Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit.

Jinhua Zuo,Qing Wang,Yunbo Luo,Benzhong Zhu,Yunxiang Wang,Lipu Gao

doi:10.3390/genes9050266

Abstract

DNA methylation is an essential feature of epigenetic regulation and plays a role in various physiological and biochemical processes at CG, CHG, and CHH sites in plants. LeERF1 is an ethylene response factor (ERF) found in tomatoes which plays an important role in ethylene signal transduction. To explore the characteristics of DNA methylation in the ethylene pathway, sense-/antisense-LeERF1 transgenic tomato fruit were chosen for deep sequencing and bioinformatics parsing. The methylation type with the greatest distribution was CG, (71.60–72.80%) and CHH was found least frequently (10.70–12.50%). The level of DNA methylation was different among different tomato genomic regions. The differentially methylated regions (DMRs) and the differentially expressed genes (DEGs) were conjointly analyzed and 3030 different expressed genes were found, of which several are involved in ethylene synthesis and signaling transduction (such as ACS, ACO, MADS-Box, ERFs, and F-box). Furthermore, the relationships between DNA methylation and microRNAs (miRNAs) were also deciphered, providing basic information for the further study of DNA methylation and small RNAs involved in the ethylene pathway.

Highlights

DNA methylation is a type of epigenetic modification process that is necessary for the control of genome activity in animals and plants [1]
DNA methylation is largely considered to function in the transcriptional silencing of transposable elements (TEs) to maintain genome stability and integrity as well as possibly regulating specific genes, such as those subjected to genomic imprinting [4,11,12,13,14]
Zhongshu4) and sense-/antisense-LeERF1 transgenic tomato plants were grown in a greenhouse

Summary

Introduction

DNA methylation is a type of epigenetic modification process that is necessary for the control of genome activity in animals and plants [1]. Genes 2018, 9, 266; doi:10.3390/genes9050266 www.mdpi.com/journal/genes methyltransferase (MET1) and CHG methylation is set up mainly by the plant-specific enzyme, chromomethylase 3 (CMT3) [5,6,7]. For methylation at nonsymmetrical (CHH) sites, two important enzymes assigned as domains rearranged methyltransferases (DRM1 and DRM2) are in charge [8,9]. In this process, methylation is guided by small (typically 24 nucleotide) RNAs known as small interfering RNAs (siRNAs) [9,10]. DNA methylation is largely considered to function in the transcriptional silencing of transposable elements (TEs) to maintain genome stability and integrity as well as possibly regulating specific genes, such as those subjected to genomic imprinting [4,11,12,13,14]

Methods

Results

Conclusion