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Series GSE143923 Query DataSets for GSE143923
Status Public on Feb 08, 2020
Title Active DNA Demethylation Regulates Plant Gamete and Zygote Genome Reprogramming
Organism Oryza sativa Japonica Group
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Fertilization constitutes a critical step in the plant life cycle during which the gamete genomes undergo reprogramming in preparation for embryogenesis. However, it is unclear whether and how DNA methylation that epigenetically regulates gene expression is reprogramed during fertilization. Here, we characterized DNA methylation patterns and investigated the function of DNA glycosylases in rice eggs, sperms and unicellular zygotes. We found that DNA methylation is extensively reprogramed at non-CG sites in euchromatin regions upon fertilization, which intensifies during early embryogenesis. Genetic and genomic analysis revealed that rice DNA glycosylase genes DNG702, DNG701 and DNG704 demethylate at distinct and complementary loci in egg, sperm, and zygote genomes and are required for zygotic gene expression and development. The results indicate that active demethylation takes place in the gametes and the zygote to reprogram DNA methylation and zygotic genome activation in plant.
 
Overall design BS-seq and RNA-seq of gametes and unicellular zygote of wild type, dng702, dng701/4 knock out mutant
 
Contributor(s) Zhou SL, Li X, Zhou DX
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Submission date Jan 19, 2020
Last update date Feb 08, 2020
Contact name shaoli zhou
E-mail(s) zhoushaoli@webmail.hzau.edu.cn
Organization name Huazhong Agricultural University
Department National Key Laboratory of Crop Genetic Improvement
Street address shizishan street
City Wuhan
State/province Hubei
ZIP/Postal code 430070
Country China
 
Platforms (1)
GPL13834 Illumina HiSeq 2000 (Oryza sativa Japonica Group)
Samples (26)
GSM4276680 BS-seq of WT egg replicate 1
GSM4276681 BS-seq of WT egg replicate 2
GSM4276682 BS-seq of WT sperm replicate 1
Relations
BioProject PRJNA602160
SRA SRP243106

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE143923_14-E_call_methylation.50bp.CGmap.gz 83.4 Mb (ftp)(http) CGMAP
GSE143923_14-S_call_methylation.50bp.CGmap.gz 56.3 Mb (ftp)(http) CGMAP
GSE143923_14-Z_call_methylation.50bp.CGmap.gz 152.2 Mb (ftp)(http) CGMAP
GSE143923_14-vs-DJ-E-gene_exp.diff.gz 1.3 Mb (ftp)(http) DIFF
GSE143923_14-vs-DJ-Z-gene_exp.diff.gz 1.3 Mb (ftp)(http) DIFF
GSE143923_2-E_call_methylation.50bp.CGmap.gz 72.3 Mb (ftp)(http) CGMAP
GSE143923_2-S_call_methylation.50bp.CGmap.gz 50.2 Mb (ftp)(http) CGMAP
GSE143923_2-vs-DJ-E-gene_exp.diff.gz 1.3 Mb (ftp)(http) DIFF
GSE143923_DJ-E_call_methylation.50bp.CGmap.gz 84.5 Mb (ftp)(http) CGMAP
GSE143923_DJ-S_call_methylation.50bp.CGmap.gz 38.0 Mb (ftp)(http) CGMAP
GSE143923_DJ-Z_call_methylation.50bp.CGmap.gz 69.2 Mb (ftp)(http) CGMAP
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Raw data are available in SRA
Processed data are available on Series record

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