Format

Send to

Choose Destination
Gene. 2014 Oct 25;550(2):230-7. doi: 10.1016/j.gene.2014.08.034. Epub 2014 Aug 20.

Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum.

Author information

1
College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
2
College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China. Electronic address: zbz@cau.edu.cn.

Abstract

Recent studies have reported that decreased level of DNA cytosine methylation in the global genome was closely related to the initiation of tomato (Solanum lycopersicum) fruit ripening. However, genome-scale analysis of cytosine-5 DNA methyltransferases (C5-MTases) and demethylases in tomato has not been engaged. In this study, 7 C5-MTases and 3 demethylases were identified in tomato genome, which probably contributed to DNA cytosine methylation level in tomato. The 7 C5-MTases were categorized into 4 subgroups, and the 3 demethylases were classified into 2 subgroups based on phylogenetic analyses. Comprehensive analysis of their structure and genomic localization was also performed in this paper. According to online RNA-seq data, 4 S. lycopersicum C5-MTase (SlC5-MTase) genes (SlMET, SlDRM1L1, SlDRM5, SlMET3L) were expressed higher than others, and one DNA demethylase gene (SlDML) was significantly changed during tomato fruit development and ripening. Furthermore, all these five gene expressions at breaker (BK) stage changed with 1-methylcyclopropene (1-MCP) treatment, indicating that they were regulated by ethylene directly or indirectly in tomato fruit. In addition, subcellular localization analysis indicated that SlDRM1L1 and SlDRM5 located in the nucleus might have responsibility for RNA-directed DNA methylation (RdDM). Collectively, this paper provided a framework for gene discovery and functional characterization of C5-MTases and DNA demethylases in other Solanaceae species.

KEYWORDS:

DNA methylation; Phylogenetic analyses; Subcellular localization; Tomato fruit ripening

PMID:
25149677
DOI:
10.1016/j.gene.2014.08.034
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Elsevier Science
Loading ...
Support Center