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Series GSE58549 Query DataSets for GSE58549
Status Public on Jun 17, 2014
Title DNA Methylation Identifies Epigenetic Variation across Embryo and Endosperm in Maize (Zea may)
Organism Zea mays
Experiment type Methylation profiling by high throughput sequencing
Summary Epigenetic modification plays important roles in plant and animal development. DNA methylation can impact the transposable element (TE) silencing, gene imprinting and regulate gene expression.Through a genome-wide analysis, DNA methylation peaks were respectively characterized and mapped in maize embryo and endosperm genome. Distinct methylation level across maize embryo and endosperm was observed. The maize embryo genome contained more DNA methylation peaks than endosperm. However, the endosperm chloroplast genome contained more DNA methylation peaks to compare with the embryo chloroplast genome. DNA methylation regions were characterized and mapped in genome. More CG island (CGI) shore are methylated than CGI in maize suggested that DNA methylation level is not positively correlated with CpG density. The DNA methylation occurred more frequently in the promoter sequence and transcriptional termination region (TTR) than other regions of the genes. The result showed that 99% TEs we characterized are methylated in maize embryo, but some (34.8%) of them are not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated two regions between embryo and endosperm are High CpG content promoters (HCPs) and high CpG content TTRs (HCTTRs). DNA methylation peaks distinction of mitochondria and chloroplast DNA were less than the nucleus DNA. Our results indicated that DNA methylation is associated with the gene silencing or gene activation in maize endosperm and embryo. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 17 endosperm-specific expressed imprinting genes were hypomethylated in endosperm and were hypermethylated in embryo. The expression of a maize DEMETER -like (DME-like) gene and MBD101 gene (MBD4 homolog) which direct bulk genome DNA demethylation were higher in endosperm than in embryo. These two genes may be associated with the distinct methylation level across maize embryo and endosperm.The methylomes of maize embryo and endosperm was obtained by MeDIP-seq method. The global mapping of maize embryo and endosperm methylation in this study broadened our knowledge of DNA methylation patterns in maize genome, and provided useful information for future studies on maize seed development and regulation of metabolic pathways in different seed tissues.
Overall design Examination of DNA methylated modifications in 2 maize tissues.
Contributor(s) Wang X, Wang P
Citation(s) 25612809
Submission date Jun 16, 2014
Last update date May 15, 2019
Contact name Xingjun Wang
Organization name Shandong Academy of Agricultural Sciences
Department Biotechnology Research Center
Street address 202#, Gongye Bei Road
City Ji'nan
State/province Shandong
ZIP/Postal code 250100
Country China
Platforms (1)
GPL15463 Illumina HiSeq 2000 (Zea mays)
Samples (2)
GSM1413338 Embryo DNA_MeDIP
GSM1413339 Endosperm DNA_MeDIP
BioProject PRJNA252856
SRA SRP043298

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Supplementary file Size Download File type/resource
GSE58549_RAW.tar 6.2 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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