Methylation Changes During Soybean Seed Development
Ontology highlight
ABSTRACT:
ORGANISM(S): Glycine max
PROVIDER: GSE34637 | GEO | 2011/12/22
SECONDARY ACCESSION(S): PRJNA151265
REPOSITORIES: GEO
Similar Datasets
Project description:What methylation changes are occurring during seed development largely remains unknown. To uncover the possible role of DNA methylation during the transition from seed differentiation to maturation and dormany in soybean, we characterized the methylome of whole seeds representing the differentiation (GLOB stage), maturation (early- (EM), mid- (B1) and late- (AA1) maturation stages), and dormancy (DRY stage) phases of soybean seed development using Illumina sequencing. In addition, we characterized the methylome of the mid-maturation stage embryonic axis (B1-AX) to examine methylation differences, if any, between an embryonic region compared to the whole seed. Illumina sequencing of bisulfite-converted genomic DNA from globular stage (GLOB), early-maturation stage (EM), mid-maturation stage (B1), and late-maturation stage (AA1) seeds, dormancy stage (DRY) and mid-maturation embryonic axis (B1-AX).
2011-12-22 | E-GEOD-34637 | biostudies-arrayexpress
Project description:There are four major seed developmental phases in Arabidopsis seed development: morphogenesis, maturation, dormancy and germination. What methylation changes occurring in the different phases, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of four major seed developmental phases of Arabidopsis using Illumina sequencing: global stage (glob) and linear cotyledon stage (lcot) for morphogenesis phase; mature green stage (mg) and post mature green stage (pmg) for maturation phase; dry seed (dry) for dormancy phase; leaves (leaf) from 4 week plant for vegetative tissues.
2015-04-22 | GSE68132 | GEO
Project description:There are four major seed developmental phases in Arabidopsis seed development: morphogenesis, maturation, dormancy and germination. What methylation changes occurring in the different phases, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of four major seed developmental phases of Arabidopsis using Illumina sequencing: global stage (glob) and linear cotyledon stage (lcot) for morphogenesis phase; mature green stage (mg) and post mature green stage (pmg) for maturation phase; dry seed (dry) for dormancy phase; leaves (leaf) from 4 week plant for vegetative tissues. Illumina sequencing of bisulfite-converted genomic DNA from six seed developmental stages in Arabidopsis: global stage (glob), linear cotyledon stage (lcot), mature green stage (mg), post mature green stage (pmg), dry seed (dry) and leaves (leaf) from 4 week plant.
2015-04-22 | E-GEOD-68132 | biostudies-arrayexpress
Project description:Seeds are comprised of three major parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. Each seed part undergoes distinct developmental programs during seed development. What methylation changes occur in the different seed parts, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of three major parts of cotyledon stage seeds, the seed coat, embryonic cotyledons, and embryonic axis, using Illumina sequencing. Illumina sequencing of bisulfite-converted genomic DNA from three parts of soybean cotyledon stage seeds: seed coat (COT-SC), embryonic cotyledons (COT-COT), and embryonic axis (COT-AX).
2014-05-17 | E-GEOD-57762 | biostudies-arrayexpress
Project description:What methylation changes are occurring in different compartments of early maturation stage seed largely remains unknown. To uncover the possible role of DNA methylation in different compartments of early maturation stage seed, we characterized the methylome of two major compartments in embryonic cotyledon: cotyledon abaxial parenchyma (EM-COT-ABPY) and cotyledon adaxial parenchyma (EM-COT-ADPY) using Illumina sequencing. Illumina sequencing of bisulfite-converted genomic DNA from cotyledon abaxial parenchyma (EM-COT-ABPY) and cotyledon adaxial parenchyma (EM-COT-ADPY) compartments.
2012-05-11 | E-GEOD-37893 | biostudies-arrayexpress
Project description: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.
2011-05-10 | GSE29134 | GEO
Project description: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. 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.
2011-05-10 | E-GEOD-29134 | biostudies-arrayexpress
Project description:Seed maturation, dormancy and germination are distinct physiological processes. Transition from maturation to dormancy, and from dormancy into germination are not only critical developmental phases in the plant life cycle but are also important agricultural traits. These developmental processes and their phase transitions are fine determined and coordinately regulated by genetic makeup and environmental cues. SCARECROW-LIKE15 (SCL15) has been demonstrated to be essential for repressing the seed maturation programme in vegetative tissues (Gao et al., Nat Commun, 2015, 6:7243). Here we report that SCL15 is also important for seed dormancy maintenance, germination timing and seed vigor performance based on the effects of SCL15 mutation on plant germination, growth and reproduction when compared with wild type Arabidopsis and over-expression lines 35S:SCL15 and Napin:SCL15. Seed dormancy is enhanced by the mutation of SCL15 in a GA signaling dependent way, indicating that SCL15 plays a negative role for primary dormancy release. Seed germination is positively regulated by SCL15 through interaction with ABA, GA and auxin signaling. SCL15 acts as positive regulator of seed vigor and effect of SCL15 mRNA abundance on seed reserve accumulation and seed development during late embryogenesis may contribute to the seed vigor performance.
2020-11-04 | GSE160707 | GEO
Project description:Seeds are comprised of three majors parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. Each seed parts undergo distinct developmental programs during seed development. What methylation changes occurring in the different seed parts, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of three major parts of an early maturation stage seed: seed coat, embryonic cotyledons, and embryonic axis using Illumina sequencing. Illumina sequencing of bisulfite-converted genomic DNA from three parts of an mid-maturation (B1) stage seed: seed coat (B1-SC), embryonic cotyledons (B1-COT), and embryonic axis (B1-AX).
2013-08-26 | E-GEOD-41061 | biostudies-arrayexpress
Project description:This series contain all stages Arabidopsis plant development. Stages of development includes unfertilized ovule, 24-Hr post-fertilization seed, globular stage seed, cotyledon stage seed, mature green seed, post-mature green seed, post-germination seedling, rosette leaf, root, stem, and floral bud. Keywords = Arabidopsis Keywords = Seed development Keywords = seedling Keywords = germination Keywords = leaf Keywords = root Keywords = stem Keywords = floral bud Keywords: ordered
2005-01-01 | GSE680 | GEO