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| 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.
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| 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.
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| 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 |
| E-mail(s) |
duzhenhai93220@gmail.com
|
| Organization name |
Tsinghua University
|
| Street address |
Qinghua Yuan, Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platforms (2) |
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| Samples (49)
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| Relations |
| BioProject |
PRJNA484983 |
| SRA |
SRP156597 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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