Analysis of Global Methylome and Gene Expression during Carbon Reserve Mobilization in Stems under Soil Drying

Wang, Guan-Qun; Li, Haoxuan; Meng, Shuan; Yang, Jianchang; Ye, Nenghui; Zhang, Jianhua

doi:10.1104/pp.20.00141

Cited by 24 publications

(14 citation statements)

References 51 publications

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“…Promoters of DPT-encoding genes did indeed contain fewer TF binding sites (median of 5 instead of the of 6 regulatory elements for GPTs, P <0.0001; Supplementary Figure 8A, Supplementary Table 15), and TATA-boxes (23.4% vs. 25.7%, P =0.002; Supplementary Figure 8A, Supplementary Table 15), and DPTs were longer than GPTs (1.19× difference, P =1.99×10 -41 ; Figure 3, Supplementary Table 7), all in agreement with a housekeeping role. Furthermore, gbM levels were higher for the less abundant DPTs than for the more abundant GPTs (1.25× difference, P =8.12×10 -11 ; Figure 3), matching previous observations on gbM and gene expression for field-grown rice (Wang et al, 2020). All of these patterns were similar overall for Japonica (Supplementary Figures 3 and 8B, Supplementary Tables 8 and 15).…”

Section: Main Textsupporting

confidence: 88%

Fitness costs and benefits of gene expression plasticity in rice under drought

Groen

Hamann

Ćalić

et al. 2021

Preprint

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Genome-wide gene expression changes in response to environmental variability have been widely documented, but we lack detailed and comprehensive understanding of the interplay between this form of phenotypic plasticity and natural selection. Selection on expression plasticity may be limited by environment-specific costs, and plasticity may in turn affect selection on baseline expression levels. Here, we address this fundamental issue by measuring selection on drought-induced plasticity of leaf transcripts in field-grown rice populations. Selection disfavored switching off housekeeping genes under drought. This stress-induced dysregulation did not constrain selection on baseline transcript levels, suggesting compensatory evolution may be possible. Selection rarely acted strongly on individual transcripts but worked polygenically on gradual (continuous) plasticity of co-expressed gene modules regulating photosynthesis via known drought-responsive transcription factors. Finally, selection was tied to inefficient gene architectural features and metabolic costs of expression. Our study provides a genome-wide view of costs and benefits of gene expression plasticity.

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Section: Main Textsupporting

confidence: 88%

Fitness costs and benefits of gene expression plasticity in rice under drought

Groen

Hamann

Ćalić

et al. 2021

Preprint

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“…Then, the above constructed vectors were mixed well for the transient expression assay in the rice protoplasts. This transient expression assay was performed as described previously (Wang et al 2019a , b ; Wang et al 2020 ). The primers used were listed in Additional file 2 : Table S5.…”

Section: Methodsmentioning

confidence: 99%

Global Survey of Alternative Splicing in Rice by Direct RNA Sequencing During Reproductive Development: Landscape and Genetic Regulation

Shen

et al. 2021

Rice

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Alternative splicing is a widespread phenomenon, which generates multiple isoforms of the gene product. Reproductive development is the key process for crop production. Although numerous forms of alternative splicing have been identified in model plants, large-scale study of alternative splicing dynamics during reproductive development in rice has not been conducted. Here, we investigated alternative splicing of reproductive development of young panicles (YP), unfertilized florets (UF) and fertilized florets (F) in rice using direct RNA sequencing, small RNA sequencing, and degradome sequencing. We identified a total of 35,317 alternative splicing (AS) events, among which 67.2% splicing events were identified as novel alternative splicing events. Intron retention (IR) was the most abundant alternative splicing subtype. Splicing factors that differentially expressed and alternatively spliced could result in global alternative splicing. Global analysis of miRNAs-targets prediction revealed that alternative spliced transcripts affected miRNAs’ targets during development. Degradome sequencing detected only 6.8% of the differentially alternative splicing transcripts, suggesting a productive transcripts generation during development. In addition, alternative splicing isoforms of Co-like, a transcription factor, interacted with Casein kinase 1-like protein HD1 (CKI) examined in luciferase assay, which could modulate normal male-floral organs development and flowering time. These results reveal that alternative splicing is intensely associated with developmental stages, and a high complexity of gene regulation.

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“…Sometimes, antagonism between DNA methyltransferase and demethylase affects the dynamic DNA methylation changes. For instance, drought induces DNA methylation levels in rice, but gene expression of methyltransferase and demethylase were both increased (Wang et al, 2020a). In this study, it is shown that the expression of some DNA methyltransferases and demethylase could enhance DNA methylation in specific contexts, and inhibit the methylation levels in others.…”

Section: Discussionmentioning

confidence: 63%

“…The regulation patterns varied from different plants between DNA methyltransferase and demethylase. During the fruit development, the expression of demethylase and DNA methylation level showed an opposite trend in orange and tomato (Huang et al, 2019;Wang et al, 2020a). The expression of DNA methyltransferase and demethylase could only affect methylation levels in specific contexts in some plants.…”

Section: Discussionmentioning

confidence: 97%

DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

et al. 2021

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Grain filling is a crucial process for crop yield and quality. Certain studies already gained insight into the molecular mechanism of grain filling. However, it is unclear whether epigenetic modifications are associated with grain filling in foxtail millet. Global DNA methylation and transcriptome analysis were conducted in foxtail millet spikelets during different stages to interpret the epigenetic effects of the grain filling process. The study employed the whole-genome bisulfite deep sequencing and advanced bioinformatics to sequence and identify all DNA methylation during foxtail millet grain filling; the DNA methylation-mediated gene expression profiles and their involved gene network and biological pathway were systematically studied. One context of DNA methylation, namely, CHH methylation, was accounted for the largest percentage, and it was gradually increased during grain filling. Among all developmental stages, the methylation levels were lowest at T2, followed by T4, which mainly occurred in CHG. The distribution of differentially methylated regions (DMR) was varied in the different genetic regions for three contexts. In addition, gene expression was negatively associated with DNA methylation. Evaluation of the interconnection of the DNA methylome and transcriptome identified some stage-specific differentially expressed genes associated with the DMR at different stages compared with the T1 developmental stage, indicating the potential function of epigenetics on the expression regulation of genes related to the specific pathway at different stages of grain development. The results demonstrated that the dynamic change of DNA methylation plays a crucial function in gene regulation, revealing the potential function of epigenetics in grain development in foxtail millet.

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Analysis of Global Methylome and Gene Expression during Carbon Reserve Mobilization in Stems under Soil Drying

Cited by 24 publications

References 51 publications

Fitness costs and benefits of gene expression plasticity in rice under drought

Fitness costs and benefits of gene expression plasticity in rice under drought

Global Survey of Alternative Splicing in Rice by Direct RNA Sequencing During Reproductive Development: Landscape and Genetic Regulation

DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

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