Plant DNA Methylation Responds to Nutrient Stress
Abstract
:1. Introduction
2. Plant DNA Methylation Patterns
3. Effects of Nutrient Stress on Plant DNA Methylation
3.1. Effects of Nitrogen Stress on Plant DNA Methylation
3.2. Effects of Phosphorus Stress on Plant DNA Methylation
3.3. Effects of Other Nutrient Stresses on Plant DNA Methylation
4. Methodology of Plant DNA Methylation
5. Issues and Prospects
Author Contributions
Funding
Conflicts of Interest
References
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Element | Plant | Genome Region | Treatment | Mode of Action | Methodology | Reference |
---|---|---|---|---|---|---|
N | Arabidopsis thaliana | RDR2 | −N | RDR2 expression corrlated with morphological traits | Quantitative real-time PCR | [76] |
N | Arabidopsis thaliana | AT1G55420, AT1G55430 and AT1G55440 | −N | DNA methylation change in recognition gene regions (AT1G55420, AT1G55430 and AT1G55440) | WGBS | [77] |
N | Leymus chinensis | Genomic | −N | Cytosine methylation changes more around transposable elements | AFLP, MSAP, SSAP | [78] |
N | Rice | Genomic | −N | Heritable alteration in DNA methylation | MSAP | [64] |
N | Rice | Genomic | N content decrease by the knockdown of OsNAR2.1 | DNA methylation levels increase in OsNAR2.1 RNAi lines | WGBS, MeDIP | [79] |
N | Rice | Genomic | N content decrease in the parent seed | Plant DNA methylation changes induced by parent seed N content | WGBS | [80] |
P | Rice | Genomic | −P | DNA methylation occurred preferentially in TEs | MethylC-Seq | [82] |
P | Arabidopsis thaliana | Genomic | −P | Gene-wide methylation changes | WGBS | [83] |
P | Arabidopsis thaliana | Genomic | −P | Over 160 DMRs induce by P deficiency | Genome-Wide DNA methylation | [84] |
P | Tomato | Genomic | −P | Global methylation level increase | WGBS | [65] |
P | Populus trichocarpa | Genomic | −P | Differentially methylated miRNAs | WGBS | [85] |
P | Soybean | Genomic | −P | Differential methylation, and siRNAs modulated TE activity by guiding CHH methylation | BGS | [86] |
Zn | Maize | Genomic | −Zn | Major methylation loss, mostly in transposable elements | BGS | [87] |
Fe | Rice | Genomic | −Fe | Hypermethylation, especially for the CHH | MethylC-Seq | [88] |
Fe | Barley | Genomic | −Fe | Eleven DNA bands differently methylated the | MSAP | [89] |
S | Arabidopsis thaliana | SULTR1.1 and SULTR1.2 | −S | DNA methylation of SULTR1.1 and SULTR1.2 changes in msa1 | WGBS | [73] |
Methods | Coverage | Reference Genome | Advantage | Limitation | Reference |
---|---|---|---|---|---|
HPLC | Genomic DNA | No | Do not need a reference genome | Complicated operating system | [91] |
SSAP | CG region | No | High economic efficiency without a reference genome | Not specifically designed to detect methylation | [97] |
AFLP | CG region | No | High economic efficiency without a reference genome | Not specifically designed to detect methylation | [97] |
MSAP | CG region | No | High economic efficiency without a reference genome | Miss methylation states | [99] |
BGS | Genomic DNA | Yes | Detects the presence of 5mC at the single-nucleotide resolution accurately | Only in the specific region | [106] |
WGBS/ MethylC-Seq | Genomic DNA | Yes | High sensitivity to DNA | High price | [109] |
RRBS | Promoters and CpG islands | Yes | Efficient and accurate on the high-density and representative genes | Limited by enzyme cleavage sites | [115] |
MeDIP-Seq | CG region | Yes | Detects the CpG island of the whole genome rapidly and accurately | Cannot analyze the single base and needs correction with different densities of CpG | [116] |
MBD-Seq | CG region | Yes | Separated different DNA methylation according to CpG density | Antibodies may cross-react | [126] |
MS-SSCA | Individual CpG site | No | Fast | Primer design is complex | [128] |
Ms-SNuPE | CG region | No | Analysis of C and T content representing the degree of DNA methylation | The number of each analysis is small | [127] |
EpiTYPER™ | CG region | No | Fast and reproducible | DNA methylation status is unclear, with overlapping CpGs | [129] |
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Fan, X.; Peng, L.; Zhang, Y. Plant DNA Methylation Responds to Nutrient Stress. Genes 2022, 13, 992. https://doi.org/10.3390/genes13060992
Fan X, Peng L, Zhang Y. Plant DNA Methylation Responds to Nutrient Stress. Genes. 2022; 13(6):992. https://doi.org/10.3390/genes13060992
Chicago/Turabian StyleFan, Xiaoru, Lirun Peng, and Yong Zhang. 2022. "Plant DNA Methylation Responds to Nutrient Stress" Genes 13, no. 6: 992. https://doi.org/10.3390/genes13060992
APA StyleFan, X., Peng, L., & Zhang, Y. (2022). Plant DNA Methylation Responds to Nutrient Stress. Genes, 13(6), 992. https://doi.org/10.3390/genes13060992