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Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

ABSTRACT: Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

PROVIDER: PRJNA481746 | ENA |

REPOSITORIES: ENA

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Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

Project description:5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, while mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, while mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small-interfering RNAs and H3K9me2, without gaining CHH methylation. This suggests that spontaneous epialelles that arise in plant cell cultures are stably maintained by small RNA independently of the canonical RNA-directed DNA methylation pathway. In contrast, loci that fail to produce siRNA are targeted for demethylation when cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.

2020-12-03 | GSE155958 | GEO

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

2020-12-03 | GSE157670 | GEO

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

Project description:Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

| PRJNA481749 | ENA

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

Project description:Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

| PRJNA656207 | ENA

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

Project description:Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

| PRJNA481750 | ENA

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

Project description:Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

| PRJNA662359 | ENA

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

Project description:5-methyl cytosine in plant genomes occurs in all sequence contexts, especially in heterochromatin, transposons and other repeats. During replication, nascent cytosines in symmetric contexts (CG) are guided for methylation by hemi-methyl C on the parental DNA strands of both daughter chromatids. However nascent cytosines in the asymmetric CHH context or in symmetric CHG (where H=A, T or C) use modified histones and 24-nt small interfering RNAs to restore methylation to each daughter chromatid. Here, we use fluorescent activated sorting of EdU-labeled nuclei to examine DNA methylation dynamics in dividing cell cultures of Arabidopsis thaliana. We find that CG methylation becomes transiently asymmetric during late S phase, but is rapidly restored during each cell division, while CHG methylation remains asymmetric and is substantially reduced. Levels of mCHH are extremely low in dividing cells, accompanied by a shift from 24-nt to 21-nt epigenetically activated small RNAs (easiRNAs) and a loss of histone lysine-9 methylation. When cell division arrests, RNA-directed CHH methylation is restored, but only at loci that retained 24-nt siRNAs. Comparisons with methylation patterns in pollen suggest that DNA methylation reprogramming in microspores (G2), sperm cells (S phase) and the vegetative nucleus (which is quiescent) reflect their cell cycle stage. Our results also account for the loss of non-CG methylation in plants micropropagated as clones, which undergo methylation reprogramming in the absence of fertilization.

2020-12-03 | GSE117315 | GEO

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

2020-12-03 | GSE117316 | GEO

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-12-03 | GSE117318 | GEO

Loss of Karma transposon methylation underlies oil palm somaclonal mantling

Project description:The oil palm fruit abnormality, mantled, is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for breeding and oil production. Widely regarded as epigenetic, mantling had defied explanation, and has become an icon of unsustainability in environmentally sensitive tropical plantation crops. We identified the MANTLED gene using Epigenome Wide Association analysis of genetically identical palms from multiple clonal lineages. Hypomethylation of a LINE retrotransposon related to rice Karma, found in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is correlated with alternative splicing and loss of small RNA. DNA methylation is regained in spontaneous revertants accounting for non-Medelian inheritance of the Good Karma and Bad Karma epialleles. Thus epigenetic regulation of transposable elements results in somaclonal variation and provides a means to cull mantled nursery palms before committing limiting plantation resources to clonal propagation. DNA methylation profiling was performed using the McrBC DNA methylation dependent fractionation and microarray hybridization method as described in Lippman, Z., Gendrel, A. V., Colot, V. & Martienssen, R. Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods 2, 219-224 (2005). DNA methylation profiling was performed on 54 parthenocarpic mantled ramet, 43 normal ramet and 1 ortet adult leaf samples. For each sample, two independent fractionations of total genomic DNA and DNA methylation-depleted DNA were performed. Each total DNA/methylation-depleted DNA pair was differentially labeled and hydrized to a custon Nimblegen microarray in a dye-swapped design (4 array hybridizations per sample).

2015-09-09 | E-GEOD-68410 | biostudies-arrayexpress

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