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Series GSE118263 Query DataSets for GSE118263
Status Public on Dec 17, 2019
Title Polycomb group proteins regulate chromatin architecture in mouse oocytes and early embryos
Organism Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary In mammals, chromatin organization undergoes drastic reorganization during oocyte development. However, the dynamics of three-dimensional chromatin structure in this process is poorly characterized. Using low-input Hi-C (genome-wide chromatin conformation capture), we found that a unique chromatin organization gradually appears during mouse oocyte growth. Oocytes at late stages show self-interacting, cohesin-independent compartmental domains marked by H3K27me3, therefore termed Polycomb-associating domains (PADs). PADs and inter-PAD (iPAD) regions form compartment-like structures with strong inter-domain interactions among nearby PADs. PADs disassemble upon meiotic resumption from diplotene arrest but briefly reappear on the maternal genome after fertilization. Upon maternal depletion of Eed, PADs are largely intact in oocytes, but their reestablishment after fertilization is compromised. By contrast, depletion of Polycomb repressive complex 1 (PRC1) proteins attenuates PADs in oocytes, which is associated with substantial gene de-repression in PADs. These data reveal a critical role of Polycomb in regulating chromatin architecture during mammalian oocyte growth and early development.
Overall design Mouse primordial germ cells (PGCs) are collected by FACs with OG2 mice. WT mouse oocytes were collected from C57BL/6N mice. And WT preimplantation embryos were obtained from crosses of C57BL/6N and PWK/PhJ. Ring1 KO Rnf2 flfl and Ring1 Rnf2 dKO FGOs were collected from Ring1-/-Rnf2flox/flox and Ring1-/-Rnf2 flox/flox; Zp3-Cre mice. Eed flfl and Eed CKO oocytes were collected from Eed flox/flox and Eed flox/flox; Gdf9-Cre mice. Eed flwt late 2cell were obtained from crosses of Eed flox/flox females and PWK/PhJ males. Eed mNull late 2cell were obtained from crosses of Eed flox/flox; Gdf9-Cre females and PWK?PhJ males. Hi-C experiments were performed in these PGCs, oocytes and embryos at various stages. CUT&RUN experiments were performed in Eed flfl and Eed CKO oocytes. RNA-seq experiments were performed in Ring1 KO Rnf2 flfl, Ring1 Rnf2 dKO FGOs, Eed flfl and Eed CKO FGOs.
Contributor(s) Du Z, Zheng H, Kawamura Y, Zhang K, Peters A, Xie W
Citation(s) 31837995
Submission date Aug 07, 2018
Last update date Dec 17, 2019
Contact name Zhenhai Du
Organization name Tsinghua University
Street address Qinghua Yuan, Haidian District
City Beijing
ZIP/Postal code 100084
Country China
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (49)
GSM3323879 Hi-C E11.5 PGC rep1
GSM3323880 Hi-C E11.5 PGC rep2
GSM3323881 Hi-C E13.5 female PGC rep1
BioProject PRJNA484983
SRA SRP156597

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
GSE118263_E11.5_PGC_rep12_allValidPairs.txt.gz 3.0 Gb (ftp)(http) TXT
GSE118263_E13.5_female_PGC_rep12_allValidPairs.txt.gz 3.6 Gb (ftp)(http) TXT
GSE118263_E13.5_male_PGC_rep12_allValidPairs.txt.gz 2.7 Gb (ftp)(http) TXT
GSE118263_Eed_CKO_FGO_rep12_allValidPairs.txt.gz 1.3 Gb (ftp)(http) TXT
GSE118263_Eed_control_and_mutant_FGO_RNAseq_FPKM.txt.gz 578.3 Kb (ftp)(http) TXT
GSE118263_Eed_flfl_FGO_rep12_allValidPairs.txt.gz 1.3 Gb (ftp)(http) TXT
GSE118263_Eed_flwt_late_2cell_rep12_allValidPairs.txt.gz 2.6 Gb (ftp)(http) TXT
GSE118263_Eed_flwt_late_2cell_rep12_maternal_allValidPairs.txt.gz 825.2 Mb (ftp)(http) TXT
GSE118263_Eed_flwt_late_2cell_rep12_paternal_allValidPairs.txt.gz 818.5 Mb (ftp)(http) TXT
GSE118263_Eed_mNull_late_2cell_rep12_allValidPairs.txt.gz 2.2 Gb (ftp)(http) TXT
GSE118263_Eed_mNull_late_2cell_rep12_maternal_allValidPairs.txt.gz 690.7 Mb (ftp)(http) TXT
GSE118263_Eed_mNull_late_2cell_rep12_paternal_allValidPairs.txt.gz 666.0 Mb (ftp)(http) TXT
GSE118263_FGO_rep123_allValidPairs.txt.gz 3.3 Gb (ftp)(http) TXT
GSE118263_GOII_DMSO_24h_rep12_allValidPairs.txt.gz 427.9 Mb (ftp)(http) TXT
GSE118263_GOII_alpha_amanitin_24h_rep12_allValidPairs.txt.gz 640.5 Mb (ftp)(http) TXT
GSE118263_GOII_before_treatment_rep12_allValidPairs.txt.gz 875.8 Mb (ftp)(http) TXT
GSE118263_GOII_rep12_allValidPairs.txt.gz 3.6 Gb (ftp)(http) TXT
GSE118263_GOI_rep12_allValidPairs.txt.gz 3.1 Gb (ftp)(http) TXT
GSE118263_GSK126_20h_rep123_allValidPairs.txt.gz 2.6 Gb (ftp)(http) TXT
GSE118263_GSK126_20h_rep123_maternal_allValidPairs.txt.gz 1.1 Gb (ftp)(http) TXT
GSE118263_GSK126_20h_rep123_paternal_allValidPairs.txt.gz 659.7 Mb (ftp)(http) TXT
GSE118263_GVBD_rep12_allValidPairs.txt.gz 2.3 Gb (ftp)(http) TXT
GSE118263_RAW.tar 38.3 Gb (http)(custom) TAR (of BW, TXT)
GSE118263_Ring1_KO_Rnf2_flfl_FGO_rep123_allValidPairs.txt.gz 587.7 Mb (ftp)(http) TXT
GSE118263_Ring1_Rnf2_dKO_FGO_rep123_allValidPairs.txt.gz 503.4 Mb (ftp)(http) TXT
GSE118263_control_for_GVBD_rep12_allValidPairs.txt.gz 1.8 Gb (ftp)(http) TXT
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