Retro-Element Gypsy-163 Is Differentially Methylated in Reproductive Tissues of Apomictic and Sexual Plants of Cenchrus ciliaris

Rathore, Priyanka; Raina, S. N.; Kumar, Suresh; Bhat, Vishnu

doi:10.3389/fgene.2020.00795

Cited by 10 publications

(13 citation statements)

References 67 publications

(79 reference statements)

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“…Moreover, a higher rate of CG methylation and a higher expression of retrotransposon transcripts was reported in sexual genotypes of E. curvula when compared to apomictic ones [45]. Otherwise, a recent work carried out in Cenchrus ciliaris showed that transcripts of Gy163, an LTR retrotransposon, are more expressed in the reproductive tissues of apomictic than of sexual plants, and this was correlated with reduced methylation level [98]. A recent study about the role of miRNA-mRNA interactions in apomixis development in E. curvula found that a transposon sequence was specifically repressed in the sexual genotype, most likely due to interactions with miRNAs [99].…”

Section: Discussionmentioning

confidence: 95%

Differential Epigenetic Marks Are Associated with Apospory Expressivity in Diploid Hybrids of Paspalum rufum

Soliman

Podio

Marconi

et al. 2021

Plants

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Apomixis seems to emerge from the deregulation of preexisting genes involved in sexuality by genetic and/or epigenetic mechanisms. The trait is associated with polyploidy, but diploid individuals of Paspalum rufum can form aposporous embryo sacs and develop clonal seeds. Moreover, diploid hybrid families presented a wide apospory expressivity variation. To locate methylation changes associated with apomixis expressivity, we compare relative DNA methylation levels, at CG, CHG, and CHH contexts, between full-sib P. rufum diploid genotypes presenting differential apospory expressivity. The survey was performed using a methylation content-sensitive enzyme ddRAD (MCSeEd) strategy on samples at premeiosis/meiosis and postmeiosis stages. Based on the relative methylation level, principal component analysis and heatmaps, clearly discriminate samples with contrasting apospory expressivity. Differential methylated contigs (DMCs) showed 14% of homology to known transcripts of Paspalum notatum reproductive transcriptome, and almost half of them were also differentially expressed between apomictic and sexual samples. DMCs showed homologies to genes involved in flower growth, development, and apomixis. Moreover, a high proportion of DMCs aligned on genomic regions associated with apomixis in Setaria italica. Several stage-specific differential methylated sequences were identified as associated with apospory expressivity, which could guide future functional gene characterization in relation to apomixis success at diploid and tetraploid levels.

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Section: Discussionmentioning

confidence: 95%

Differential Epigenetic Marks Are Associated with Apospory Expressivity in Diploid Hybrids of Paspalum rufum

Soliman

Podio

Marconi

et al. 2021

Plants

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“…The RE Ty3-gypsy was found to be differentially methylated/expressed in the reproductive tissues of apomictic and sexual plants. Hypomethylation was observed in CHH context in reproductive (aposporous initial and mature embryo sac) tissues of apomictic plants, which was directly correlated with the activity of the RE (Rathore et al, 2020). Thus, epigenetic regulation of seed development appears to be a common process in different plant species.…”

Section: Genome Imprinting and Heterosismentioning

confidence: 94%

“…In Arabidopsis as well as in other plants, the heterochromatic regions are enriched with methylcytosines, generally in the repetitive sequences and TEs. However, TEs and 5-mC are also found to be interspersed in the euchromatic regions (Zhang et al, 2006;Rathore et al, 2020). The dynamics of DNA base methylation depends on the reversibility of the processes, which also controls switching on/off the gene.…”

Section: Dynamics Of Dna Methylationmentioning

confidence: 99%

“…This gets repatterned and/or released when the inbreds are crossed to develop a hybrid. Further, understanding the epigenetic regulation of embryo development might uncover the mysteries of apomixis (asexual reproduction through seeds) in a plant (Koltunow and Grossniklaus, 2003;Kumar, 2017;Rathore et al, 2020). If apomixis is successfully incorporated in commercial seed crops, heterosis can be preserved over the generations to overcome the current limitations of hybrid seed production.…”

Section: Genome Imprinting and Heterosismentioning

confidence: 99%

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Dynamics of DNA Methylation and Its Functions in Plant Growth and Development

2021

Self Cite

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Epigenetic modifications in DNA bases and histone proteins play important roles in the regulation of gene expression and genome stability. Chemical modification of DNA base (e.g., addition of a methyl group at the fifth carbon of cytosine residue) switches on/off the gene expression during developmental process and environmental stresses. The dynamics of DNA base methylation depends mainly on the activities of the writer/eraser guided by non-coding RNA (ncRNA) and regulated by the developmental/environmental cues. De novo DNA methylation and active demethylation activities control the methylation level and regulate the gene expression. Identification of ncRNA involved in de novo DNA methylation, increased DNA methylation proteins guiding DNA demethylase, and methylation monitoring sequence that helps maintaining a balance between DNA methylation and demethylation is the recent developments that may resolve some of the enigmas. Such discoveries provide a better understanding of the dynamics/functions of DNA base methylation and epigenetic regulation of growth, development, and stress tolerance in crop plants. Identification of epigenetic pathways in animals, their existence/orthologs in plants, and functional validation might improve future strategies for epigenome editing toward climate-resilient, sustainable agriculture in this era of global climate change. The present review discusses the dynamics of DNA methylation (cytosine/adenine) in plants, its functions in regulating gene expression under abiotic/biotic stresses, developmental processes, and genome stability.

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“…In plants, epigenetic mechanisms, such as DNA methylation, histone modifications, and small non-coding RNAs, are known to regulate gene expression changes in response to developmental and environmental cues (e.g. [28][29][30][31][32][33] ). Based on this evidence, epigenetic mechanisms are currently considered potentially important regulators of plants response to stress.…”

Section: Introductionmentioning

confidence: 99%

Molecular basis of intraspecific differentiation for heavy metal tolerance in the copper moss Scopelophila cataractae

Boquete

Schmid²,

Wagemaker

et al. 2022

Preprint

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Bryophytes’ remarkable capacity to tolerate extreme abiotic conditions allows us to enhance our understanding of the diversity of molecular mechanisms involved in plant stress response. Here, we used next generation sequencing to study DNA methylation and gene expression changes in plants from four populations of the metallophyte moss Scopelophila cataractae experimentally exposed to either Cd or Cu. These populations previously showed differences in tolerance to both metals, so here, we aimed at uncovering the molecular basis of this phenotypic differentiation. We found no evidence of genetic differentiation among the populations studied. The epigenetic data, however, showed limited but significant population-specific changes in DNA methylation in response to both metals. Exposure to acute Cu stress in the laboratory led to the downregulation of genes involved in heavy metal tolerance in both populations regardless of their tolerance level, but this response was quantitatively higher in the most tolerant. We propose that chronic exposure to varying levels of heavy metals in the field led to potentially non-genetically-based intraspecific differentiation for heavy metal tolerance in S. cataractae. The most tolerant plants invested more in constitutive protection and were more efficient in entering a conservative state when faced with acute Cu stress.

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Retro-Element Gypsy-163 Is Differentially Methylated in Reproductive Tissues of Apomictic and Sexual Plants of Cenchrus ciliaris

Cited by 10 publications

References 67 publications

Differential Epigenetic Marks Are Associated with Apospory Expressivity in Diploid Hybrids of Paspalum rufum

Differential Epigenetic Marks Are Associated with Apospory Expressivity in Diploid Hybrids of Paspalum rufum

Dynamics of DNA Methylation and Its Functions in Plant Growth and Development

Molecular basis of intraspecific differentiation for heavy metal tolerance in the copper moss Scopelophila cataractae

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