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Kong W, Li B, Wang Q, Wang B, Duan X, Ding L, Lu Y, Liu LW, La H. Analysis of the DNA methylation patterns and transcriptional regulation of the NB-LRR-encoding gene family in Arabidopsis thaliana. Plant Mol Biol 2018; 96:563-575. [PMID: 29525832 DOI: 10.1007/s11103-018-0715-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/02/2018] [Indexed: 05/26/2023]
Abstract
The relationships between transcription and methylation were revealed in Arabidopsis thaliana NB-LRR-encoding genes in wild type (Col-0) and different mutants. Plant nucleotide-binding, leucine-rich repeat (NB-LRR) proteins constitute a large family that plays predominant roles in disease resistance. However, the regulation of NB-LRR-encoding genes at the transcriptional level is still poorly understood. Recently, DNA cytosine methylation in eukaryotes has been described as serving an important function in regulating gene expression. Here, we analysed the DNA methylation patterns of NB-LRR-encoding genes in Arabidopsis thaliana in samples from a wild type (Col-0) and ago4, met1, cmt3, drm1/2, and ddm1 mutants. Our results revealed that the vast majority of the NB-LRR-encoding genes in Col-0 were methylated, and the DNA methylation occurred predominantly in the CG sequence context. Moreover, DNA methylation was widely distributed in both the promoters and the bodies of most NB-LRR-encoding genes. Our results also showed that the loss of AGO4, MET1, CMT3, DRM1/2 or DDM1 functions generally led to decreased cytosine methylation in the NB-LRR-encoding genes. Analysis of the available transcriptome data from the wild type and the met1, cmt3, drm1/2 and ddm1 mutants revealed that differences in the transcription levels between the wild type and mutants were statistically significant for 63 of the NB-LRR-encoding genes. Of these genes, 38 were significantly upregulated, and the other 25 were significantly downregulated. Some NB-LRR-encoding genes with differential expression levels, which were revealed by the mRNA-Seq data, were confirmed to be significantly upregulated or downregulated in the mutants compared to the wild type by using quantitative RT-PCR. These data suggest that some Arabidopsis NB-LRR-encoding genes are likely to be regulated by altered DNA methylation patterns.
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Affiliation(s)
- Weiwen Kong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Bin Li
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Qianqian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Bin Wang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiaoke Duan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Li Ding
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yanke Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Li-Wei Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Honggui La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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