Dataset Information

Genomic methylation patterns in pre-meiotic gynoecia of wild-type and RdDM mutants of Arabidopsis.

ABSTRACT:

Introduction

Although DNA methylation patterns are generally considered to be faithfully inherited in Arabidopsis thaliana (Arabidopsis), there is evidence of reprogramming during both male and female gametogenesis. The gynoecium is the floral reproductive organ from which the ovules develop and generate meiotically derived cells that give rise to the female gametophyte. It is not known whether the gynoecium can condition genomic methylation in the ovule or the developing female gametophyte.

Methods

We performed whole genome bisulfite sequencing to characterize the methylation patterns that prevail in the genomic DNA of pre-meiotic gynoecia of wild-type and three mutants defective in genes of the RNA-directed DNA methylation pathway (RdDM): ARGONAUTE4 (AGO4), ARGONAUTE9 (AGO9), and RNA-DEPENDENT RNA POLYMERASE6 (RDR6).

Results

By globally analyzing transposable elements (TEs) and genes located across the Arabidopsis genome, we show that DNA methylation levels are similar to those of gametophytic cells rather than those of sporophytic organs such as seedlings and rosette leaves. We show that none of the mutations completely abolishes RdDM, suggesting strong redundancy within the methylation pathways. Among all, ago4 mutation has the strongest effect on RdDM, causing more CHH hypomethylation than ago9 and rdr6. We identify 22 genes whose DNA methylation is significantly reduced in ago4, ago9 and rdr6 mutants, revealing potential targets regulated by the RdDM pathway in premeiotic gyneocia.

Discussion

Our results indicate that drastic changes in methylation levels in all three contexts occur in female reproductive organs at the sporophytic level, prior to the alternation of generations within the ovule primordium, offering a possibility to start identifying the function of specific genes acting in the establishment of the female gametophytic phase of the Arabidopsis life cycle.

SUBMITTER: Ortiz-Vasquez Q

PROVIDER: S-EPMC10040562 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Publications

Genomic methylation patterns in pre-meiotic gynoecia of wild-type and RdDM mutants of Arabidopsis.

Ortiz-Vasquez Quetzely Q León-Martínez Gloria G Barragán-Rosillo Carlos C González-Orozco Eduardo E Deans Samuel S Aldridge Billy B Vickers Martin M Feng Xiaoqi X Vielle-Calzada Jean-Philippe JP

Frontiers in plant science 20230313

<h4>Introduction</h4>Although DNA methylation patterns are generally considered to be faithfully inherited in Arabidopsis thaliana (Arabidopsis), there is evidence of reprogramming during both male and female gametogenesis. The gynoecium is the floral reproductive organ from which the ovules develop and generate meiotically derived cells that give rise to the female gametophyte. It is not known whether the gynoecium can condition genomic methylation in the ovule or the developing female gametoph ...[more]

PMID: 36993852

Similar Datasets

Project description:BackgroundSeveral studies showed genome-wide DNA methylation during Arabidopsis embryogenesis and germination. Although it has been known that the change of DNA methylation mainly occurs at CHH context mediated by small RNA-directed DNA methylation pathway during seed ripening and germination, the causality of the methylation difference exhibited in natural Arabidopsis ecotypes has not been thoroughly studied.ResultsIn this study we compared DNA methylation difference using comparative pairwise multi-omics dynamics in Columbia-0 (Col) and Cape Verde Island (Cvi) ecotypes. Arabidopsis genome was divided into two regions, common regions in both ecotypes and Col-specific regions, depending on the reads mapping of whole genome bisulfite sequencing libraries from both ecotypes. Ecotype comparison was conducted within common regions and the levels of DNA methylation on common regions and Col-specific regions were also compared. we confirmed transcriptome were relatively dynamic in stage-wise whereas the DNA methylome and small RNAome were more ecotype-dependent. While the global CG methylation remains steady during maturation and germination, we found genic CG methylation differs the most between the two accessions. We also found that ecotype-specific differentially methylated regions (eDMR) are positively correlated with ecotype-specifically expressed 24-nt small RNA clusters. In addition, we discovered that Col-specific regions enriched with transposable elements (TEs) and structural variants that tend to become hypermethylated, and TEs in Col-specific regions were longer in size, more pericentromeric, and more hypermethylated than those in the common regions. Through the analysis of RdDM machinery mutants, we confirmed methylation on Col-specific region as well as on eDMRs in common region are contributed by RdDM pathway. Lastly, we demonstrated that highly variable sequences between ecotypes (HOT regions) were also affected by RdDM-mediated regulation.ConclusionsThrough ecotype comparison, we revealed differences and similarities of their transcriptome, methylome and small RNAome both in global and local regions. We validated the contribution of RdDM causing differential methylation of common regions. Hypermethylated ecotype-specific regions contributed by RNA-directed DNA methylation pathway largely depend on the presence of TEs and copy-gain structural variations. These ecotype-specific regions are frequently associated with HOT regions, providing evolutionary insights into the epigenome dynamics within a species.

Dataset Information

Genomic methylation patterns in pre-meiotic gynoecia of wild-type and RdDM mutants of Arabidopsis.

Introduction

Methods

Results

Discussion

Publications

Genomic methylation patterns in pre-meiotic gynoecia of wild-type and RdDM mutants of Arabidopsis.

Similar Datasets

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