Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.)

Zhang, Hongyu; Ali, Asif; Hou, Feixue; Wu, Tingkai; Guo, Daiming; Zeng, Xiufeng; Wang, Fangfang; Zhao, Huixia; Chen, Xiaoqiong; Xu, Peizhou; Wu, Xiaoyun

doi:10.1186/s12870-018-1553-5

Cited by 8 publications

(8 citation statements)

References 60 publications

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“…The methylation levels varied among genic regions (Table 1) and the promoter showed the highest methylation ratio in all contexts. Our result is consistent with other species, including rice (Zhang et al, 2018a), chickpea (Bhatia, Khemka, Jain, & Garg, 2018b), lotus (Lin et al, 2019) and black poplar (Ding et al, 2018) where promoter regions were the most heavily methylated as compared to the other genic regions. In contrast, promoter regions are barely methylated in Arabidopsis (Zhang et al, 2006).…”

Section: F I G U R Esupporting

confidence: 92%

Machine learning analyses of methylation profiles uncovers tissue‐specific gene expression patterns in wheat

et al. 2020

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DNA methylation is a mechanism of epigenetic modification in eukaryotic organisms. Generally, methylation within genes promoter inhibits regulatory protein binding and represses transcription, whereas gene body methylation is associated with actively transcribed genes. However, it remains unclear whether there is interaction between methylation levels across genic regions and which site has the biggest impact on gene regulation. We investigated and used the methylation patterns of the bread wheat cultivar Chinese Spring to uncover differentially expressed genes (DEGs) between roots and leaves, using six machine learning algorithms and a deep neural network. As anticipated, genes with higher expression in leaves were mainly involved in photosynthesis and pigment biosynthesis processes whereas genes that were not differentially expressed between roots and leaves were involved in protein processes and membrane structures. Methylation occurred preponderantly (60%) in the CG context, whereas 35 and 5% of methylation occurred in CHG and CHH contexts, respectively. Methylation levels were highly correlated (r = 0.7 to 0.9) between all genic regions, except within the promoter (r = 0.4 to 0.5). Machine learning models gave a high (0.81) prediction accuracy of DEGs. There was a strong correlation (p-value = 9.20×10 −10) between all features and gene expression, suggesting that methylation across all genic regions contribute to gene regulation. However, the methylation of the promoter, the CDS and the exon in CG context was the most impactful. Our study provides more insights into the interplay between DNA methylation and gene expression and paves the way for identifying tissue-specific genes using methylation profiles.

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Section: F I G U R Esupporting

confidence: 92%

Machine learning analyses of methylation profiles uncovers tissue‐specific gene expression patterns in wheat

et al. 2020

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“…A study on rice (Oryza sativa L.) found that the relative level of DNA methylation in diploid fish was higher than that in haploid fish. The methylation in CG sequence context did not differ between haploid and diploid fish [28]. In animals, DNA methylation occurs in the CG context, and it commonly occurs within all sequence contexts (CG, CHG and CHH) in plants [29].…”

Section: Discussionmentioning

confidence: 84%

Genome-wide DNA Methylation and Gene Expression Patterns of Androgenetic Haploid Tiger Pufferfish (Takifugu Rubripes) Provide Insights into Haploid Syndrome

Wang

Zhou

et al. 2021

Preprint

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Androgenesis is an important chromosome set manipulation technique used in sex control in aquaculture. Haploid embryos exhibit haploid syndrome and show abnormalities and even die during early embryonic development. In this study, we used whole genome bisulfite sequencing (WGBS) to investigate the genome-wide DNA methylation profiles in haploid females (1n-X) and males (1n-Y), and diploid females (2n-XX) and males (2n-XY) of tiger pufferfish (Takifugu rubripes), an economically important ﬁsh in China. A total of 96.32 Gb clean data was produced. Analysis of differentially methylated regions (DMRs) showed that haploids had more hyper-methylated regions than diploids, which may be related to abnormal development and early embryonic death in haploids. There were 7,838 hyper-methylated differentially methylated genes (DMGs) and 4,755 hypo-methylated DMGs in haploid vs. diploid comparisons in both females and males. These DMGs were mainly related to genomic stability maintenance and cell cycle regulation. slf1, actr8, gas2, and pbrm1 genes were detected to validate the methylation sequencing. After combining the methylation data with the corresponding transcriptome data, we identified several genes, including guca2a, myoc, fezf2, rprml, telo2, s100a1, and marveld1, which exhibited differential expression levels modulated by DNA methylation. In conclusion, our study revealed different methylation and expression profiles between haploid and diploid T. rubripes for the first time. Several DMGs were identified between different ploidy levels, which may be related to haploid syndrome formation. The results expand the understanding of the effects of ploidy on the early development of teleosts and provide knowledge about target genes and networks to improve the survival rate of haploids.

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“…e . the DNA methylation [ 9 ]. In plants, this modification occurs in three sequence contexts: CpG, CpHpG and CpHpH (where H = A, T or C).…”

Section: Introductionmentioning

confidence: 99%

“…It is usually assumed that DNA methylation in the gene promoter and first exon leads to the reduction in gene expression [ 10 , 11 ]. Numerous properties of the plant genome such as, its morphology, stability, differentiation, gene expression, transposable elements (TEs) transposition, chromatin structure and genome protection against mutational changes were reported to be affected by methylation [ 8 , 9 ].…”

Section: Introductionmentioning

confidence: 99%

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Salt stress and salt shock differently affect DNA methylation in salt-responsive genes in sugar beet and its wild, halophytic ancestor

et al. 2021

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Here we determined the impact of salt shock and salt stress on the level of DNA methylation in selected CpG islands localized in promoters or first exons of sixteen salt-responsive genes in beets. Two subspecies differing in salt tolerance were subjected for analysis, a moderately salt-tolerant sugar beet Beta vulgaris ssp. vulgaris cv. Huzar and a halophytic beet, Beta vulgaris ssp. maritima. The CpG island methylation status was determined. All target sequences were hyper- or hypomethylated under salt shock and/or salt stress in one or both beet subspecies. It was revealed that the genomic regions analyzed were highly methylated in both, the salt treated plants and untreated controls. Methylation of the target sequences changed in a salt-dependent manner, being affected by either one or both treatments. Under both shock and stress, the hypomethylation was a predominant response in sugar beet. In Beta vulgaris ssp. maritima, the hypermethylation occurred with higher frequency than hypomethylation, especially under salt stress and in the promoter-located CpG sites. Conversely, the hypomethylation of the promoter-located CpG sites predominated in sugar beet plants subjected to salt stress. This findings suggest that DNA methylation may be involved in salt-tolerance and transcriptomic response to salinity in beets.

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Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.)

Cited by 8 publications

References 60 publications

Machine learning analyses of methylation profiles uncovers tissue‐specific gene expression patterns in wheat

Machine learning analyses of methylation profiles uncovers tissue‐specific gene expression patterns in wheat

Genome-wide DNA Methylation and Gene Expression Patterns of Androgenetic Haploid Tiger Pufferfish (Takifugu Rubripes) Provide Insights into Haploid Syndrome

Salt stress and salt shock differently affect DNA methylation in salt-responsive genes in sugar beet and its wild, halophytic ancestor

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