Lipophilic-Signals Lead to Organ-Specific Gene Expression Changes in Arabidopsis Seedlings
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ABSTRACT:
PROVIDER: PRJNA554610 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9682380_1.fastq.gz | Fastqsanger.gz | |||
| SRR9682380_2.fastq.gz | Fastqsanger.gz | |||
| SRR9682390_1.fastq.gz | Fastqsanger.gz | |||
| SRR9682390_2.fastq.gz | Fastqsanger.gz | |||
| SRR9682400_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Using RNA-seq and differential expression analysis, we examined the NAE-type and organ-specific genetic pathways involved in transducing ear;y signals into downstream physiological changes involved in Arabidopsis seedling growth. Methods: Intact seedlings and dissected cotyledon and root mRNA profiles of 3-day-old Arabidopsis seedlings treated with DMSO, 40 µM NAE 18:2 or 80 µM NAE 18:3 were generated by deep sequencing, in triplicate, using the Illumina Next-Seq 500 system. The sequence reads that passed quality filters were analyzed using STAR followed by DESeq2. qRT–PCR validation was performed using SYBR Green assays Results: Using RNA-seq and differential expression analysis, we identified early (1 h) transcriptional changes induced by the exogenous treatment of NAE 18:2 and NAE 18:3 in cotyledons, roots and intact seedlings. These two treatments led to a significant enrichment in ABA-response and chitin-response genes in organs where the treatments led to changes in development. In Arabidopsis seedlings, NAE 18:2 treatment led to the repression of genes involved in cell wall biogenesis and organization in roots and seedlings. In addition, cotyledons, roots, and seedlings treated with NAE 18:3 also showed a decrease in transcripts that encode proteins involved in growth processes. NAE 18:3 also led to changes in the abundance of transcripts involved in the modulation of chlorophyll biosynthesis and catabolism in cotyledons. Overall, NAE 18:2 and NAE 18:3 treatment led to lipid-type and organ-specific gene expression changes that include overlapping and non-overlapping gene sets. These data will provide future, rich opportunities to examine the genetic pathways involved in transducing early signals into downstream physiological changes in seedling growth. Conclusions: A detailed transcriptional analyses provided insight into the early organ-specific molecular responses to NAE 18:2 and NAE 18:3. Using this experimental and computational approach, we gained an unbiased view of the NAE 18:2- and NAE 18:3-modulated transcriptome changes that are activated and lead to downstream changes in seedling development. NAE 18:2 and NAE 18:3 induced the expression of several genes also induced by ABA or chitin treatment. The overlap with ABA-response genes corroborates previously work; however, this is the first time chitin-response genes have been identified as part of the NAE-modulation of seedling growth. Overall, the bioinformatic analyses presented here supports the hypothesis that NAE 18:2 and NAE 18:3 elicit organ-specific and signal- specific molecular changes that precede developmental changes in Arabidopsis seedlings. Further, these data provide novel insights into the genetic programs that are modulated by NAE 18:2 and NAE 18:3 at the organ-specific level in Arabidopsis seedlings, and will facilitate future studies of the corresponding signaling networks.
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Project description:In plants, N-acylethanolamines (NAEs) are most abundant in desiccated seeds and their levels decline during germination and early seedling establishment. However, endogenous NAE levels rise in seedlings when ABA or environmental stress is applied, and this results in an inhibition of further seedling development. When the most abundant, polyunsaturated NAEs of linoleic acid (18:2) and linolenic acid (18:3) were exogenously applied, seedling development was affected in an organ-specific manner. NAE 18:2 primarily affected primary root elongation and NAE 18:3 primarily affected cotyledon greening and expansion and overall seedling growth. The molecular components and signaling mechanisms involved in this pathway are not well understood. In addition, the bifurcating nature of this pathway provides a unique system in which to study the spatial aspects and interaction of these lipid-specific and organ-targeted signaling pathways. Using whole transcriptome sequencing (RNA-seq) and differential expression analysis, we identified early (1-3 hr) transcriptional changes induced by the exogenous treatment of NAE 18:2 and NAE 18:3 in cotyledons, roots, and seedlings. These two treatments led to a significant enrichment in ABA-response and chitin-response genes in organs where the treatments led to changes in development. In Arabidopsis seedlings, NAE 18:2 treatment led to the repression of genes involved in cell wall biogenesis and organization in roots and seedlings. In addition, cotyledons, roots, and seedlings treated with NAE 18:3 also showed a decrease in transcripts that encode proteins involved in growth processes. NAE 18:3 also led to changes in the abundance of transcripts involved in the modulation of chlorophyll biosynthesis and catabolism in cotyledons. Overall, NAE 18:2 and NAE 18:3 treatment led to lipid-type and organ-specific gene expression changes that include overlapping and non-overlapping gene sets. These data will provide future, rich opportunities to examine the genetic pathways involved in transducing early signals into downstream physiological changes in seedling growth.
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Project description:Epigenetic modifications, such as DNA methylation where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence the ability of plants to respond to changing environmental conditions. One approach to determining the association between DNA methylation, phenotypic variation, and gene expression, is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree species of Quercus lobata with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that foliar application of 5-azayctidine lead to a 3-6% absolute reduction and 6.1-43% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. We also show that the demethylation treatment had minimal impact on the soil microbiome. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings, and but no significant differences in fluctuating asymmetry (i.e., deviations from bilateral symmetry) of leaves compared to control seedlings. Finally, treated seedlings showed differential expression of a total of 23 genes relative to control seedlings, the majority of which were upregulated. Overall, this study provides evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings.
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Project description:Tocopherols (Vitamin E) are lipophilic antioxidants that are synthesized by all plants and are particularly abundant in seeds. Two tocopherol deficient mutant loci were used to examine how tocopherol deficiency impacts global gene expression during the critical peroid of germination and early seedling development when tocopherols are essential. vte1 lacks all tocopherols, but accumulates the tocopherol pathway intermediate DMPBQ,. vte2 which lacks all tocopherols and pathway intermediates. We used microarrays to examine the global gene expression in early seedlings and identify distinct classes of genes whose expression is affected by tocopherol deficient mutants vte1 and vte2. Keywords: genetic modification
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Project description:Tocopherols (Vitamin E) are lipophilic antioxidants that are synthesized by all plants and are particularly abundant in seeds. Two tocopherol deficient mutant loci were used to examine how tocopherol deficiency impacts global gene expression during the critical peroid of germination and early seedling development when tocopherols are essential. vte1 lacks all tocopherols, but accumulates the tocopherol pathway intermediate DMPBQ,. vte2 which lacks all tocopherols and pathway intermediates. We used microarrays to examine the global gene expression in early seedlings and identify distinct classes of genes whose expression is affected by tocopherol deficient mutants vte1 and vte2. Experiment Overall Design: Arabidopsis seedlings were grown on media containing MS salts at 22C and RNA was extracted from 1 (1D)and 3 (3D)day old seedlings following cold treatment to break dormancy and synchronize germination (5 days at 6C) . We sought to compare the two tocopherol deficient mutants vte1 (VTE1) and vte2 (VTE2) with each other and the corresponding wild-type background Columbia-0 (COL).
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