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Series GSE130115 Query DataSets for GSE130115
Status Public on Dec 26, 2019
Title Allelic histone-to-DNA methylation switch establishes secondary DMR to maintain noncanonical imprinting
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Faithful maintenance of genomic imprinting is essential for mammalian development. While germline DNA methylation-dependent (canonical) imprinting is relatively stable during development, the recently discovered oocyte-derived H3K27me3-mediated noncanonical imprinting is mostly transient in early embryos with only a few genes maintain imprinted expression in the extraembryonic lineage. How these few noncanonical imprinted genes maintain their extraembryonic-specific imprinting is unknown. Here we report that maintenance of extraembryonic-specific noncanonical imprinting requires maternal allele-specific de novo DNA methylation (secondary differentially methylation regions; DMRs) at implantation. The secondary DMRs are located at the gene promoters with paternal allele-specific H3K4me3 preformed during preimplantation development. Importantly, genetic ablation of Eed and DNA methyltransferases revealed that both maternal H3K27me3 and zygotic Dnmt3a/3b are required for establishing secondary DMRs and for maintaining noncanonical imprinting. Thus, our study not only reveals the mechanism underlying maintenance of noncanonical imprinting, but also sheds light on how histone modifications in oocytes and preimplantation embryos may shape the secondary DMRs in post-implantation embryos.
 
Overall design Two RNA-seq replicates were performed for Dnmt3l control (CTR) and maternal KO (matKO) morula samples;
One replicate of whole genome bisulfite sequencing (WGBS) was performed for Eed CTR and matKO E6.5 extraembryonic ectoderm (ExE);
Two and seven RNA-seq replicates were performed for WT and Dnmt3a/3b double KO (DKO) E6.5 ExE;
Three RRBS replicates were performed for WT and Dnmt3a/3b DKO E6.5 ExE;
Two H3K27me3 CUT&RUN replicates were performed for WT and Dnmt3a/3b DKO E6.5 ExE;
Two H3K4me3 CUT&RUN replicates were performed for Eed CTR and matKO morula;
One H3K4me3 CUT&RUN replicate was performed for Eed CTR and matKO trophectoderm (TE).
 
Contributor(s) Chen Z, Yin Q, Azusa I, Zhang C, Zhang Y
Citation(s) 32064321
Submission date Apr 21, 2019
Last update date Feb 24, 2020
Contact name Zhiyuan Chen
E-mail(s) Zhiyuan.chen@cchmc.org
Organization name Cincinnati Children's Hospital Medical Center
Street address 3333 Burnet Avenue
City Cincinnati
State/province Ohio
ZIP/Postal code 45229
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (31)
GSM3732305 Dnmt3l_CTR_morula_B6129xPWK_RNAseq_rep1
GSM3732306 Dnmt3l_CTR_morula_B6129xPWK_RNAseq_rep2
GSM3732307 Dnmt3l_matKO_morula_B6129xPWK_RNAseq_rep1
Relations
BioProject PRJNA533990
SRA SRP193267

Download family Format
SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE130115_RAW.tar 3.4 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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