RNA directed DNA methylation and seed plant genome evolution

Mbichi, Ruth Wambui; Wang, Qingfeng; Wan, Tao

doi:10.1007/s00299-020-02558-4

Cited by 21 publications

(13 citation statements)

References 74 publications

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“…Our results show that although the tea plant genome is rich in TEs, the TEs within the tea plant genome were found to be highly methylated. A likely explanation is that the transcriptional suppression of TEs in tea plant by DNA methylation allows them to accumulate high copy numbers with minimal deleterious consequences to the host (Deniz et al, 2019; Wambui Mbichi et al, 2020), which thereby helps to maintain the genomic stability of the tea plant.…”

Section: Discussionmentioning

confidence: 99%

Divergent DNA methylation contributes to duplicated gene evolution and chilling response in tea plants

Tong

Huang

et al. 2021

The Plant Journal

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Summary The tea plant (Camellia sinensis) is a thermophilic cash crop and contains a highly duplicated and repeat‐rich genome. It is still unclear how DNA methylation regulates the evolution of duplicated genes and chilling stress in tea plants. We therefore generated a single‐base‐resolution DNA methylation map of tea plants under chilling stress. We found that, compared with other plants, the tea plant genome is highly methylated in all three sequence contexts, including CG, CHG and CHH (where H = A, T, or C), which is further proven to be correlated with its repeat content and genome size. We show that DNA methylation in the gene body negatively regulates the gene expression of tea plants, whereas non‐CG methylation in the flanking region enables a positive regulation of gene expression. We demonstrate that transposable element‐mediated methylation dynamics significantly drives the expression divergence of duplicated genes in tea plants. The DNA methylation and expression divergence of duplicated genes in the tea plant increases with evolutionary age and selective pressure. Moreover, we detect thousands of differentially methylated genes, some of which are functionally associated with chilling stress. We also experimentally reveal that DNA methyltransferase genes of tea plants are significantly downregulated, whereas demethylase genes are upregulated at the initial stage of chilling stress, which is in line with the significant loss of DNA methylation of three well‐known cold‐responsive genes at their promoter and gene body regions. Overall, our findings underscore the importance of DNA methylation regulation and offer new insights into duplicated gene evolution and chilling tolerance in tea plants.

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Section: Discussionmentioning

confidence: 99%

Divergent DNA methylation contributes to duplicated gene evolution and chilling response in tea plants

Tong

Huang

et al. 2021

The Plant Journal

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“…To prevent this threat, DNA methylation mechanisms can be triggered by various mechanisms [ 66 ]. DNA methylation was considered one of the key components in understanding divergence in genome evolution among plants [ 67 ]. The expansion of wheat DMT genes might contribute to the large genome size of wheat.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and transcriptional characterization of DNA methyltransferases conferring temperature-sensitive male sterility in wheat

Feng

Liu

et al. 2021

BMC Genomics

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Background DNA methyltransferase (DMT) genes contribute to plant stress responses and development by de novo establishment and subsequent maintenance of DNA methylation during replication. The photoperiod and/or temperature-sensitive genic male sterile (P/TGMS) lines play an important role in hybrid seed production of wheat. However, only a few studies have reported on the effect of DMT genes on temperature-sensitive male sterility of wheat. Although DMT genes have been investigated in some plant species, the identification and analysis of DMT genes in wheat (Triticum aestivum L.) based on genome-wide levels have not been reported. Results In this study, a detailed overview of phylogeny of 52 wheat DMT (TaDMT) genes was presented. Homoeolog retention for TaDMT genes was significantly above the average retention rate for whole-wheat genes, indicating the functional importance of many DMT homoeologs. We found that the strikingly high number of TaDMT genes resulted mainly from the significant expansion of the TaDRM subfamily. Intriguingly, all 5 paralogs belonged to the wheat DRM subfamily, and we speculated that tandem duplications might play a crucial role in the TaDRM subfamily expansion. Through the transcriptional analysis of TaDMT genes in a TGMS line BS366 and its hybrids with the other six fertile lines under sterile and fertile conditions, we concluded that TaCMT-D2, TaMET1-B1, and TaDRM-U6 might be involved in male sterility in BS366. Furthermore, a correlation analysis showed that TaMET1-B1 might negatively regulate the expression of TaRAFTIN1A, an important gene for pollen development, so we speculated regarding an epigenetic regulatory mechanism underlying the male sterility of BS366 via the interaction between TaMET1-B1 and TaRAFTIN1A. Conclusions Our findings presented a detailed phylogenic overview of the DMT genes and could provide novel insights into the effects of DMT genes on TGMS wheat.

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“…, 2015; Wambui Mbichi et al. , 2020), the features of the regions that overlapped with the 24‐nt siRNA‐covered regions were examined. It was found that over 62% of Fe‐deficiency‐induced hyper CHH‐DMRs overlapped with the 24‐nt siRNA clusters in both roots and shoots (Figure 5c).…”

Section: Resultsmentioning

confidence: 99%

DNA methylation is involved in acclimation to iron‐deficiency in rice (Oryza sativa)

et al. 2021

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SUMMARY Iron (Fe) is an essential micronutrient in plants, and Fe limitation significantly affects plant growth, yield and food quality. While many studies have reported the transcriptomic profile and pursue molecular mechanism in response to Fe limitation, little is known if epigenetic factors play a role in response to Fe‐deficiency. In this study, whole‐genome bisulfite sequencing analysis, high‐throughput RNA‐Seq of mRNA, small RNA and transposable element (TE) expression with root and shoot organs of rice seedlings under Fe‐sufficient and Fe‐deficient conditions were performed. The results showed that widespread hypermethylation, especially for the CHH context, occurred after Fe‐deficiency. Integrative analysis of methylation and transcriptome revealed that the transcript abundance of Fe‐deficiency‐induced genes was negatively correlated with nearby TEs and positively with the 24‐nucleotide siRNAs. The ability of methylation to affect the physiology and molecular response to Fe‐deficiency was tested using an exogenous DNA methyltransferase inhibitor (5‐azacytidine), and genetically using a mutant for domains rearranged methyltransferase 2 (DRM2), that lacks CHH methylation. Both approaches resulted in decreased growth and Fe content in rice plants. Thus, alterations in specific methylation patterns, directed by siRNAs, play an important role in acclimation of rice to Fe‐deficient conditions. Furthermore, comparison with other reports suggests this may be a universal mechanism to acclimate to limited nutrient availability.

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RNA directed DNA methylation and seed plant genome evolution

Cited by 21 publications

References 74 publications

Divergent DNA methylation contributes to duplicated gene evolution and chilling response in tea plants

Divergent DNA methylation contributes to duplicated gene evolution and chilling response in tea plants

Genome-wide identification and transcriptional characterization of DNA methyltransferases conferring temperature-sensitive male sterility in wheat

DNA methylation is involved in acclimation to iron‐deficiency in rice (Oryza sativa)

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