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

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 ex...

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Autores principales: Zuo, Jinhua, Wang, Yunxiang, Zhu, Benzhong, Luo, Yunbo, Wang, Qing, Gao, Lipu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977206/
https://www.ncbi.nlm.nih.gov/pubmed/29883429
http://dx.doi.org/10.3390/genes9050266
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author Zuo, Jinhua
Wang, Yunxiang
Zhu, Benzhong
Luo, Yunbo
Wang, Qing
Gao, Lipu
author_facet Zuo, Jinhua
Wang, Yunxiang
Zhu, Benzhong
Luo, Yunbo
Wang, Qing
Gao, Lipu
author_sort Zuo, Jinhua
collection PubMed
description 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.
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spelling pubmed-59772062018-05-31 Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit Zuo, Jinhua Wang, Yunxiang Zhu, Benzhong Luo, Yunbo Wang, Qing Gao, Lipu Genes (Basel) Article 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. MDPI 2018-05-21 /pmc/articles/PMC5977206/ /pubmed/29883429 http://dx.doi.org/10.3390/genes9050266 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zuo, Jinhua
Wang, Yunxiang
Zhu, Benzhong
Luo, Yunbo
Wang, Qing
Gao, Lipu
Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit
title Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit
title_full Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit
title_fullStr Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit
title_full_unstemmed Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit
title_short Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit
title_sort comparative analysis of dna methylation reveals specific regulations on ethylene pathway in tomato fruit
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977206/
https://www.ncbi.nlm.nih.gov/pubmed/29883429
http://dx.doi.org/10.3390/genes9050266
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