Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development

Proceedings of the National Academy of Sciences of the United States of America
Jer-Young LinRobert B Goldberg

Abstract

We profiled soybean and Arabidopsis methylomes from the globular stage through dormancy and germination to understand the role of methylation in seed formation. CHH methylation increases significantly during development throughout the entire seed, targets primarily transposable elements (TEs), is maintained during endoreduplication, and drops precipitously within the germinating seedling. By contrast, no significant global changes in CG- and CHG-context methylation occur during the same developmental period. An Arabidopsis ddcc mutant lacking CHH and CHG methylation does not affect seed development, germination, or major patterns of gene expression, implying that CHH and CHG methylation does not play a significant role in seed development or in regulating seed gene activity. By contrast, over 100 TEs are transcriptionally de-repressed in ddcc seeds, suggesting that the increase in CHH-context methylation may be a failsafe mechanism to reinforce transposon silencing. Many genes encoding important classes of seed proteins, such as storage proteins, oil biosynthesis enzymes, and transcription factors, reside in genomic regions devoid of methylation at any stage of seed development. Many other genes in these classes have similar me...Continue Reading

Associated Datasets

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Citations

Dec 22, 2017·The Plant Journal : for Cell and Molecular Biology·Wu JiaoZ Jeffrey Chen
May 31, 2020·Plants·Kai Katsuya-GaviriaRaquel Iglesias-Fernández
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Dec 25, 2021·Genome Research·Chenxin LiVenkatesan Sundaresan

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Datasets Mentioned

BETA
GSE29134

Methods Mentioned

BETA
laser capture microdissection
BS-Seq
dissection
RNA-Seq
methylome sequencing

Software Mentioned

Bowtie
genome
EdgeR
BS Seeker

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