scholarly journals Maternal components of RNA ‐directed DNA methylation are required for seed development in Brassica rapa

2018 ◽  
Vol 94 (4) ◽  
pp. 575-582 ◽  
Author(s):  
Jeffrey W. Grover ◽  
Timmy Kendall ◽  
Abdul Baten ◽  
Diane Burgess ◽  
Michael Freeling ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Seed Development ◽  
Brassica Rapa

scholarly journals Embryo CHH hypermethylation is mediated by RdDM and is autonomously directed in Brassica rapa

2020 ◽  
Author(s):  
Tania Chakraborty ◽  
Timmy Kendall ◽  
Jeffrey W. Grover ◽  
Rebecca A. Mosher
Keyword(s):  
Dna Methylation ◽  
Seed Development ◽  
Embryo Development ◽  
Brassica Rapa ◽  
Small Rnas ◽  
Cytosine Methylation ◽  
Mature Plant ◽  
Seed Abortion ◽  
Compelling Evidence ◽  
Methylation Patterns

AbstractBackgroundRNA directed DNA methylation (RdDM) initiates cytosine methylation in all contexts, and maintains asymmetric CHH methylation (where H is any base other than G). Mature plant embryos show one of the highest levels of CHH methylation, and it has been suggested that RdDM is responsible for this hypermethylation. Because loss of RdDM in Brassica rapa causes seed abortion, embryo methylation might play a role in seed development. RdDM is required in the maternal sporophyte, suggesting that small RNAs from the maternal sporophyte might translocate to the developing embryo, triggering DNA methylation that prevents seed abortion. This raises the question whether embryo hypermethylation is autonomously regulated by the embryo itself or influenced by the maternal sporophyte.ResultsHere, we demonstrate that B. rapa embryos are hypermethylated in both euchromatin and heterochromatin and that this process requires RdDM. Contrary to current models, B. rapa embryo hypermethylation is not correlated with demethylation of the endosperm. We also show that maternal somatic RdDM is not sufficient for global embryo hypermethylation, and we find no compelling evidence for maternal somatic influence over embryo methylation at any locus. Decoupling of maternal and zygotic RdDM leads to successful seed development despite loss of embryo CHH hypermethylation.ConclusionsWe conclude that embryo CHH hypermethylation is conserved, autonomously controlled, and not required for embryo development. Furthermore, maternal somatic RdDM, while required for seed development, does not directly influence embryo methylation patterns.

DNA Methylation of Seed in Response to Heat Stress in Brassica rapa L.

2011 ◽  
Vol 37 (9) ◽  
pp. 1597-1604 ◽  
Author(s):  
Gui-Zhen GAO ◽  
Fei YING ◽  
Bi-Yun CHEN ◽  
Hao LI ◽  
Xiao-Dan LÜ ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Heat Stress ◽  
Brassica Rapa

scholarly journals DNA Methylation Alterations at 5′-CCGG Sites in the Interspecific and Intraspecific Hybridizations Derived from Brassica rapa and B. napus

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e65946 ◽  
Author(s):  
Wanshan Xiong ◽  
Xiaorong Li ◽  
Donghui Fu ◽  
Jiaqin Mei ◽  
Qinfei Li ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brassica Rapa

scholarly journals Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

DNA Research ◽  
2018 ◽  
Vol 25 (5) ◽  
pp. 511-520 ◽  
Author(s):  
Satoshi Takahashi ◽  
Kenji Osabe ◽  
Naoki Fukushima ◽  
Shohei Takuno ◽  
Naomi Miyaji ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brassica Rapa ◽  
Small Rna ◽  
Histone H3 ◽  
Rna Expression ◽  
Genome Wide

scholarly journals Dynamic Changes of Genome-Wide DNA Methylation during Soybean Seed Development

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Yong-qiang Charles An ◽  
Wolfgang Goettel ◽  
Qiang Han ◽  
Arthur Bartels ◽  
Zongrang Liu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Seed Development ◽  
Soybean Seed ◽  
Dynamic Changes ◽  
Genome Wide

Changes in DNA methylation levels during seed development in Jatropha curcas

2016 ◽  
Vol 95 (S1) ◽  
pp. 13-18 ◽  
Author(s):  
PRATIMA PANDEY ◽  
ANOOP ANAND MALIK ◽  
KAMLESH KUMAR ◽  
MADAN SINGH NEGI ◽  
SHASHI BHUSHAN TRIPATHI
Keyword(s):  
Dna Methylation ◽  
Seed Development ◽  
Jatropha Curcas

scholarly journals Seed Genome Hypomethylated Regions Are Enriched In Transcription Factor Genes

2018 ◽  
Author(s):  
Min Chen ◽  
Jer-Young Lin ◽  
Jungim Hur ◽  
Julie M. Pelletier ◽  
Russell Baden ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Seed Development ◽  
Mammalian Cells ◽  
Fatty Acid Biosynthesis ◽  
Developmental Stages ◽  
Storage Proteins ◽  
Seed Formation ◽  
Epigenetic Events ◽  
Transcription Factor Genes

AbstractThe precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators, such as ABI3 and FUS3, are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes, and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from post-fertilization through dormancy and germination for regions that contain < 5% or < 0.4% bulk methylation in CG-, CHG-, and CHH-contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5 to 76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor genes, and other developmental genes, that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue - and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development - probably by the action of specific transcription factors and epigenetic events at the chromatin level.SignificanceWe scanned soybean and Arabidopsis seed genomes for hypomethylated regions, or DNA Methylation Valleys (DMVs), present in mammalian cells. A significant fraction of seed genomes contain DMV regions that have < 5% bulk DNA methylation, or, in many cases, no detectable DNA methylation. Methylation levels of seed DMVs do not vary detectably during seed development with respect to time, region, and tissue, and are present prior to fertilization. Seed DMVs are enriched in transcription factor genes and other genes critical for seed development, and are also decorated with histone marks that fluctuate with developmental stage, resembling in significant ways their animal counterparts. We conclude that many genes playing important roles in seed formation are regulated in the absence of detectable DNA methylation events, and suggest that selective action of transcriptional activators and repressors, as well as chromatin epigenetic events play important roles in making a seed - particularly embryo formation.

scholarly journals Parent-of-origin effects on seed development in Arabidopsis thaliana require DNA methylation

Development ◽  
2000 ◽  
Vol 127 (11) ◽  
pp. 2493-2502 ◽  
Author(s):  
S. Adams ◽  
R. Vinkenoog ◽  
M. Spielman ◽  
H.G. Dickinson ◽  
R.J. Scott
Keyword(s):  
Dna Methylation ◽  
Seed Development ◽  
High Weight ◽  
Transgenic Arabidopsis ◽  
Parental Genome ◽  
Wild Type ◽  
Low Weight ◽  
Parental Imprinting ◽  
Parent Of Origin ◽  
Origin Effects

Some genes in mammals and flowering plants are subject to parental imprinting, a process by which differential epigenetic marks are imposed on male and female gametes so that one set of alleles is silenced on chromosomes contributed by the mother while another is silenced on paternal chromosomes. Therefore, each genome contributes a different set of active alleles to the offspring, which develop abnormally if the parental genome balance is disturbed. In Arabidopsis, seeds inheriting extra maternal genomes show distinctive phenotypes such as low weight and inhibition of mitosis in the endosperm, while extra paternal genomes result in reciprocal phenotypes such as high weight and endosperm overproliferation. DNA methylation is known to be an essential component of the parental imprinting mechanism in mammals, but there is less evidence for this in plants. For the present study, seed development was examined in crosses using a transgenic Arabidopsis line with reduced DNA methylation. Crosses between hypomethylated and wild-type diploid plants produced similar seed phenotypes to crosses between plants with normal methylation but different ploidies. This is consistent with a model in which hypomethylation of one parental genome prevents silencing of alleles that would normally be active only when inherited from the other parent - thus phenocopying the effects of extra genomes. These results suggest an important role for methylation in parent-of-origin effects, and by inference parental imprinting, in plants. The phenotype of biparentally hypomethylated seeds is less extreme than the reciprocal phenotypes of uniparentally hypomethylated seeds. The observation that development is less severely affected if gametes of both sexes (rather than just one) are ‘neutralized’ with respect to parent-of-origin effects supports the hypothesis that parental imprinting is not necessary to regulate development.

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