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Genome Biol. 2017 Sep 15;18(1):171. doi: 10.1186/s13059-017-1251-x.

Dynamic DNA methylation reconfiguration during seed development and germination.

Author information

1
Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
2
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
3
Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan.
4
Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. ecker@salk.edu.
5
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. ecker@salk.edu.
6
Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. ecker@salk.edu.

Abstract

BACKGROUND:

Unlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of gene expression and genome integrity. In animals, reprogramming erases and re-establishes DNA methylation during development. However, knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. To better understand epigenetic reconfiguration in the embryo, which forms the plant body, we compared time-series methylomes of dry and germinating seeds to publicly available seed development methylomes.

RESULTS:

Time-series whole genome bisulfite sequencing reveals extensive gain of CHH methylation during seed development and drastic loss of CHH methylation during germination. These dynamic changes in methylation mainly occur within transposable elements. Active DNA methylation during seed development depends on both RNA-directed DNA methylation and heterochromatin formation pathways, whereas global demethylation during germination occurs in a passive manner. However, an active DNA demethylation pathway is initiated during late seed development.

CONCLUSIONS:

This study provides new insights into dynamic DNA methylation reprogramming events during seed development and germination and suggests possible mechanisms of regulation. The observed sequential methylation/demethylation cycle suggests an important role of DNA methylation in seed dormancy.

KEYWORDS:

Arabidopsis thaliana; DNA methylation; Dry seed; Embryogenesis; Germination

PMID:
28911331
PMCID:
PMC5599895
DOI:
10.1186/s13059-017-1251-x
[Indexed for MEDLINE]
Free PMC Article

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