Epigenetic modifications in plants: an evolutionary perspective

Plant genomes are modified by an array of epigenetic marks that help regulate plant growth and reproduction. Although plants share many epigenetic features with animals and fungi, some epigenetic marks are unique to plants. In different organisms, the same epigenetic mark can play different roles and/or similar functions can be carried out by different epigenetic marks. Furthermore, while the enzymatic systems responsible for generating or eliminating epigenetic marks are often conserved, there are also cases where they are quite divergent between plants and other organisms. DNA methylation and methylation of histone tails on the lysine 4, 9, and 27 positions are among the best characterized epigenetic marks in both plants and animals. Recent studies have greatly enhanced our knowledge about the pattern of these marks in various genomes and provided insights into how they are established and maintained and how they function. This review focuses on the conservation and divergence of the pathways that mediate these four types of epigenetic marks.     

Homosexuality via canalized sexual development: A testing protocol for a new epigenetic model

We recently synthesized and reinterpreted published studies to advance an epigenetic model for the development of homosexuality (HS). The model is based on epigenetic marks laid down in response to the XX vs. XY karyotype in embryonic stem cells. These marks boost sensitivity to testosterone in XY fetuses and lower it in XX fetuses, thereby canalizing sexual development. Our model predicts that a subset of these canalizing epigenetic marks stochastically carry over across generations and lead to mosaicism for sexual development in opposite‐sex offspring – the homosexual phenotype being one such outcome. Here, we begin by outlining why HS has been under‐appreciated as a commonplace phenomenon in nature, and how this trend is currently being reversed in the field of neurobiology. We next briefly describe our epigenetic model of HS, develop a set of predictions, and describe how epigenetic profiles of human stem cells can provide for a strong test of the model.     

Structural biology-based insights into combinatorial readout and crosstalk among epigenetic marks

Epigenetic mechanisms control gene regulation by writing, reading and erasing specific epigenetic marks. Within the context of multi-disciplinary approaches applied to investigate epigenetic regulation in diverse systems, structural biology techniques have provided insights at the molecular level of key interactions between upstream regulators and downstream effectors. The early structural efforts focused on studies at the single domain-single mark level have been rapidly extended to research at the multiple domain–multiple mark level, thereby providing additional insights into connections within the complicated epigenetic regulatory network. This review focuses on recent results from structural studies on combinatorial readout and crosstalk among epigenetic marks. It starts with an overview of multiple readout of histone marks associated with both single and dual histone tails, as well as the potential crosstalk between them. Next, this review further expands on the simultaneous readout by epigenetic modules of histone and DNA marks, thereby establishing connections between histone lysine methylation and DNA methylation at the nucleosomal level. Finally, the review discusses the role of pre-existing epigenetic marks in directing the writing/erasing of certain epigenetic marks. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.     

Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

The expansion of repressive epigenetic marks has been implicated in heterochromatin formation during embryonic development, but the general applicability of this mechanism is unclear. Here we show that nuclear rearrangement of repressive histone marks H3K9me3 and H3K27me3 into nonoverlapping structural layers characterizes senescence-associated heterochromatic foci (SAHF) formation in human fibroblasts. However, the global landscape of these repressive marks remains unchanged upon SAHF formation, suggesting that in somatic cells, heterochromatin can be formed through the spatial repositioning of pre-existing repressively marked histones. This model is reinforced by the correlation of presenescent replication timing with both the subsequent layered structure of SAHFs and the global landscape of the repressive marks, allowing us to integrate microscopic and genomic information. Furthermore, modulation of SAHF structure does not affect the occupancy of these repressive marks, nor vice versa. These experiments reveal that high-order heterochromatin formation and epigenetic remodeling of the genome can be discrete events.     

Epigenetic control

Epigenetics refers to mitotically and/or meiotically heritable variations in gene expression that are not caused by changes in DNA sequence. Epigenetic mechanisms regulate all biological processes from conception to death, including genome reprogramming during early embryogenesis and gametogenesis, cell differentiation and maintenance of a committed lineage. Key epigenetic players are DNA methylation and histone post‐translational modifications, which interplay with each other, with regulatory proteins and with non‐coding RNAs, to remodel chromatin into domains such as euchromatin, constitutive or facultative heterochromatin and to achieve nuclear compartmentalization. Besides epigenetic mechanisms such as imprinting, chromosome X inactivation or mitotic bookmarking which establish heritable states, other rapid and transient mechanisms, such as histone H3 phosphorylation, allow cells to respond and adapt to environmental stimuli. However, these epigenetic marks can also have long‐term effects, for example in learning and memory formation or in cancer. Erroneous epigenetic marks are responsible for a whole gamut of diseases including diseases evident at birth or infancy or diseases becoming symptomatic later in life. Moreover, although epigenetic marks are deposited early in development, adaptations occurring through life can lead to diseases and cancer. With epigenetic marks being reversible, research has started to focus on epigenetic therapy which has had encouraging success. As we witness an explosion of knowledge in the field of epigenetics, we are forced to revisit our dogma. For example, recent studies challenge the idea that DNA methylation is irreversible. Further, research on Rett syndrome has revealed an unforeseen role for methyl‐CpG‐binding protein 2 (MeCP2) in neurons. J. Cell. Physiol. 219: 243–250, 2009. © 2009 Wiley‐Liss, Inc.     

Epigenetic programming: from gametes to blastocyst

Embryo development requires a series of cell fate decisions; cell lineages are established early during development and must be "remembered" through multiple cell divisions. It is increasingly evident that epigenetic marks, DNA methylation, histone modifications, and noncoding RNAs, have a critical role in this cell memory during development. During gametogenesis, epigenetic programming results in the production of spermatozoa and oocytes with distinctive chromatin. The goal of this article is to review what is known about the epigenetic marks in mature gametes and how these marks change during early embryo development. An understanding of the role of epigenetic programming during normal development will lay the basis for the elucidation of its role when development goes awry and the consequence is a birth defect.     

Epigenetics and its implications for plant biology 2. The 'epigenetic epiphany': epigenetics, evolution and beyond

SCOPE: In the second part of a two-part review, the ubiquity and universality of epigenetic systems is emphasized, and attention is drawn to the key roles they play, ranging from transducing environmental signals to altering gene expression, genomic architecture and defence. KEY ISSUES: The importance of transience versus heritability in epigenetic marks is examined, as are the potential for stable epigenetic marks to contribute to plant evolution, and the mechanisms generating novel epigenetic variation, such as stress and interspecific hybridization. FUTURE PROSPECTS: It is suggested that the ramifications of epigenetics in plant biology are immense, yet unappreciated. In contrast to the ease with which the DNA sequence can be studied, studying the complex patterns inherent in epigenetics poses many problems. Greater knowledge of patterns of epigenetic variation may be informative in taxonomy and systematics, as well as population biology and conservation.     

Linking inter-individual variability to endocrine disruptors: insights for epigenetic inheritance

Endocrine disrupting chemicals (EDCs) can induce a myriad of adverse health effects. An area of active investigation is the multi- and transgenerational inheritance of EDC-induced adverse health effects referring to the transmission of phenotypes across multiple generations via the germline. The inheritance of EDC-induced adverse health effects across multiple generations can occur independent of genetics, spurring much research into the transmission of underlying epigenetic mechanisms. Epigenetic mechanisms play important roles in the development of an organism and are responsive to environmental exposures. To date, rodent studies have demonstrated that acquired epigenetic marks, particularly DNA methylation, that are inherited following parental EDC exposure can escape embryonic epigenome reprogramming. The acquired epimutations can lead to subsequent adult-onset diseases. Increasing studies have reported inter-individual variations that occur with epigenetic inheritance. Factors that underlie differences among individuals could reveal previously unidentified mechanisms of epigenetic transmission. In this review, we give an overview of DNA methylation and posttranslational histone modification as the potential mechanisms for disease transmission, and define the requirements for multi- and transgenerational epigenetic inheritance. We subsequently evaluate rodent studies investigating how acquired changes in epigenetic marks especially DNA methylation across multiple generations can vary among individuals following parental EDC exposure. We also discuss potential sources of inter-individual variations and the challenges in identifying these variations. We conclude our review discussing the challenges in applying rodent generational studies to humans.

     

Translational Epigenetics: Clinical Approaches to Epigenome Therapeutics for Cancer

Cancer epigenetics research is now entering an exciting phase of translational epigenetics whereby novel epigenome therapeutics is being developed for application in clinical settings. Epigenetics refers to all heritable and potentially reversible changes in gene or genome functioning that occurs without altering the nucleotide sequence of the DNA. A range of different epigenetic “marks” can activate or repress gene expression. While epigenetic alterations are associated with most cancers, epigenetic dysregulation can also have a causal role in cancer etiology. Epigenetically disrupted stem or progenitor cells could have an early role in neoplastic transformations, while perturbance of epigenetic regulatory mechanisms controlling gene expression in cancer-relevant pathways will also be a contribution factor. The reversibility of epigenetic marks provides the possibility that the activity of key cancer genes and pathways can be regulated as a therapeutic approach. The growing availability of a range of chemical agents which can affect epigenome functioning has led to a range of epigenetic-therapeutic approaches for cancer and intense interest in the development of second-generation epigenetic drugs (epi-drugs) which would have greater specificity and efficacy in clinical settings. The latest developments in this exciting arena of translational cancer epigenetics were presented at a recent conference on “Epigenetics and New Therapies in Cancer” at the Spanish National Cancer Research Center (CNIO), Spain.     

Epigenetic memory transmission through mitosis and meiosis in plants

Gene activities can be regulated by epigenetic modifications of nucleotides and chromatin that are stably propagated through somatic cell divisions and, in some cases, across generations. The mechanisms that control epigenetic marks have recently been uncovered using model organisms, such as the flowering plant Arabidopsis thaliana. In Arabidopsis, perturbation of epigenetic gene activity often results in heritable developmental phenotypes. Stable, but potentially reversible, changes in epigenetic status can also be sources for phenotypic variations in natural plant populations.     

Advances in understanding molecular regulation of innate immune memory

The epigenetic and functional reprogramming of immune genes during induction of trained immunity is accompanied by the metabolic rewiring of cellular state. This memory is induced in the hematopoietic niche and propagated to daughter cells, generating epigenetically and metabolically reprogrammed innate immune cells that are greatly enhanced in their capacity to resolve inflammation. In particular, these cells show accumulation of H3K4me3 and H3K27Ac epigenetic marks on multiple immune gene promoters and associated enhancers. However, the mechanism governing how these epigenetic marks accumulate at discrete immune gene loci has been poorly understood, until now. Here, we discuss some recent advances in the regulation of trained immunity, with a particular focus on the mechanistic role of a novel class of long non-coding RNAs in the establishment of epigenetic marks on trained immune gene promoters.     

Reproductive barrier and genomic imprinting in the endosperm of flowering plants

In flowering plants, success or failure of seed development is determined by various genetic mechanisms. During sexual reproduction, double fertilization produces the embryo and endosperm, which both contain maternally and paternally derived genomes. In endosperm, a reproductive barrier is often observed in inter-specific crosses. Endosperm is a tissue that provides nourishment for the embryo within the seed, in a similar fashion to the placenta of mammals, and for the young seedling after germination. This review considers the relationship between the reproductive barrier in endosperm and genomic imprinting. Genomic imprinting is an epigenetic mechanism that results in mono-allelic gene expression that is parent-of-origin dependent. In Arabidopsis, recent studies of several imprinted gene loci have identified the epigenetic mechanisms that determine genomic imprinting. A crucial feature of genomic imprinting is that the maternally and paternally derived imprinted genes must carry some form of differential mark, usually DNA methylation and/or histone modification. Although the epigenetic marks should be complementary on maternally and paternally imprinted genes within a single species, it is possible that neither the patterns of epigenetic marks nor expression of imprinted genes are the same in different species. Moreover, in hybrid endosperm, the regulation of expression of imprinted genes can be affected by upstream regulatory mechanisms in the male and female gametophytes. Species-specific variations in epigenetic marks, the copy number of imprinted genes, and the epigenetic regulation of imprinted genes in hybrids might all play a role in the reproductive barriers observed in the endosperm of interspecific and interploidy crosses. These predicted molecular mechanisms might be related to earlier models such as the "endosperm balance number" (EBN) and "polar nuclei activation" (PNA) hypotheses.     

Enhanced targeted DNA methylation of the CMV and endogenous promoters with dCas9-DNMT3A3L entails distinct subsequent histone modification changes in CHO cells

With the emergence of new CRISPR/dCas9 tools that enable site specific modulation of DNA methylation and histone modifications, more detailed investigations of the contribution of epigenetic regulation to the precise phenotype of cells in culture, including recombinant production subclones, is now possible. These also allow a wide range of applications in metabolic engineering once the impact of such epigenetic modifications on the chromatin state is available.In this study, enhanced DNA methylation tools were targeted to a recombinant viral promoter (CMV), an endogenous promoter that is silenced in its native state in CHO cells, but had been reactivated previously (β-galactoside α-2,6-sialyltransferase 1) and an active endogenous promoter (α-1,6-fucosyltransferase), respectively. Comparative ChIP-analysis of histone modifications revealed a general loss of active promoter histone marks and the acquisition of distinct repressive heterochromatin marks after targeted methylation. On the other hand, targeted demethylation resulted in autologous acquisition of active promoter histone marks and loss of repressive heterochromatin marks. These data suggest that DNA methylation directs the removal or deposition of specific histone marks associated with either active, poised or silenced chromatin. Moreover, we show that de novo methylation of the CMV promoter results in reduced transgene expression in CHO cells. Although targeted DNA methylation is not efficient, the transgene is repressed, thus offering an explanation for seemingly conflicting reports about the source of CMV promoter instability in CHO cells.Importantly, modulation of epigenetic marks enables to nudge the cell into a specific gene expression pattern or phenotype, which is stabilized in the cell by autologous addition of further epigenetic marks. Such engineering strategies have the added advantage of being reversible and potentially tunable to not only turn on or off a targeted gene, but also to achieve the setting of a desirable expression level.     

Epigenetic changes during aging and their reprogramming potential

The aging process results in significant epigenetic changes at all levels of chromatin and DNA organization. These include reduced global heterochromatin, nucleosome remodeling and loss, changes in histone marks, global DNA hypomethylation with CpG island hypermethylation, and the relocalization of chromatin modifying factors. Exactly how and why these changes occur is not fully understood, but evidence that these epigenetic changes affect longevity and may cause aging, is growing. Excitingly, new studies show that age-related epigenetic changes can be reversed with interventions such as cyclic expression of the Yamanaka reprogramming factors. This review presents a summary of epigenetic changes that occur in aging, highlights studies indicating that epigenetic changes may contribute to the aging process and outlines the current state of research into interventions to reprogram age-related epigenetic changes.     

Long-term and transgenerational effects of in vitro culture on mouse embryos

The mouse is a convenient model to analyze the impact of in vitro culture (IVC) on the long-term health and physiology of the offspring, and the possible inheritance of these altered phenotypes. The preimplantation period of mammalian development has been identified as an early ‘developmental window’ during which environmental conditions may influence the pattern of future growth and physiology. Suboptimal culture media can cause severe alterations in mRNA expression in the embryo, which are associated with embryo quality reduction. In addition, the embryonic epigenetic reprogramming may also be severely affected by IVC, modifying epigenetic marks particularly in imprinted genes and epigenetically sensitive alleles. These altered epigenetic marks can persist after birth, resulting in adult health problems such as obesity, increased anxiety and memory deficits. Furthermore, some epigenetic modifications have been found to be transmitted to the offspring (epigenetic transgenerational inheritance), thereby providing a suitable model to asses risks of cross-generational effects of perturbing early embryo development. This review will highlight how preimplantation environment changes can not only affect developmental processes taking place at that time, but can also have an impact further, affecting offspring health and physiology; and how they may be transmitted to the next generation. We will also analyze the emerging role of epigenetics as a mechanistic link between the early environment and the later phenotype of the developing organism.