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Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 May 2020) | Viewed by 57135

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Special Issue Editors

Dr. Maria Beatrice Bitonti

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Laboratory of Plant Biology, Department of Biology, Ecology and Earth Science, University of Calabria, 87036 Cosenza, Italy
Interests: cell commitment and differentiation; plant development; plant growth plasticity; plant stress response; gene expression; DNA methylation
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Leonardo Bruno

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Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
Interests: plant development; epigenetic and chromatin-related control plant growth plasticity and response to stress

Special Issue Information

Dear Colleagues,

Plant genomics is a branch of biology which aims to explore all the aspects of an entire genome, from genetic composition to structure, from organization to functions, and genetic connections. Currently, the advance of ‘omics’ technologies and bioinformatics tools have largely contributed to dissecting the genetic architecture of plant genomes and also to identifying key genes and their combinatorial interaction in plant growth and development. The recent new approaches on genome editing have further enriched this expanding field. Moreover, in recent years, an enhanced focus has been paid to understanding epigenetics and genome-wide distribution of epigenetic changes, which appears essential for dissecting all aspects of genetic studies.

Epigenetics refers to all molecular pathways which determine changes in genome structure and activity without alteration in the DNA sequence, resulting in stable heritable and nonheritable phenotypes. Overall, these pathways act through chromatin remodeling processes tracing the chromatin/epigenetic landscape of the genome (epigenome). Moreover, they interplay with each other rather than working separately and contribute to the control of several nuclear processes, such as DNA transcription, replication, recombination, and repair.

Typically, epigenetic machinery includes variants and post-translational modifications of histones, covalent modifications of DNA bases, like cytosine methylation, and biogenesis of noncoding RNAs, including long and short noncoding RNAs. However, the epigenomics field is ever-broadening, and new epigenetic/epitranscriptomic changes have been identified in all the kingdoms of living organisms, involving a network of chromatin-modifying enzymes, chromatin remodeling complexes, signaling kinases, and also cellular metabolism.

The currently available literature has evidenced that naturally occurring epigenetic processes are essential for defining cell identities and regulating several functions of living organisms which can be adversely affected when they occur incorrectly. This is particularly documented in animal systems by advanced research carried out in the field of human health. Consistently, in plant the epigenetic processes, in addition to playing a role in heritable genetic diversity and evolution, are essential for growth and development. Moreover, epigenetic changes can also arise under the influence of the environment and be connected to or driven by biotic and abiotic agents, thus contributing to plant growth plasticity and stress response. However, despite all this information, many aspects of the molecular and cellular mechanisms which operate in and are modulated by epigenetic processes in plants need to be clarified.

This Special issue will collect meaningful original research, reviews, and perspectives related to all these aspects of plant epigenetics. Contributions dealing with the potential of epigenetic variations for planning new crop-improvement strategies and plant biotechnologies will also be welcome.

Dr. M. Beatrice Bitonti
Guest Editor

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Keywords

DNA methylation
histone modifications
noncoding RNAs
plant evolution
plant development and differentiation
plant growth plasticity
plant stress response
crop improvement
biotechnological strategies

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Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects 2.0 in International Journal of Molecular Sciences (2 articles)

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23 pages, 1876 KiB

Open AccessArticle

Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both

by Jack Colicchio, John Kelly and Lena Hileman

Int. J. Mol. Sci. 2020, 21(20), 7552; https://doi.org/10.3390/ijms21207552 - 13 Oct 2020

Cited by 4 | Viewed by 2039

Abstract

Organisms alter development in response to environmental cues. Recent studies demonstrate that they can transmit this plasticity to progeny. While the phenotypic and transcriptomic evidence for this “transgenerational plasticity” has accumulated, genetic and developmental mechanisms remain unclear. Plant defenses, gene expression and DNA methylation are modified as an outcome of parental wounding in Mimulus guttatus. Here, we sequenced M. guttatus small RNAs (sRNA) to test their possible role in mediating transgenerational plasticity. We sequenced sRNA populations of leaf-wounded and control plants at 1 h and 72 h after damage and from progeny of wounded and control parents. This allowed us to test three components of an a priori model of sRNA mediated transgenerational plasticity—(1) A subset of sRNAs will be differentially expressed in response to wounding, (2) these will be associated with previously identified differentially expressed genes and differentially methylated regions and (3) changes in sRNA abundance in wounded plants will be predictive of sRNA abundance, DNA methylation, and/or gene expression shifts in the following generation. Supporting (1) and (2), we found significantly different sRNA abundances in wounded leaves; the majority were associated with tRNA fragments (tRFs) rather than small-interfering RNAs (siRNA). However, siRNAs responding to leaf wounding point to Jasmonic Acid mediated responses in this system. We found that different sRNA classes were associated with regions of the genome previously found to be differentially expressed or methylated in progeny of wounded plants. Evidence for (3) was mixed. We found that non-dicer sRNAs with increased abundance in response to wounding tended to be nearby genes with decreased expression in the next generation. Counter to expectations, we did not find that siRNA responses to wounding were associated with gene expression or methylation changes in the next generation and within plant and transgenerational sRNA plasticity were negatively correlated. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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21 pages, 2107 KiB

Open AccessArticle

m⁶A RNA Methylation in Marine Plants: First Insights and Relevance for Biological Rhythms

by Miriam Ruocco, Luca Ambrosino, Marlene Jahnke, Maria Luisa Chiusano, Isabel Barrote, Gabriele Procaccini, João Silva and Emanuela Dattolo

Int. J. Mol. Sci. 2020, 21(20), 7508; https://doi.org/10.3390/ijms21207508 - 12 Oct 2020

Cited by 10 | Viewed by 3201

Abstract

Circadian regulations are essential for enabling organisms to synchronize physiology with environmental light-dark cycles. Post-transcriptional RNA modifications still represent an understudied level of gene expression regulation in plants, although they could play crucial roles in environmental adaptation. N⁶-methyl-adenosine (m⁶A) is the most prevalent mRNA modification, established by “writer” and “eraser” proteins. It influences the clockwork in several taxa, but only few studies have been conducted in plants and none in marine plants. Here, we provided a first inventory of m⁶A-related genes in seagrasses and investigated daily changes in the global RNA methylation and transcript levels of writers and erasers in Cymodocea nodosa and Zostera marina. Both species showed methylation peaks during the dark period under the same photoperiod, despite exhibiting asynchronous changes in the m⁶A profile and related gene expression during a 24-h cycle. At contrasting latitudes, Z. marina populations displayed overlapping daily patterns of the m⁶A level and related gene expression. The observed rhythms are characteristic for each species and similar in populations of the same species with different photoperiods, suggesting the existence of an endogenous circadian control. Globally, our results indicate that m⁶A RNA methylation could widely contribute to circadian regulation in seagrasses, potentially affecting the photo-biological behaviour of these plants. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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17 pages, 3618 KiB

Open AccessArticle

Epigenetic Analysis through MSAP-NGS Coupled Technology: The Case Study of White Poplar Monoclonal Populations/Stands

by Francesco Guarino, Berthold Heinze, Stefano Castiglione and Angela Cicatelli

Int. J. Mol. Sci. 2020, 21(19), 7393; https://doi.org/10.3390/ijms21197393 - 07 Oct 2020

Cited by 4 | Viewed by 2069

Abstract

Over the last several decades, several lines of evidence have shown that epigenetic modifications modulate phenotype and mediate an organism’s response to environmental stimuli. Plant DNA is normally highly methylated, although notable differences exist between species. Many biomolecular techniques based on PCR have been developed to analyse DNA methylation status, however a qualitative leap was made with the advent of next-generation sequencing (NGS). In the case of large, repetitive, or not-yet-sequenced genomes characterised by a high level of DNA methylation, the NGS analysis of bisulphite pre-treated DNA is expensive and time consuming, and moreover, in some cases data analysis is a major challenge. Methylation-sensitive amplification polymorphism (MSAP) analysis is a highly effective method to study DNA methylation. The method is based on the comparison of double DNA digestion profiles (EcoRI-HpaII and EcoRI-MspI) to reveal methylation pattern variations. These are often attributable to pedoclimatic and stress conditions which affect all organisms during their lifetime. In our study, five white poplar (Populus alba L.) specimens were collected from different monoclonal stands in the Maltese archipelago, and their DNA was processed by means of an innovative approach where MSAP analysis was followed by NGS. This allowed us to identify genes that were differentially methylated among the different specimens and link them to specific biochemical pathways. Many differentially methylated genes were found to encode transfer RNAs (tRNAs) related to photosynthesis or light reaction pathways. Our results clearly demonstrate that this combinatorial method is suitable for epigenetic studies of unsequenced genomes like P. alba (at the time of study), and to identify epigenetic variations related to stress, probably caused by different and changing pedoclimatic conditions, to which the poplar stands have been exposed. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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13 pages, 895 KiB

Open AccessArticle

CG Demethylation Leads to Sequence Mutations in an Anther Culture of Barley Due to the Presence of Cu, Ag Ions in the Medium and Culture Time

by Piotr T. Bednarek and Renata Orłowska

Int. J. Mol. Sci. 2020, 21(12), 4401; https://doi.org/10.3390/ijms21124401 - 20 Jun 2020

Cited by 17 | Viewed by 2221

Abstract

During plant tissue cultures the changes affecting regenerants have a broad range of genetic and epigenetic implications. These changes can be seen at the DNA methylation and sequence variation levels. In light of the latest studies, DNA methylation change plays an essential role in determining doubled haploid (DH) regenerants. The present study focuses on exploring the relationship between DNA methylation in CG and CHG contexts, and sequence variation, mediated by microelements (CuSO₄ and AgNO₃) supplemented during barley anther incubation on induction medium. To estimate such a relationship, a mediation analysis was used based on the results previously obtained through metAFLP method. Here, an interaction was observed between DNA demethylation in the context of CG and the time of culture. It was also noted that the reduction in DNA methylation was associated with a total decrease in the amount of Cu and Ag ions in the induction medium. Moreover, the total increase in Cu and Ag ions increased sequence variation. The importance of the time of tissue culture in the light of the observed changes resulted from the grouping of regenerants obtained after incubation on the induction medium for 28 days. The present study demonstrated that under a relatively short time of tissue culture (28 days), the multiplication of the Cu²⁺ and Ag⁺ ion concentrations (‘Cu*Ag’) acts as a mediator of demethylation in CG context. Change (increase) in the demethylation in CG sequence results in the decrease of ‘Cu*Ag’, and that change induces sequence variation equal to the value of the indirect effect. Thus, Cu and Ag ions mediate sequence variation. It seems that the observed changes at the level of methylation and DNA sequence may accompany the transition from direct to indirect embryogenesis Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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25 pages, 3399 KiB

Open AccessArticle

Genome-Wide Identification of Epigenetic Regulators in Quercus suber L.

by Helena G. Silva, Rómulo S. Sobral, Alexandre P. Magalhães, Leonor Morais-Cecílio and M. Manuela R. Costa

Int. J. Mol. Sci. 2020, 21(11), 3783; https://doi.org/10.3390/ijms21113783 - 27 May 2020

Cited by 11 | Viewed by 3550

Abstract

Modifications of DNA and histones, including methylation and acetylation, are critical for the epigenetic regulation of gene expression during plant development, particularly during environmental adaptation processes. However, information on the enzymes catalyzing all these modifications in trees, such as Quercus suber L., is still not available. In this study, eight DNA methyltransferases (DNA Mtases) and three DNA demethylases (DDMEs) were identified in Q. suber. Histone modifiers involved in methylation (35), demethylation (26), acetylation (8), and deacetylation (22) were also identified in Q. suber. In silico analysis showed that some Q. suber DNA Mtases, DDMEs and histone modifiers have the typical domains found in the plant model Arabidopsis, which might suggest a conserved functional role. Additional phylogenetic analyses of the DNA and histone modifier proteins were performed using several plant species homologs, enabling the classification of the Q. suber proteins. A link between the expression levels of each gene in different Q. suber tissues (buds, flowers, acorns, embryos, cork, and roots) with the functions already known for their closest homologs in other species was also established. Therefore, the data generated here will be important for future studies exploring the role of epigenetic regulators in this economically important species. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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20 pages, 1097 KiB

Open AccessArticle

Epigenetic Patterns and Geographical Parthenogenesis in the Alpine Plant Species Ranunculus kuepferi (Ranunculaceae)

by Christoph C. F. Schinkel, Eleni Syngelaki, Bernhard Kirchheimer, Stefan Dullinger, Simone Klatt and Elvira Hörandl

Int. J. Mol. Sci. 2020, 21(9), 3318; https://doi.org/10.3390/ijms21093318 - 07 May 2020

Cited by 10 | Viewed by 2539

Abstract

Polyploidization and the shift to apomictic reproduction are connected to changes in DNA cytosine-methylation. Cytosine-methylation is further sensitive to environmental conditions. We, therefore, hypothesize that DNA methylation patterns would differentiate within species with geographical parthenogenesis, i.e., when diploid sexual and polyploid apomictic populations exhibit different spatial distributions. On natural populations of the alpine plant Ranunculus kuepferi, we tested differences in methylation patterns across two cytotypes (diploid, tetraploid) and three reproduction modes (sexual, mixed, apomictic), and their correlation to environmental data and geographical distributions. We used methylation-sensitive amplified fragment-length polymorphism (methylation-sensitive AFLPs) and scored three types of epiloci. Methylation patterns differed independently between cytotypes versus modes of reproduction and separated three distinct combined groups (2x sexual + mixed, 4x mixed, and 4x apomictic), with differentiation of 4x apomicts in all epiloci. We found no global spatial autocorrelation, but instead correlations to elevation and temperature gradients in 22 and 36 epiloci, respectively. Results suggest that methylation patterns in R. kuepferi were altered by cold conditions during postglacial recolonization of the Alps, and by the concomitant shift to facultative apomixis, and by polyploidization. Obligate apomictic tetraploids at the highest elevations established a distinct methylation profile. Methylation patterns reflect an ecological gradient rather than the geographical differentiation. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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Review

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18 pages, 1069 KiB

Open AccessReview

Plant Volatile Organic Compounds Evolution: Transcriptional Regulation, Epigenetics and Polyploidy

by Jesús Picazo-Aragonés, Anass Terrab and Francisco Balao

Int. J. Mol. Sci. 2020, 21(23), 8956; https://doi.org/10.3390/ijms21238956 - 25 Nov 2020

Cited by 57 | Viewed by 5503

Abstract

Volatile organic compounds (VOCs) are emitted by plants as a consequence of their interaction with biotic and abiotic factors, and have a very important role in plant evolution. Floral VOCs are often involved in defense and pollinator attraction. These interactions often change rapidly over time, so a quick response to those changes is required. Epigenetic factors, such as DNA methylation and histone modification, which regulate both genes and transcription factors, might trigger adaptive responses to these evolutionary pressures as well as regulating the rhythmic emission of VOCs through circadian clock regulation. In addition, transgenerational epigenetic effects and whole genome polyploidy could modify the generation of VOCs’ profiles of offspring, contributing to long-term evolutionary shifts. In this article, we review the available knowledge about the mechanisms that may act as epigenetic regulators of the main VOC biosynthetic pathways, and their importance in plant evolution. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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21 pages, 1025 KiB

Open AccessReview

Application of the MSAP Technique to Evaluate Epigenetic Changes in Plant Conservation

by María Elena González-Benito, Miguel Ángel Ibáñez, Michela Pirredda, Sara Mira and Carmen Martín

Int. J. Mol. Sci. 2020, 21(20), 7459; https://doi.org/10.3390/ijms21207459 - 10 Oct 2020

Cited by 15 | Viewed by 2832

Abstract

Epigenetic variation, and particularly DNA methylation, is involved in plasticity and responses to changes in the environment. Conservation biology studies have focused on the measurement of this variation to establish demographic parameters, diversity levels and population structure to design the appropriate conservation strategies. However, in ex situ conservation approaches, the main objective is to guarantee the characteristics of the conserved material (phenotype and epi-genetic). We review the use of the Methylation Sensitive Amplified Polymorphism (MSAP) technique to detect changes in the DNA methylation patterns of plant material conserved by the main ex situ plant conservation methods: seed banks, in vitro slow growth and cryopreservation. Comparison of DNA methylation patterns before and after conservation is a useful tool to check the fidelity of the regenerated plants, and, at the same time, may be related with other genetic variations that might appear during the conservation process (i.e., somaclonal variation). Analyses of MSAP profiles can be useful in the management of ex situ plant conservation but differs in the approach used in the in situ conservation. Likewise, an easy-to-use methodology is necessary for a rapid interpretation of data, in order to be readily implemented by conservation managers. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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33 pages, 758 KiB

Open AccessReview

Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses

by Vasily V. Ashapkin, Lyudmila I. Kutueva, Nadezhda I. Aleksandrushkina and Boris F. Vanyushin

Int. J. Mol. Sci. 2020, 21(20), 7457; https://doi.org/10.3390/ijms21207457 - 09 Oct 2020

Cited by 92 | Viewed by 7831

Abstract

Unlike animals, plants are immobile and could not actively escape the effects of aggressive environmental factors, such as pathogenic microorganisms, insect pests, parasitic plants, extreme temperatures, drought, and many others. To counteract these unfavorable encounters, plants have evolved very high phenotypic plasticity. In a rapidly changing environment, adaptive phenotypic changes often occur in time frames that are too short for the natural selection of adaptive mutations. Probably, some kind of epigenetic variability underlines environmental adaptation in these cases. Indeed, isogenic plants often have quite variable phenotypes in different habitats. There are examples of successful “invasions” of relatively small and genetically homogenous plant populations into entirely new habitats. The unique capability of quick environmental adaptation appears to be due to a high tendency to transmit epigenetic changes between plant generations. Multiple studies show that epigenetic memory serves as a mechanism of plant adaptation to a rapidly changing environment and, in particular, to aggressive biotic and abiotic stresses. In wild nature, this mechanism underlies, to a very significant extent, plant capability to live in different habitats and endure drastic environmental changes. In agriculture, a deep understanding of this mechanism could serve to elaborate more effective and safe approaches to plant protection. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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23 pages, 974 KiB

Open AccessReview

Plant Elongator—Protein Complex of Diverse Activities Regulates Growth, Development, and Immune Responses

by Magdalena Jarosz, Mieke Van Lijsebettens and Magdalena Woloszynska

Int. J. Mol. Sci. 2020, 21(18), 6912; https://doi.org/10.3390/ijms21186912 - 22 Sep 2020

Cited by 7 | Viewed by 3659

Abstract

Contrary to the conserved Elongator composition in yeast, animals, and plants, molecular functions and catalytic activities of the complex remain controversial. Elongator was identified as a component of elongating RNA polymerase II holoenzyme in yeast, animals, and plants. Furthermore, it was suggested that Elonagtor facilitates elongation of transcription via histone acetyl transferase activity. Accordingly, phenotypes of Arabidopsis elo mutants, which show development, growth, or immune response defects, correlate with transcriptional downregulation and the decreased histone acetylation in the coding regions of crucial genes. Plant Elongator was also implicated in other processes: transcription and processing of miRNA, regulation of DNA replication by histone acetylation, and acetylation of alpha-tubulin. Moreover, tRNA modification, discovered first in yeast and confirmed in plants, was claimed as the main activity of Elongator, leading to specificity in translation that might also result indirectly in a deficiency in transcription. Heterologous overexpression of individual Arabidopsis Elongator subunits and their respective phenotypes suggest that single Elongator subunits might also have another function next to being a part of the complex. In this review, we shall present the experimental evidence of all molecular mechanisms and catalytic activities performed by Elongator in nucleus and cytoplasm of plant cells, which might explain how Elongator regulates growth, development, and immune responses. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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19 pages, 775 KiB

Open AccessReview

Knowing When to Silence: Roles of Polycomb-Group Proteins in SAM Maintenance, Root Development, and Developmental Phase Transition

by Bowen Yan, Yanpeng Lv, Chunyu Zhao and Xiaoxue Wang

Int. J. Mol. Sci. 2020, 21(16), 5871; https://doi.org/10.3390/ijms21165871 - 15 Aug 2020

Cited by 13 | Viewed by 4069

Abstract

Polycomb repressive complex 1 (PRC1) and PRC2 are the major complexes composed of polycomb-group (PcG) proteins in plants. PRC2 catalyzes trimethylation of lysine 27 on histone 3 to silence target genes. Like Heterochromatin Protein 1/Terminal Flower 2 (LHP1/TFL2) recognizes and binds to H3K27me3 generated by PRC2 activities and enrolls PRC1 complex to further silence the chromatin through depositing monoubiquitylation of lysine 119 on H2A. Mutations in PcG genes display diverse developmental defects during shoot apical meristem (SAM) maintenance and differentiation, seed development and germination, floral transition, and so on so forth. PcG proteins play essential roles in regulating plant development through repressing gene expression. In this review, we are focusing on recent discovery about the regulatory roles of PcG proteins in SAM maintenance, root development, embryo development to seedling phase transition, and vegetative to reproductive phase transition. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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17 pages, 741 KiB

Open AccessReview

Epigenetic Landmarks of Leaf Senescence and Crop Improvement

by Agnieszka Ostrowska-Mazurek, Piotr Kasprzak, Szymon Kubala, Magdalena Zaborowska and Ewa Sobieszczuk-Nowicka

Int. J. Mol. Sci. 2020, 21(14), 5125; https://doi.org/10.3390/ijms21145125 - 20 Jul 2020

Cited by 14 | Viewed by 3537

Abstract

This review synthesizes knowledge on epigenetic regulation of leaf senescence and discusses the possibility of using this knowledge to improve crop quality. This control level is implemented by different but interacting epigenetic mechanisms, including DNA methylation, covalent histone modifications, and non-covalent chromatin remodeling. The genetic and epigenetic changes may act alone or together and regulate the gene expression, which may result in heritable (stress memory) changes and may lead to crop survival. In the review, the question also arises whether the mitotically stable epigenetic information can be used for crop improvement. The barley crop model for early and late events of dark-induced leaf senescence (DILS), where the point of no return was defined, revealed differences in DNA and RNA modifications active in DILS compared to developmental leaf senescence. This suggests the possibility of a yet-to-be-discovered epigenetic-based switch between cell survival and cell death. Conclusions from the analyzed research contributed to the hypothesis that chromatin-remodeling mechanisms play a role in the control of induced leaf senescence. Understanding this mechanism in crops might provide a tool for further exploitation toward sustainable agriculture: so-called epibreeding. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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28 pages, 3036 KiB

Open AccessReview

Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation

by Estephania Zluhan-Martínez, Vadim Pérez-Koldenkova, Martha Verónica Ponce-Castañeda, María de la Paz Sánchez, Berenice García-Ponce, Sergio Miguel-Hernández, Elena R. Álvarez-Buylla and Adriana Garay-Arroyo

Int. J. Mol. Sci. 2020, 21(14), 4925; https://doi.org/10.3390/ijms21144925 - 12 Jul 2020

Cited by 5 | Viewed by 4086

Abstract

The Retinoblastoma protein (pRb) is a key cell cycle regulator conserved in a wide variety of organisms. Experimental analysis of pRb’s functions in animals and plants has revealed that this protein participates in cell proliferation and differentiation processes. In addition, pRb in animals and its orthologs in plants (RBR), are part of highly conserved protein complexes which suggest the possibility that analogies exist not only between functions carried out by pRb orthologs themselves, but also in the structure and roles of the protein networks where these proteins are involved. Here, we present examples of pRb/RBR participation in cell cycle control, cell differentiation, and in the regulation of epigenetic changes and chromatin remodeling machinery, highlighting the similarities that exist between the composition of such networks in plants and animals. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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23 pages, 1773 KiB

Open AccessReview

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

by Barbara Wójcikowska, Anna M. Wójcik and Małgorzata D. Gaj

Int. J. Mol. Sci. 2020, 21(7), 2307; https://doi.org/10.3390/ijms21072307 - 26 Mar 2020

Cited by 50 | Viewed by 8885

Abstract

Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted. Full article

(This article belongs to the Special Issue Role of Epigenetic Mechanisms in Plants: From Basic to Applicative Aspects)

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