Dynamic Changes in DNA Methylation Occur in TE Regions and Affect Cell Proliferation During Leaf-to-callus Transition in Arabidopsis

Overview

Journal Epigenetics

Specialty Genetics

Date 2021 Jan 7

PMID 33406971

Citations 14

Authors

Sangrea Shim

Hong Gil Lee

Ok-Sun Park

Hosub Shin

Kyounghee Lee

Hongwoo Lee

Jin Hoe Huh

Pil Joon Seo

Affiliations

Soon will be listed here.

Abstract

Plant somatic cells can be reprogrammed into pluripotent cell mass, called callus, through a two-step tissue culture method. Incubation on callus-inducing medium triggers active cell proliferation to form a pluripotent callus. Notably, DNA methylation is implicated during callus formation, but a detailed molecular process regulated by DNA methylation remains to be fully elucidated. Here, we compared genome-wide DNA methylation profiles between leaf and callus tissues in using whole-genome bisulphite-sequencing. Global distribution of DNA methylation showed that CHG methylation was increased, whereas CHH methylation was reduced especially around transposable element (TE) regions during the leaf-to-callus transition. We further analysed differentially expressed genes around differentially methylated TEs (DMTEs) during the leaf-to-callus transition and found that genes involved in cell cycle regulation were enriched and also constituted a coexpression gene network along with pluripotency regulators. In addition, a conserved DNA sequence analysis for upstream -elements led us to find a putative transcription factor associated with cell fate transition. CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) was newly identified as a regulator of plant regeneration, and consistently, the mutant displayed altered phenotypes in callus proliferation. Overall, these results suggest that DNA methylation coordinates cell cycle regulation during callus formation, and CCA1 may act as a key upstream coordinator at least in part in the processes.

Citing Articles

The DNA methylation-demethylation balance prevents development of multiple megaspore mother cells in Arabidopsis.

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DEMETER DNA demethylase reshapes the global DNA methylation landscape and controls cell identity transition during plant regeneration.

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