromatin remodeling proteins are found to be associated with human diseases, including cancer. Targeting chromatin remodeling pathways is currently evolving as a major therapeutic strategy in the treatment of several cancers.

Enhancer of zeste homolog 2 (EZH2) is a histone-lysine N-methyltransferase enzyme encoded by EZH2 gene, that participates in histone methylation and, ultimately, transcriptional repression. EZH2 catalyzes the addition of methyl groups to histone H3 at lysine 27, by using the cofactor S-adenosyl-L-methionine. Methylation activity of EZH2 facilitates heterochromatin formation thereby silences gene function. Remodeling of chromosomal heterochromatin by EZH2 is also required during cell mitosis.

In molecular biology, a Tudor domain is a conserved protein structural domain originally identified in the Tudor protein encoded in Drosophila. The Tudor gene was found in a Drosophila screen for maternal factors that regulate embryonic development or fertility. Mutations here are lethal for offspring, inspiring the name Tudor, as a reference to the Tudor King Henry VIII and the several miscarriages experienced by his wives.

<span class="mw-page-title-main">PRC2</span>

PRC2 is one of the two classes of polycomb-group proteins or (PcG). The other component of this group of proteins is PRC1.

<span class="mw-page-title-main">Cancer epigenetics</span> Field of study in cancer research

Cancer epigenetics is the study of epigenetic modifications to the DNA of cancer cells that do not involve a change in the nucleotide sequence, but instead involve a change in the way the genetic code is expressed. Epigenetic mechanisms are necessary to maintain normal sequences of tissue specific gene expression and are crucial for normal development. They may be just as important, if not even more important, than genetic mutations in a cell's transformation to cancer. The disturbance of epigenetic processes in cancers, can lead to a loss of expression of genes that occurs about 10 times more frequently by transcription silencing than by mutations. As Vogelstein et al. points out, in a colorectal cancer there are usually about 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations. However, in colon tumors compared to adjacent normal-appearing colonic mucosa, there are about 600 to 800 heavily methylated CpG islands in the promoters of genes in the tumors while these CpG islands are not methylated in the adjacent mucosa. Manipulation of epigenetic alterations holds great promise for cancer prevention, detection, and therapy. In different types of cancer, a variety of epigenetic mechanisms can be perturbed, such as the silencing of tumor suppressor genes and activation of oncogenes by altered CpG island methylation patterns, histone modifications, and dysregulation of DNA binding proteins. There are several medications which have epigenetic impact, that are now used in a number of these diseases.

Epigenome editing or Epigenome engineering is a type of genetic engineering in which the epigenome is modified at specific sites using engineered molecules targeted to those sites. Whereas gene editing involves changing the actual DNA sequence itself, epigenetic editing involves modifying and presenting DNA sequences to proteins and other DNA binding factors that influence DNA function. By "editing” epigenomic features in this manner, researchers can determine the exact biological role of an epigenetic modification at the site in question.

Transposable elements are short strands of repetitive DNA that can self-replicate and translocate within the eukaryotic genome, and are generally perceived as parasitic in nature. Their transcription can lead to the production of dsRNAs, which resemble retroviruses transcripts. While most host cellular RNA has a singular, unpaired sense strand, dsRNA possesses sense and anti-sense transcripts paired together, and this difference in structure allows an host organism to detect dsRNA production, and thereby the presence of transposons. Plants lack distinct divisions between somatic cells and reproductive cells, and also have, generally, larger genomes than animals, making them an intriguing case-study kingdom to be used in attempting to better understand the epigenetics function of transposable elements.

Melanoma is a rare but aggressive malignant cancer that originates from melanocytes. These melanocytes are cells found in the basal layer of the epidermis that produce melanin under the control of melanocyte-stimulating hormone. Despite the fact that melanoma represents only a small number of all skin cancers, it is the cause of more than 50% of cancer-related deaths. The high metastatic qualities and death rate, and also its prevalence among people of younger ages have caused melanoma to become a highly researched malignant cancer. Epigenetic modifications are suspected to influence the emergence of many types of cancer-related diseases, and are also suspected to have a role in the development of melanoma.

Epigenetics is the study of changes in gene expression that occur via mechanisms such as DNA methylation, histone acetylation, and microRNA modification. When these epigenetics changes are heritable, they can influence evolution. Current research indicates that epigenetics has influenced evolution in a number of organisms, including plants and animals.

Elizabeth Salisbury Dennis is an Australian scientist working mainly in the area of plant molecular biology. She is currently a chief scientist at the plant division of CSIRO Canberra. She was elected a Fellow of the Australian Academy of Technological Sciences and Engineering (FTSE) in 1987, and the Australian Academy of Science in 1995. She jointly received the inaugural Prime Minister's Science Prize together with Professor Jim Peacock in 2000 for her outstanding achievements in science and technology.

Epigenetics of human development is the study of how epigenetics effects human development.

H3K27me3 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the tri-methylation of lysine 27 on histone H3 protein.

RNA-directed DNA methylation (RdDM) is a biological process in which non-coding RNA molecules direct the addition of DNA methylation to specific DNA sequences. The RdDM pathway is unique to plants, although other mechanisms of RNA-directed chromatin modification have also been described in fungi and animals. To date, the RdDM pathway is best characterized within angiosperms, and particularly within the model plant Arabidopsis thaliana. However, conserved RdDM pathway components and associated small RNAs (sRNAs) have also been found in other groups of plants, such as gymnosperms and ferns. The RdDM pathway closely resembles other sRNA pathways, particularly the highly conserved RNAi pathway found in fungi, plants, and animals. Both the RdDM and RNAi pathways produce sRNAs and involve conserved Argonaute, Dicer and RNA-dependent RNA polymerase proteins.

Transgenerational epigenetic inheritance in plants involves mechanisms for the passing of epigenetic marks from parent to offspring that differ from those reported in animals. There are several kinds of epigenetic markers, but they all provide a mechanism to facilitate greater phenotypic plasticity by influencing the expression of genes without altering the DNA code. These modifications represent responses to environmental input and are reversible changes to gene expression patterns that can be passed down through generations. In plants, transgenerational epigenetic inheritance could potentially represent an evolutionary adaptation for sessile organisms to quickly adapt to their changing environment.

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