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Series GSE29134 Query DataSets for GSE29134
Status Public on May 10, 2011
Title Epigenetic Regulation of the Transition from Seed Maturation to Germination in Soybean
Organism Glycine max
Experiment type Expression profiling by high throughput sequencing
Summary How epigenetics is involved in the transition from seed maturation to seed germination largely remains elusive. To uncover the possible role of epigenetics in gene expression during the transition from seed maturation to seed germination in soybean, the transcriptome of cotyledons from four stages of soybean seed maturation and germination, including mid-late maturation, late maturation, seed dormancy and seed germination, were profiled by Illumina sequencing. For the genes that are quantitatively regulated at the four stages, two antagonistic epigenetic marks, H3K4me3 and H3K27me3, together with the binding of RNA polymerase II, were investigated at the four stages by chromatin immunoprecipitation (ChIP). For 10 out of 16 genes examined, the relative enrichment of histone modification marks (H3K4me3 and H3K27me3) and RNA polymerase II binding on their promoter regions correlates well with their relative expression levels at four stages, suggesting the involvement of epigenetics in transcriptional regulation. A striking finding is that seed germination-specific genes start to show open chromatin (H3K4me3) during late seed maturation although their transcripts do not accumulate, which is further supported by RNA polymerase II binding. Together, our results provide the first evidence that seed germination genes can be primed for transcription (open chromatin and RNA polymerase II binding) during seed maturation, highlighting that the transition from seed maturation to seed germination starts at late seed maturation stages at both the genetic and epigenetic levels.
Overall design Illumina sequencing of transcripts from cotyledons of mid-maturation (B1 stage) and late maturation (AA1 stage) seeds, whole dry seeds, and cotyledons of seedlings six days after imbibition.
Contributor(s) Goldberg RB, Xie Z, Kawashima T, Le BH, Henry KF
Citation(s) 29078418
Submission date May 08, 2011
Last update date Jul 19, 2019
Contact name Bob Goldberg
Phone 310-825-3270
Organization name University of California, Los Angeles
Department Molecular, Cell and Developmental Biology
Street address 610 Charles E Young Drive East
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
Platforms (1)
GPL11192 Illumina Genome Analyzer II (Glycine max)
Samples (4)
GSM721277 B1 stage cotyledons
GSM721278 AA1 stage cotyledons
GSM721279 Dry seed
SRA SRP006750
BioProject PRJNA140453

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GSE29134_RAW.tar 940.0 Kb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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