Genome-wide analysis of day/night DNA methylation differences in Populus nigra

Ding, Changjun; Liang, Lisong; Su, Xiaohua; Zhang, Bingyu

doi:10.1371/journal.pone.0190299

Cited by 22 publications

(19 citation statements)

References 41 publications

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“…The relationship between the gene expression and methylation level was not linear in our study; 109 of 254 DEG-DMR pairs showed negative regulation. This result was consistent with the previous MeDIP-seq studies [ 15 , 16 ], such as Hu et al [ 16 ] found that down-regulated genes did not show significant hypermethylation. The negative regulations of DEG-DMR pairs might due to other regulatory mechanisms, such as DNA hypermethylation of DNA methylation monitoring sequence (MEMS) in the promoter of the ROS1 could concomitantly increase ROS1 expression [ 53 ].…”

Section: Discussionsupporting

confidence: 93%

“…Recently, Yan et al [ 14 ] reported that rice mutants exhibited abnormal spikelets or male sterility as well as SNPs in important meiosis-related genes. Immunoprecipitation of methylated DNA by monoclonal antibodies specific to 5-methylcytidine sequencing (MeDIP-Seq) can be used to detect methylated DNA in whole genomes and has been utilized in rice, maize and poplar [ 15 – 17 ]. Hypermethylation was identified in PA64S (sterile) rice compared to PA64S (fertile); and 1258 differentially methylated regions (DMRs) were identified between them [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice

Jiao

et al. 2018

PLoS ONE

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Autotetraploid rice is a useful germplasm with high biomass production; however, low fertility is the main barrier in commercial utilization. In our previous study, differential expression of meiosis-related miRNAs was found to be involved in the pollen sterility of autotetraploid rice. However, genome-wide DNA variations and methylomes associated with low fertility of autotetraploid rice are still poorly understood. Here, we measured both global DNA variations and the methylome and compared them with the transcriptome during pollen development in autotetraploid rice by high-throughput sequencing. A total of 34416 SNPs, 6993 InDels, 1003 SVs and 25 CNVs were detected, and 11367 and 41117 differentially methylated regions showed hypermethylation and hypomethylation in 02428-4x. In total, 1110 genes displayed differentially expression in 02428-4x during meiosis, of these six harbored CNVs, including four upregulated genes with gain CNVs, such as LOC_Os11g38620. We identified 122 genes by comparing with the previous data that might be associated with low fertility during pollen development in 02428-4x. Of the 122 gens, 98 were displayed methylation and differential expression, including OsMADS98, CYP703A3 and OsABCG26. The downregulation of these three genes were confirmed by qPCR during meiosis of 02428-4x, which played pivotal roles in pollen fertility. These results indicate that the low fertility of autotetraploid rice is not only caused by the differential expression of genes involved in pollen development, but also by sequence variation and differential methylation, suggesting that the reason for pollen sterility in autotetraploid rice is complex and might be affected by multiple factors.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice

Jiao

et al. 2018

PLoS ONE

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“…Genomic DNA from 40 dry seeds per sample was extracted using DNeasy Plant Kit (Qiagen) and was sheared to about 500 bp by sonication. Sheared DNA was immunoprecipitated using MagMeDIP Methylated DNA Immunoprecipitation Kit as described by the manufacturer's protocol and a previous study applied to plant samples 51 . Immunoprecipitated DNA was subjected to qRT-PCR using SYBR using the same specific primers as Chop-qPCR.…”

Section: Methodsmentioning

confidence: 99%

Mechanism of delayed seed germination caused by high temperature during grain filling in rice (Oryza sativa L.)

Suriyasak

Oyama

Ishida

et al. 2020

Sci Rep

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High temperature during grain filling considerably reduces yield and quality in rice (Oryza sativa L.); however, how high temperature affects seed germination of the next generation is not yet well understood. Here, we report that seeds from plants exposed to high temperature during the grain filling stage germinated significantly later than seeds from unstressed plants. This delay remained even after dormancy release treatments, suggesting that it was not due to primary seed dormancy determined during grain filling. In imbibed embryos of heat-stressed seeds, expression of abscisic acid (ABA) biosynthesis genes (OsNCEDs) was higher than in those of control seeds, whereas that of ABA catabolism genes (OsABA8′OHs) was lower. In the aleurone layer, despite no change in GA signaling as evidenced by no effect of heat stress on OsGAMYB gene expression, the transcripts of α-amylase genes OsAmy1C, OsAmy3B, and OsAmy3E were significantly down-regulated in heat-stressed seeds in comparison with controls. Changes in promoter methylation levels were consistent with transcriptional changes of ABA catabolism-related and α-amylase genes. These data suggest that high temperature during grain filling results in DNA methylation of ABA catabolism-related and α-amylase gene promoters, delaying germination of heat-stressed seeds.

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“…DNA methylation, a key epigenetic modification, typically involves the addition of a methyl group to the fifth carbon of cytosine to produce 5-methylcytosine (5mC) in eukaryotic genomes [9,10]. Although the relationship between DNA methylation and its effect on gene expression is complex [11,12], an increasing body of evidence suggests that DNA methylation plays a role in various biological processes during plant growth and development [12,13], such as morphogenesis [14], gender determination [15,16], vegetative propagation [17], and response to abiotic stress [18][19][20][21]. In plants, cytosine methylation is primarily found in three sequence contexts: CG, CHG, and CHH (where H = A, T or C) [22].…”

Section: Introductionmentioning

confidence: 99%

DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems

Yang

Liu

et al. 2020

BMC Genomics

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Background: As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNAdependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation. Results: The overall average percentages of CG, CHG, and CHH methylation in poplar stems were~53.6%,~37.7%, and 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation. Conclusions: DNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.

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Genome-wide analysis of day/night DNA methylation differences in Populus nigra

Cited by 22 publications

References 41 publications

Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice

Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice

Mechanism of delayed seed germination caused by high temperature during grain filling in rice (Oryza sativa L.)

DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems

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