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Global transcriptomic analysis of Arabidopsis thaliana ecotype Columbia-0 subjected to magnesium deficiency

ABSTRACT: Global transcriptomic analysis of Arabidopsis thaliana ecotype Columbia-0 subjected to magnesium deficiency

PROVIDER: PRJNA588176 | ENA |

REPOSITORIES: ENA

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Global transcriptomic analysis of Arabidopsis thaliana ecotype Columbia-0 subjected to magnesium deficiency

Project description:Magnesium (Mg) is essential for many biological processes in plant cells and its deficiency causes yield reduction in crop systems. Low Mg status reportedly impacts on photosynthesis, sucrose partitioning and biomass allocation. However, earlier responses to Mg deficiency are scarcely described. Generally, symptoms of nutrient deficiency appear in specific ages of leaves. Therefore, we hypothesised that transcriptional responses to Mg deficiency are different depending on the ages of leaves, and performed a global transcriptomic analysis in two types of leaves; source and sink leaves of the model plant species Arabidopsis thaliana to reveal the earlier responses to Mg deficiency. The global transcriptomic study revealed that short-term Mg deficiency triggers the expression of defence response genes in sink leaves. In roots, although short-term Mg deficiency enhanced the Mg2+ uptake from the environmnet, transcriptional levels of genes encoding putative Mg2+ transporters in roots were unchanged, suggesting non-transcriptional regulation of Mg2+ uptake in roots.

2020-04-29 | GSE140070 | GEO

2-week-old Arabidopsis seedlings (Columbia ecotype)

Project description:Comparison of TopHat alignments and assessment of spurious splice junctions for 32nt and 76nt read lengths. Total RNA from 2-week-old Arabidopsis thaliana (ecotype Columbia) seedlings grown on MS plates was isolated using RNeasy Plant Mini Kit from Qiagen. To remove any contaminating DNA, RNA was treated with DNAse. Isolation of poly (A) mRNA and preparation of cDNA library were carried out using the Illumina TrueSeq RNA kit. Sequencing (72 cycle) was done on Illumina Genome Analyzer II.

2011-09-24 | GSE32318 | GEO

Proteomic analysis of Citrus sinensis roots and leaves in response to long-term magnesium-deficiency

Project description:After long-term magnesium-deficiency treatment, 2D electrophoresis and mass spectrum were conducted to investigate different proteiomic profile in Citrus sinensis roots and leaves samples.

2015-04-13 | PXD001871 | Pride

Methylomic biomarkers for magnesium deficiency and colon neoplasia prevention

Project description:Methylomic biomarkers for magnesium deficiency and colon neoplasia prevention

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Methylomic biomarkers for magnesium deficiency and colon neoplasia prevention

Project description:Methylomic biomarkers for magnesium deficiency and colon neoplasia prevention

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MicroRNA regulatory mechanisms on Citrus sinensis leaves to magnesium-deficiency

Project description:In China, magnesium (Mg)-deficiency often occurs in citrus orchards, and is responsible for the loss of yield and poor fruit quality. However, very limited data are available on Mg-deficiency-responsive microRNAs (miRNAs) in higher plants. Using Illumina sequencing, we isolated 93 (91 known and 2 novel) up- and 90 (83 known and 7 novel) down-regulated miRNAs from Mg-deficient Citrus sinensis leaves. In addition to the remarkable metabolic flexibility as indicated by the great alteration of miRNA expression, the adaptive responses of leaf miRNAs to Mg-deficiency might also involve the following aspects: (a) accelerating protein turnover and amino acid biosynthesis by repressing the expression of miR2919, miR7812, miR5904 and miR5742; (b) up-regulating stress-related genes by down-regulating miR2919, miR164 and miR7812; (c) enhancing cell transport due to decreased expression of miR2919, miR3946, miR7533, miR1222, miR779, miR6143 and miR2868 and increased expression of miR395, miR1077, miR1160 and miR8019; (d) activating lipid metabolism-related genes by repressing miR158, miR1222, miR7533 and miR3946; (e) inducing cell wall-related genes by decreasing miR7533, miR779 and miR2868 expression; and (f) maintaing primary meristems by down-regulating miR6135. To conclude, we identified some candidate miRNAs that might contribute to Mg-deficiency tolerance. Our results are usefult not only for increasing our understaning of the molecular mechanisms on plant Mg-deficiency tolerance at post-transcriptional level, but also for obtaining the key miRNAs for plant Mg-deficiency tolerance.

2016-12-07 | GSE75758 | GEO

2-week-old Arabidopsis seedlings (Columbia ecotype)

2011-09-24 | E-GEOD-32318 | biostudies-arrayexpress

Methylomic Biomarkers for Magnesium Deficiency in the Personalized Prevention of Colorectal Cancer Trial

Project description:Based on the magnesium (Mg) tolerance test, the "gold standard" test of Mg status, more than 50% US participants had Mg deficiency. Observations suggest that the associations between high Mg intake and disease risks may completely differ by the underlying Mg status. Due to major limitations, the Mg tolerance test is not used in conventional clinical practice and rarely used in research. Instead, serum Mg is used for clinical diagnosis. However, serum Mg performs very poorly at identifying those with Mg deficiency. There is a great need to develop implementable, sensitive, and specific biomarkers which can be easily used for identifying people with Mg deficiency. It is known that DNA methylation changes are inducible by environmental exposures, including nutrients, and reversible when the exposure disappears. We propose to identify 5-hmC/5-mC biomarkers for Mg deficiency by a 4- phase EWAS study in the "Personalized Prevention of Colorectal Cancer Trial [PPCCT, R01CA149633; PI, Dai & Yu]" with a total of 240 participants. Mg tolerance test will be used as the gold standard. Finally, using newly identified biomarkers, we will evaluate if 12-week Mg treatment reduces TRPM7 expression, essential in Mg homeostasis and colorectal carcinogenesis, in rectal tissues only among those with Mg deficiency.

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Arabidopsis thaliana strain:ecotype Col-0

Project description:Arabidopsis thaliana strain:ecotype Col-0 Raw sequence reads

| PRJNA485392 | ENA

Arabidopsis thaliana ecotype Columbia [Col-0]: incubated with E. coli vs. Control

Project description:To explore mechanisms involved in the plant-microbe interactions, we proceeded with genome-wide transcriptome analysis of Arabidopsis roots incubated with E. coli Bl21 for 24 hours. Control plants did not receive E. coli.

2010-12-01 | GSE22277 | GEO

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