Genome-Wide DNA Methylation Comparison between Brassica napus Genic Male Sterile Line and Restorer Line

Wang, Zhixin; Wu, Xiang-Ping; Wu, Zengxiang; An, Hong; Yi, Bin; Wen, Jing; Ma, Chaozhi; Shen, Jinxiong; Fu, Tingdong; Tu, Jinxing

doi:10.3390/ijms19092689

Cited by 19 publications

(24 citation statements)

References 47 publications

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“…However, studies have also shown that DNA methylation is not necessarily associated with the repression of gene expression, but exhibits the positive correlations with transcription activation instead [52]. In the study of Brassica napus, the gene expression of BnaA0724700D and BnaA08g08410D are up-regulated, although they exhibit opposite methylation patterns in their promoters [53]. In the present study, the increased methylation in CHH type were at the gene body region of Grb10, eIF4E and mTOR genes.…”

Section: Discussionsupporting

confidence: 38%

Early leucine programming on protein utilization and mTOR signaling by DNA methylation in zebrafish (Danio rerio)

Zhu

Wang

et al. 2020

Nutr Metab (Lond)

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Background: Early nutritional programming affects a series of metabolism, growth and development in mammals. Fish also exhibit the developmental plasticity by early nutritional programming. However, little is known about the effect of early amino acid programming on growth and metabolism. Methods: In the present study, zebrafish (Danio rerio) was used as the experimental animal to study whether early leucine stimulation can programmatically affect the mechanistic target of rapamycin (mTOR) signaling pathway, growth and metabolism in the later life, and to undercover the mechanism of epigenetic regulation. Zebrafish larvas at 3 days post hatching (dph) were raised with 1.0% leucine from 3 to 13 dph during the critical developmental stage, then back to normal water for 70 days (83 dph). Results: The growth performance and crude protein content of zebrafish in the early leucine programming group were increased, and consistent with the activation of the mTOR signaling pathway and the high expression of genes involved in the metabolism of amino acid and glycolipid. Furthermore, we compared the DNA methylation profiles between the control and leucine-stimulated zebrafish, and found that the methylation levels of CG-differentially methylated regions (DMGs) and CHH-DMGs of genes involved in mTOR signaling pathway were different between the two groups. With quantitative PCR analysis, the decreased methylation levels of CG type of Growth factor receptorbound protein 10 (Grb10), eukaryotic translation initiation factor 4E (eIF4E) and mTOR genes of mTOR signaling pathway in the leucine programming group, might contribute to the enhanced gene expression. Conclusions: The early leucine programming could improve the protein synthesis and growth, which might be attributed to the methylation of genes in mTOR pathway and the expression of genes involved in protein synthesis and glycolipid metabolism in zebrafish. These results could be beneficial for better understanding of the epigenetic regulatory mechanism of early nutritional programming.

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Section: Discussionsupporting

confidence: 38%

Early leucine programming on protein utilization and mTOR signaling by DNA methylation in zebrafish (Danio rerio)

Zhu

Wang

et al. 2020

Nutr Metab (Lond)

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“…It encodes a deleterious chimeric protein that localises to the chloroplast, affects normal function of the chloroplast to cause aborted anthers and albinotic seedlings, and high temperature treatment can partially restore male fertility caused by Bnams4 b Xia et al, 2016). Bnams4 a is a suppressor gene and may reduce the transcription level of Bnams4 b through DNA methylation Wang et al, 2018). Bnams4 c is a null allele .…”

Section: Introductionmentioning

confidence: 99%

Two young genes reshape a novel interaction network in Brassica napus

et al. 2019

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Summary New genes often drive the evolution of gene interaction networks. In Brassica napus, the widely used genic male sterile breeding system 7365ABC is controlled by two young genes, Bnams4b and BnaMs3. However, the interaction mechanism of these two young genes remains unclear. Here, we confirmed that Bnams4b interacts with the nuclear localised E3 ligase BRUTUS (BTS). Ectopic expression of AtBRUTUS (AtBTS) and comparison between Bnams4b‐transgenic Arabidopsis and bts mutants suggested that Bnams4b may drive translocation of BTS to cause various toxic defects. BnaMs3 gained an exclusive interaction with the plastid outer‐membrane translocon Toc33 compared with Bnams3 and AtTic40, and specifically compensated for the toxic effects of Bnams4b. Heat shock treatment also rescued the sterile phenotype, and high temperature suppressed the interaction between Bnams4b and BTS in yeast. Furthermore, the ubiquitin system and TOC (translocon at the outer envelope membrane of chloroplasts) component accumulation were affected in Bnams4b‐transgenic Arabidopsis plants. Taken together, these results indicate that new chimeric Bnams4b carries BTS from nucleus to chloroplast, which may disrupt the normal ubiquitin–proteasome system to cause toxic effects, and these defects can be compensated by BnaMs3−Toc33 interaction or environmental heat shock. It reveals a scenario in which two population‐specific coevolved young genes reshape a novel interaction network in plants.

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“…The consistent demethylation of the cytosines in the promoter region of PPR, the consistent methylation of the cytosines in the downstream region of bZIP, as well as the stable methylation state in the downstream regions of MYB and C2H2 contribute to rice heat tolerance [46]. Several additional TFs, including flowering control locus A (FCA), bZIP, tryptophan-arginine-lysinetyrosine (WRKY), APETALA2 (AP2), cysteine 8-cysteine 5 or cysteine 3-histidine-type zinc finger protein (C8C5C3H), and DNA binding with one finger protein (Dof), were also reported to be regulated by DNA methylation in plants [49][50][51]. The post-transcriptional regulator FCA, which has two RNAbinding motifs (RRMs), upregulates the gene mitogen-activated protein kinase 5 lacking an intact kinase domain (OstMAPKKK5).…”

Section: Discussionmentioning

confidence: 99%

“…However, the cytosines in the promoter or downstream region of the TFs MYB and C2H2 could be HNT-induced demethylated in the heat-sensitive rice strain but were unchanged in the heat-sensitive strain, which might allow for the removal of excessive ROS and reduction of cellular damage in the heat-tolerant strain. SnRK2 also plays important roles in sugar transport and starch synthesis by regulating bZIP, WRKY80, AP2, and C8C5C3H [48][49][50]58]. The cytosines in the promoter or downstream regions of bZIP and WRKY80 were HNT-induced methylated, while the cytosines in the promoter or downstream regions of AP2 and C8C5C3H were unchanged in the heat-tolerant rice strain.…”

Section: Discussionmentioning

confidence: 99%

Cytosine methylation in the promoter region of genes involved in cellular oxidation equilibrium pathways affects rice heat tolerance

Zhang

et al. 2020

Preprint

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Background High temperatures are detrimental to rice yield and quality, especially at night. Due to the predicted increases in global warming, it is imperative that crops are able to adapt to high night temperatures (HNTs) in the near future. DNA methylation is a potential mechanism for controlling gene activity and cellular phenotype under adversely environment without changing nucleotide sequence.Results Here, we reported that few CG and CHG contexts but CHH context in rice genome was strongly induced by HNT to occur cytosine methylation variation between two coisogenic rice strains with significant difference in heat tolerance. Methylation variations occurred mainly on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, two basal transcriptional factor TFIID subunit 11 and mediator of RNA polymerase II transcription subunit 31 were fully demethylated in the downstream 358-359 bp and 2-60 bp under HNT in the heat-tolerant strain, respectively. Various genes involved in ABA-related reactive oxygen species (ROS) equilibrium pathways, including the pentatricopeptide repeat domain gene PPR (LOC_Os07g28900) and the homeobox domain gene homeobox (LOC_Os01g19694), were induced by HNT to occur methylation variation on successive cytosines in the gene promoter regions of the heat-tolerant strain. Varidation among the typical heat-tolerant group and heat-sensitive group of rice germplasms, methylation rate of the cytosines in gene promoter region for gene PPR was higher and gene expression was suppressed in the heat-sensitive group, comparing to the heat-tolerant group.Conclusions The CHH context in rice genome was the main context type to occur cytosine methylation variation under HNT between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes related to abscisic acid-related oxidation and ROS scavenging contributes to rice heat tolerance. These findings provide bases to explain the molecular mechanisms behind rice heat tolerance.

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Genome-Wide DNA Methylation Comparison between Brassica napus Genic Male Sterile Line and Restorer Line

Cited by 19 publications

References 47 publications

Early leucine programming on protein utilization and mTOR signaling by DNA methylation in zebrafish (Danio rerio)

Early leucine programming on protein utilization and mTOR signaling by DNA methylation in zebrafish (Danio rerio)

Two young genes reshape a novel interaction network in Brassica napus

Cytosine methylation in the promoter region of genes involved in cellular oxidation equilibrium pathways affects rice heat tolerance

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