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RNA-seq and DNA methylomes of germinating rice and developing coleoptiles

ABSTRACT: RNA-seq and DNA methylomes of germinating rice and developing coleoptiles

OTHER RELATED OMICS DATASETS IN: GSE115373GSE115371

PROVIDER: PRJNA474719 | ENA |

REPOSITORIES: ENA

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RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)

Project description:RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)

| PRJNA474721 | ENA

RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (Methyl-Seq)

Project description:RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (Methyl-Seq)

| PRJNA474723 | ENA

RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)

Project description:RNAseq profiling of seeds and 7 time points during germination in rice under aerobic and anerobic conditions, as well as following re-oxygenation.

2018-06-11 | GSE115371 | GEO

RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (Methyl-Seq)

Project description:methylC-seq profiling of seeds, at 0 h and 24 h after imbibition and following 4-d of growth under aerobic and anerobic conditions, as well as following re-oxygenation (3dN1dA) in rice.

2018-06-11 | GSE115372 | GEO

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Acetylome analyses in the germinating rice seed

Project description:Seed germination is a complicated physiological process, during which structures of mitochondria and plastids are recovered, and metabolisms are re-activated (Han and Yang, 2015). It has been shown that metabolism reactivation is very important for rice germination (He et al., 2011b;Han et al., 2014a). It is still unknown if protein acetylation involved in and regulate these metabolisms during rice seed germination. To answer this question, we globally profiled the acetylome in rice embryos from the germinating seeds. A number of acetylated enzymes were identified. The results provide more information about the metabolism regulation in germinating seeds.

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E-GEOD-115371

Project description:RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)

2020-04-03 | E-GEOD-115371 | ExpressionAtlas

RNA-seq and DNA methylomes of germinating rice and developing coleoptiles

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-06-11 | GSE115373 | GEO

Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds [methylome]

Project description:Cytosine methylation is an important mechanism for dynamical regulation of gene expression and transposon mobility during plant developmental processes. Recently, the variation of DNA methylation has been described between wild type and DNA methylation-related mutants in Arabidopsis thaliana. However, the elaborate representation of soybean DNA methylomes remains lacking. Here, we described the epigenome maps of soybean root, stem, leaf, and cotyledon of developing seed at a single-base resolution. We confirmed the transcription start sites of genes using high-throughput sequencing and reported the DNA methylation patterns in gene and transposon regions. The correlation between gene expression and DNA methylation was revealed through transcriptome sequencing. We found CHH methylation may function in promotion of gene expression and ten cotyledon-preferred genes were identified CHH hypermethylated in cotyledon. Small RNA library sequencing showed that DNA methylation was enhanced by small RNAs not by strand-specific way, and the variation of DNA methylation between the organs was highly related with expression of small RNAs. methylomes of roots, stems, leaves, and cotyledons of developing seeds

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Comparison of transcriptomic adjustments to availability of sugar, cellular energy, and oxygen in germinating rice embryos

Project description:During germination, the availability of sugars, oxygen, or cellular energy fluctuates under dynamic environmental conditions, and the global RNA profile of rice genes can be affected by their availabilities. In the aerobically germinating rice embryos, most sugar-regulated genes are responsive to low energy and anaerobic conditions, indicating that sugar-regulation is closely associated with energy and anaerobic signaling. The interference pattern of sugar-regulation by either anaerobic or low energy conditions indicates that induction is likely the more prevalent regulatory mechanism than repression for the alteration in the expression of sugar-regulated genes in aerobically germinating rice embryos. Among the aerobically sugar-regulated genes, limited genes exhibit sugar regulation under anaerobic conditions, indicating that anaerobic conditions strongly influence sugar-regulated gene expression. Anaerobically responsive genes are highly overlapped with low-energy responsive genes. In particular, the expression levels of anaerobically downregulated genes are consistent with those induced by low energy-conditions, suggesting that anaerobic downregulation results from the prevention of aerobic respiration due to the absence of the final electron acceptor, i.e., molecular oxygen. It was noted that abscisic acid (ABA)-responsive genes were over-representative of the genes upregulated under low energy conditions, in contrast to the downregulated genes. This suggests that either ABA itself or upstream signaling components of the ABA signaling pathway are likely to be involved in the signaling pathways activated by low energy conditions.

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