Biological role and mechanism of chromatin readers in plants

Scheid, Ray; Chen, Jiani; Zhong, Xuehua

doi:10.1016/j.pbi.2021.102008

Cited by 17 publications

(12 citation statements)

References 65 publications

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“…MBD7 protects genes from expression repression and DNA hypermethylation by binding to the highly methylated CG region and recruiting histone acetyltransferases [ 14 ]. MBD9 strongly interacts with Imitation SWItch (ISWI) chromatin remodeling complexes and has been shown to be involved in DNA demethylation [ 15 – 17 ]. In Arabidopsis mutants with MBD gene knockdown, nucleolar dominance was disturbed, and their growth and development were abnormal [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

Xiao

Wang

2022

BMC Plant Biol

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Background Polyploidization promotes species formation and is widespread in angiosperms. Genome changes dramatically bring opportunities and challenges to plants after polyploidy. Methyl-CpG-Binding Domain (MBD) proteins can recognize and bind to methylation sites and they play an important role in the physiological process related to methylation in animals and plants. However, research on the influence of the allopolyploidization process on the MBD gene family is still lacking, so it is necessary to conduct a comprehensive analysis. Results In this study, twenty-two, ten and eleven MBD genes were identified in the genome of allotetraploid B. napus and its diploid ancestors, B. rapa and B. oleracea, respectively. Based on the clades of the MBD gene in Arabidopsis, rice and maize, we divided the new phylogenetic tree into 8 clades. Among them, the true MBD genes in Brassica existed in only 5 clades. Clade IV and Clade VI were unique in term of MBD genes in dicotyledons. Ka/Ks calculations showed that MBD genes underwent purifying selection in Brassica and may retain genes through sequence or functional differentiation early in evolution. In the process of allopolyploidization, the number of MBD gene introns increased, and the protein motifs changed. The MBD proteins had their own special motifs in each clade, and the MBD domains were only conserved in their clades. At the same time, the MBD genes were expressed in flower, leaf, silique, and stem tissues, and the expression levels of the different genes were significantly different, while the tissue specificity was not obvious. The allopolyploidization process may increase the number of cis-acting elements and activate the transposable elements. During allopolyploidization, the expression pattern of the MBD gene changes, which may be regulated by cis-acting elements and transposable elements. The number imbalance of cis-acting elements and transposable elements in An and Cn subgenomes may also lead to biased An subgenome expression of the MBD gene in B. napus. Conclusions In this study, by evaluating the number, structure, phylogeny and expression of the MBD gene in B. napus and its diploid ancestors, we increased the understanding of MBD genes in allopolyploids and provided a reference for future analysis of allopolyploidization.

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Section: Introductionmentioning

confidence: 99%

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

Xiao

Wang

2022

BMC Plant Biol

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“…For instance, silent or increased histone H3K9 and DNA methylation in conjunction with H3 lysine results in TE suppression in Arabidopsis, thus protecting the genomes from TE transposition and genome instability [259]. This distinctive three-layered state of silent heterochromatin is distinguishable from the polycomb gene cluster transcribed and active heterochromatin gene expression and is linked to the Arabidopsis genome [260]. There can be several different reasons for the collapse of structures and reactivation of previously silenced TEs [261].…”

Section: Te Methylation In Plant Evolutionmentioning

confidence: 99%

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Ramakrishnan

Satish

Kalendar

et al. 2021

IJMS

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Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.

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“…Because of this, readers provide interaction between epigenetic marks (modifications of histones and DNA) and other cellular processes in which a nonhistone protein is involved (Li, Y. and Li, H., 2012;Patel, 2016;Grimanell and Ingouff, 2020). For example, readers can interact with proteins that establish or remove marks from DNA and histones, contributing to the spreading or elimination of marks (Grimanell and Ingouff, 2020;Scheid et al, 2021). They can contribute to the opening of chromatin, due to the inclusion of histone variants that change the state of chromatin (Kouzarides, 2007;Sijacic et al, 2019).…”

Section: How Epigenetic Modifications Can Affect the Phenotypementioning

confidence: 99%

Paradoxes of Plant Epigenetics

Ежова

2021

Russ J Dev Biol

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Plants have a unique ability to adapt ontogenesis to changing environmental conditions and the influence of stress factors. This ability is based on the existence of two specific features of epigenetic regulation in plants, which seem to be mutually exclusive at first glance. On the one hand, plants are capable of partial epigenetic reprogramming of the genome, which can lead to adaptation of physiology and metabolism to changed environmental conditions as well as to changes in ontogenesis programs. On the other hand, plants can show amazing stability of epigenetic modifications and the ability to transmit them to vegetative and sexual generations. The combination of these inextricably linked epigenetic features not only ensures survival in the conditions of a sessile lifestyle but also underlies a surprisingly wide morphological diversity of plants, which can lead to the appearance of morphs within one population and the existence of interpopulation morphological differences. The review discusses the molecular genetic mechanisms that cause a paradoxical combination of the stability and lability properties of epigenetic modifications and underlie the polyvariance of ontogenesis. We also consider the existing approaches for studying the role of epigenetic regulation in the manifestation of polyvariance of ontogenesis and discuss their limitations and prospects.

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Biological role and mechanism of chromatin readers in plants

Cited by 17 publications

References 65 publications

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Paradoxes of Plant Epigenetics

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