Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Pleurotus Species

Pleurotus tuoliensis (Pt) and P. eryngii var. eryngii (Pe) are important edible mushrooms. The epigenetic and gene expression signatures characterizing major developmental transitions in these two mushrooms remain largely unknown. Here, we report global analyses of DNA methylation and gene expression in both mushrooms across three major developmental transitions, from mycelium to primordium and to fruit body, by whole-genome bisulfite sequencing (WGBS) and RNA-seq-based transcriptome profiling. Our results revealed that in both Pt and Pe the landscapes of methylome are largely stable irrespective of genomic features, e.g., in both protein-coding genes and transposable elements (TEs), across the developmental transitions. The repressive impact of DNA methylation on expression of a small subset of genes is likely due to TE-associated effects rather than their own developmental dynamics. Global expression of gene orthologs was also broadly conserved between Pt and Pe, but discernible interspecific differences exist especially at the fruit body formation stage, and which are primarily due to differences in trans-acting factors. The methylome and transcriptome repertories we established for the two mushroom species may facilitate further studies of the epigenetic and transcriptional regulatory mechanisms underpinning gene expression during development in Pleurotus and related genera.

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Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon

10.1101/2020.06.16.154047 ◽

2020 ◽

Cited By ~ 1

Author(s):

Michele Wyler ◽

Christoph Stritt ◽

Jean-Claude Walser ◽

Célia Baroux ◽

Anne C. Roulin

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Transposable Elements ◽

Plant Species ◽

Brachypodium Distachyon ◽

Expression Patterns ◽

Small Subset ◽

Molecular Evidence ◽

Specific Gene ◽

Plant Genomes

AbstractTransposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation and nearby gene expression in additional plant species. Here we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for eleven natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated to a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon.Significance statementTransposable elements (TEs) are a major component of plant genomes and a source of genetic and epigenetic innovations underlying adaptation to changing environmental conditions. Yet molecular evidence linking TE silencing and nearby gene expression are lacking for many plant species. We show that in the model grass Brachypodium DNA methylation spreads over very short distances around TEs, with an influence on gene expression for a small subset of TE families.

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Ploidy-dependent changes in the epigenome of symbiotic cells correlate with specific patterns of gene expression

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1704211114 ◽

2017 ◽

Vol 114 (17) ◽

pp. 4543-4548 ◽

Cited By ~ 14

Author(s):

Marianna Nagymihály ◽

Alaguraj Veluchamy ◽

Zoltán Györgypál ◽

Federico Ariel ◽

Teddy Jégu ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Medicago Truncatula ◽

The Other ◽

Small Subset ◽

Epigenetic Changes ◽

Ploidy Levels ◽

Transcriptional Reprogramming ◽

Other Hand ◽

Symbiotic Nodule

The formation of symbiotic nodule cells in Medicago truncatula is driven by successive endoreduplication cycles and transcriptional reprogramming in different temporal waves including the activation of more than 600 cysteine-rich NCR genes expressed only in nodules. We show here that the transcriptional waves correlate with growing ploidy levels and have investigated how the epigenome changes during endoreduplication cycles. Differential DNA methylation was found in only a small subset of symbiotic nodule-specific genes, including more than half of the NCR genes, whereas in most genes DNA methylation was unaffected by the ploidy levels and was independent of the genes’ active or repressed state. On the other hand, expression of nodule-specific genes correlated with ploidy-dependent opening of the chromatin as well as, in a subset of tested genes, with reduced H3K27me3 levels combined with enhanced H3K9ac levels. Our results suggest that endoreduplication-dependent epigenetic changes contribute to transcriptional reprogramming in the differentiation of symbiotic cells.

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DNA methylation mediates genetic liability to non-syndromic cleft lip/palate

10.1101/256842 ◽

2018 ◽

Author(s):

Laurence J Howe ◽

Tom G Richardson ◽

Ryan Arathimos ◽

Lucas Alvizi ◽

Maria-Rita Passos-Bueno ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Genetic Risk ◽

Cleft Lip ◽

Genome Wide Association Study ◽

Complex Trait ◽

Methylation Data ◽

Protein Coding ◽

Genetic Liability ◽

Cleft Lip Palate

AbstractBackgroundNon-syndromic cleft lip/palate (nsCL/P) is a complex trait with genetic and environmental risk factors. Around 40 distinct genetic risk loci have been identified for nsCL/P, but many reside in non-protein-coding regions with an unclear function. We hypothesised that one possibility is that the genetic risk variants influence susceptibility to nsCL/P through gene regulation pathways, such as those involving DNA methylation.MethodsUsing nsCL/P Genome-wide association study summary data and methylation data from four studies, we used Mendelian randomization and joint likelihood mapping to identify putative loci where genetic liability to nsCL/P may be mediated by variation in DNA methylation in blood.ResultsThere was evidence at three independent loci, VAX1 (10q25.3), LOC146880 (17q23.3) and NTN1 (17p13.1), that liability to nsCL/P and variation in DNA methylation might be driven by the same genetic variant. Follow up analyses using DNA methylation data, derived from lip and palate tissue, and gene expression catalogues provided further insight into possible biological mechanisms.ConclusionsGenetic variation may increase liability to nsCL/P by influencing DNA methylation and gene expression at VAX1, LOC146880 and NTN1.

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Contribution of Epigenetic Mechanisms in the Regulation of Environmentally-Induced Polyphenism in Insects

Insects ◽

10.3390/insects12070649 ◽

2021 ◽

Vol 12 (7) ◽

pp. 649

Author(s):

Gautier Richard ◽

Julie Jaquiéry ◽

Gaël Le Trionnaire

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Current Knowledge ◽

Epigenetic Mechanisms ◽

Developmental Transitions ◽

Phenotypic Changes ◽

Genome Expression ◽

Alternative Phenotypes ◽

Non Coding Rna ◽

Developmental Switches

Many insect species display a remarkable ability to produce discrete phenotypes in response to changes in environmental conditions. Such phenotypic plasticity is referred to as polyphenism. Seasonal, dispersal and caste polyphenisms correspond to the most-studied examples that are environmentally-induced in insects. Cues that induce such dramatic phenotypic changes are very diverse, ranging from seasonal cues, habitat quality changes or differential larval nutrition. Once these signals are perceived, they are transduced by the neuroendocrine system towards their target tissues where gene expression reprogramming underlying phenotypic changes occur. Epigenetic mechanisms are key regulators that allow for genome expression plasticity associated with such developmental switches. These mechanisms include DNA methylation, chromatin remodelling and histone post-transcriptional modifications (PTMs) as well as non-coding RNAs and have been studied to various extents in insect polyphenism. Differential patterns of DNA methylation between phenotypes are usually correlated with changes in gene expression and alternative splicing events, especially in the cases of dispersal and caste polyphenism. Combinatorial patterns of histone PTMs provide phenotype-specific epigenomic landscape associated with the expression of specific transcriptional programs, as revealed during caste determination in honeybees and ants. Alternative phenotypes are also usually associated with specific non-coding RNA profiles. This review will provide a summary of the current knowledge of the epigenetic changes associated with polyphenism in insects and highlights the potential for these mechanisms to be key regulators of developmental transitions triggered by environmental cues.

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