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| Status |
Public on Oct 30, 2012 |
| Title |
Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds [methylome] |
| Organism |
Glycine max |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
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.
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| Overall design |
methylomes of roots, stems, leaves, and cotyledons of developing seeds
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| |
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| Contributor(s) |
Song Q, Zhang J |
| Citation(s) |
23966636 |
| |
| Submission date |
Jan 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinsong Zhang |
| E-mail(s) |
jszhang@genetics.ac.cn
|
| Organization name |
IGDB
|
| Street address |
No.1 West Beichen Road,Chaoyang District
|
| City |
beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
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| Platforms (1) |
| GPL15087 |
Illumina Genome Analyzer IIx (Glycine max) |
|
| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE34875 |
Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds |
|
| Relations |
| SRA |
SRP010103 |
| BioProject |
PRJNA156283 |
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