Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.)

Ahmad, Fiaz; Huang, Xunhe; Lan, Hongxia; Huma, Tayyaba; Bao, Yuxin; Huang, Junjun; Zhang, H S

doi:10.4238/2014.july.7.9

Cited by 36 publications

(29 citation statements)

References 41 publications

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“…Rice contains 10 DMT family members that can be phylogenetically classified into CMT, MET ( DNMT1‐like ), DNMT2‐like and DRM ( DNMT3‐like ) clades (Chen & Zhou ; Ahmad et al . ; Qian et al . ; Fig.…”

Section: Resultsmentioning

confidence: 99%

Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium

Feng

Liu

Tao

et al. 2016

Plant Cell & Environment

158

101

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We report genome-wide single-base resolution maps of methylated cytosines and transcriptome change in Cd-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between Cd-exposed and Cd-free rice genomes. There are 2320 non-redundant differentially methylated regions detected in the genome. RNA sequencing revealed 2092 DNA methylation-modified genes differentially expressed under Cd exposure. More genes were found hypermethylated than those hypomethylated in CG, CHH and CHG (where H is A, C or T) contexts in upstream, gene body and downstream regions. Many of the genes were involved in stress response, metal transport and transcription factors. Most of the DNA methylation-modified genes were transcriptionally altered under Cd stress. A subset of loss of function mutants defective in DNA methylation and histone modification activities was used to identify transcript abundance of selected genes. Compared with wide type, mutation of MET1 and DRM2 resulted in general lower transcript levels of the genes under Cd stress. Transcripts of OsIRO2, OsPR1b and Os09g02214 in drm2 were significantly reduced. A commonly used DNA methylation inhibitor 5-azacytidine was employed to investigate whether DNA demethylation affected physiological consequences. 5-azacytidine provision decreased general DNA methylation levels of selected genes, but promoted growth of rice seedlings and Cd accumulation in rice plant.

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Section: Resultsmentioning

confidence: 99%

Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium

Feng

Liu

Tao

et al. 2016

Plant Cell & Environment

158

101

View full text Add to dashboard Cite

show abstract

“…Expression change of genes involved in DNA methylation pathways has been reported for other abiotic constraints. For example, high temperature induces a coordinated up-regulation of RdDM genes such as Drm2, NRPD1 and NRPE1 in Arabidopsis (Naydenov et al 2015), and osmotic stress reduces the expression of Met1 and Cmt3 orthologs in rice roots and shoots (Ahmad et al 2014). In maize, four of the expressed methyltransferases (ZmMet1a, ZmMet1b, ZmMet2a and ZmMet2b) showed decreased expression levels in leaves after drought and salt stress (Qian et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Low temperature triggers genome-wide hypermethylation of transposable elements and centromeres in maize

Achour

Joets

et al. 2019

Preprint

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telephone: +33 1 69 33 23 57. RUNNING TITLECold triggers hypermethylation of maize transposons ABSTRACT Characterizing the molecular processes developed by plants to respond to environmental cues is a major task to better understand local adaptation. DNA methylation is a chromatin mark involved in the transcriptional silencing of transposable elements (TEs) and gene expression regulation. While the molecular bases of DNA methylation regulation are now well described, involvement of DNA methylation in plant response to environmental cues remains poorly characterized. Here, using the TErich maize genome and analyzing methylome response to prolonged cold at the chromosome and feature scales, we investigate how genomic architecture affects methylome response to stress in a cold-sensitive genotype. Interestingly, we show that cold stress induces a genome-wide methylation increase through the hypermethylation of TE sequences and centromeres. Our work highlights a cytosine context-specific response of TE methylation that depends on TE types, chromosomal location and proximity to genes. The patterns observed can be explained by the parallel transcriptional activation of multiple DNA methylation pathways that methylate TEs in the various chromatin locations where they reside. Our results open new insights into the possible role of genome-wide DNA methylation in phenotypic response to stress. A B C

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“…8). The decreased DNA methylation may be caused by the increased JA level and the further study is needed6566.…”

Section: Discussionmentioning

confidence: 99%

Transcript profile analysis reveals important roles of jasmonic acid signalling pathway in the response of sweet potato to salt stress

Zhang

Zhai

et al. 2017

Sci Rep

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Sweet potato is an important food and bio-energy crop, and investigating the mechanisms underlying salt tolerance will provide information for salt-tolerant breeding of this crop. Here, the root transcriptomes of the salt-sensitive variety Lizixiang and the salt-tolerant line ND98 were compared to identify the genes and pathways involved in salt stress responses. In total, 8,744 and 10,413 differentially expressed genes (DEGs) in Lizixiang and ND98, respectively, were involved in salt responses. A lower DNA methylation level was detected in ND98 than in Lizixiang. In both genotypes, the DEGs, which function in phytohormone synthesis and signalling and ion homeostasis, may underlie the different degrees of salt tolerance. Significant up-regulations of the genes involved in the jasmonic acid (JA) biosynthesis and signalling pathways and ion transport, more accumulation of JA, a higher degree of stomatal closure and a lower level of Na+ were found in ND98 compared to Lizixiang. This is the first report on transcriptome responses to salt tolerance in sweet potato. These results reveal that the JA signalling pathway plays important roles in the response of sweet potato to salt stress. This study provides insights into the mechanisms and genes involved in the salt tolerance of sweet potato.

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Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.)

Cited by 36 publications

References 41 publications

Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium

Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium

Low temperature triggers genome-wide hypermethylation of transposable elements and centromeres in maize

Transcript profile analysis reveals important roles of jasmonic acid signalling pathway in the response of sweet potato to salt stress

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