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| Status |
Public on Jun 23, 2020 |
| Title |
Analysis of genome architecture during SCNT reveals a role of cohesin in impeding minor ZGA |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Somatic cell nuclear transfer (SCNT) can reprogram a somatic nucleus to a totipotent state. However, the re-organization of three-dimensional chromatin structure in this process remains poorly understood. Using low-input Hi-C, we revealed that during SCNT, the transferred nucleus first enters a mitotic-like state (premature chromatin condensation). Unlike fertilized embryos, SCNT embryos show stronger TADs at the 1-cell stage. TADs become weaker at the 2-cell stage, followed by gradual consolidation. Compartments A/B are markedly weak in 1-cell SCNT embryos and become increasingly strengthened afterward. By the 8-cell stage, somatic chromatin architecture is largely reset to embryonic patterns. Unexpectedly, we found cohesin represses minor zygotic genome activation (ZGA) genes (2-cell specific genes) in pluripotent and differentiated cells, and pre-depleting cohesin in donor cells facilitates minor ZGA and SCNT. These data reveal multi-step reprogramming of 3D chromatin architecture during SCNT and support dual roles of cohesin in TAD formation and minor ZGA repression.
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| Overall design |
Donor MEF/cumulus cells (MEF/CC), the SCNT embryos at the PCC stage (premature chromosome condensation) (1 hour after nuclear transfer) and SCNT embryos after PCC exit through “SCNT activation” using strontium chloride (SrCl2) at the 1-cell(4hours after activation, 6hours after activation and 10hours after activation), late 2-cell (28 hours after activation), and 8-cell (56 hours after activation) stages were obtained. Both MEF and CC are used for donor cells for the collection of SCNT 8-cell samples. HiC and RNA-seq were performed in these cells at various stages during SCNT embryogenesis. For the predepletion of CTCF/cohesin experiment, the short term differentiated cells with/without auxin treatment are collected for HiC experiments, RNA-seq and ChIP-seq experiments.
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| Contributor(s) |
Zhang K, Wu D, Zheng H, Wang Y, Sun Q, Liu X, Wang L, Xiong W, Wang Q, Rhodes J, Xu K, Li L, Lin Z, Yu G, Xia W, Huang B, Du Z, Yao Y, Nasmyth K, Klose R, Miao Y, Xie W |
| Citation(s) |
32579944 |
| Submission date |
Oct 26, 2019 |
| Last update date |
Jul 17, 2020 |
| Contact name |
Ke Zhang |
| E-mail(s) |
zhangke16@mails.tsinghua.edu.cn
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| Organization name |
Tsinghua university
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| Department |
School of Life Sciences
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| Lab |
Wei Xie
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| Street address |
Haidian District
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platforms (3) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21273 |
HiSeq X Ten (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (75)
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| Relations |
| BioProject |
PRJNA579764 |
| SRA |
SRP227097 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE139430_Cumulus_cell_donor_rep12_allValidPairs.txt.gz |
5.9 Gb |
(ftp)(http) |
TXT |
| GSE139430_EB_SCC1_auxin_rep12_allValidPairs.txt.gz |
629.2 Mb |
(ftp)(http) |
TXT |
| GSE139430_EB_SCC1_rep12_allValidPairs.txt.gz |
1.1 Gb |
(ftp)(http) |
TXT |
| GSE139430_MEF_donor_rep12_allValidPairs.txt.gz |
6.5 Gb |
(ftp)(http) |
TXT |
| GSE139430_PCC_rep12_merge_allValidPairs.txt.gz |
717.1 Mb |
(ftp)(http) |
TXT |
| GSE139430_PPN1_rep12_allValidPairs.txt.gz |
583.4 Mb |
(ftp)(http) |
TXT |
| GSE139430_PPN3_rep12_allValidPairs.txt.gz |
417.6 Mb |
(ftp)(http) |
TXT |
| GSE139430_PPN5_rep12_allValidPairs.txt.gz |
591.8 Mb |
(ftp)(http) |
TXT |
| GSE139430_SCC1_auxin_GSE139430_SCNT_PPN1_rep12_allValidPairs.txt.gz |
715.9 Mb |
(ftp)(http) |
TXT |
| GSE139430_SCC1_auxin_no_selection_diff_allValidPairs.txt.gz |
639.5 Mb |
(ftp)(http) |
TXT |
| GSE139430_SCC1_ctrl_GSE139430_SCNT_PPN1_rep12_allValidPairs.txt.gz |
674.0 Mb |
(ftp)(http) |
TXT |
| GSE139430_SCC1_ctrl_auxin_Neuron_fpkm.txt.gz |
145.3 Kb |
(ftp)(http) |
TXT |
| GSE139430_SCC1_ctrl_auxin_SCNT_L2C_PPN5_fpkm.txt.gz |
759.5 Kb |
(ftp)(http) |
TXT |
| GSE139430_SCC1_ctrl_no_selection_diff_allValidPairs.txt.gz |
507.6 Mb |
(ftp)(http) |
TXT |
| GSE139430_SCC1_diff_facs_select_noselect_fpkm.txt.gz |
659.0 Kb |
(ftp)(http) |
TXT |
| GSE139430_SCC1_mesc_timepoint_auxin_fpkm.txt.gz |
746.3 Kb |
(ftp)(http) |
TXT |
| GSE139430_SCNT_8C_CC_rep12_allValidPairs.txt.gz |
1.1 Gb |
(ftp)(http) |
TXT |
| GSE139430_SCNT_8C_MEF_rep12_allValidPairs.txt.gz |
616.8 Mb |
(ftp)(http) |
TXT |
| GSE139430_SCNT_Late2C_rep12_allValidPairs.txt.gz |
862.9 Mb |
(ftp)(http) |
TXT |
| GSE139430_SCNT_mESC_auxin_24h_H3K27ac_rep1_100bp_rpkm.tsv.gz |
27.2 Mb |
(ftp)(http) |
TSV |
| GSE139430_SCNT_mESC_auxin_24h_H3K9me3_rep1_100bp_rpkm.tsv.gz |
24.9 Mb |
(ftp)(http) |
TSV |
| GSE139430_SCNT_mESC_auxin_6h_H3K27ac_rep1_100bp_rpkm.tsv.gz |
21.9 Mb |
(ftp)(http) |
TSV |
| GSE139430_SCNT_mESC_auxin_6h_H3K9me3_rep1_100bp_rpkm.tsv.gz |
30.4 Mb |
(ftp)(http) |
TSV |
| GSE139430_SCNT_mESC_ctrl_H3K27ac_rep1_100bp_rpkm.tsv.gz |
23.0 Mb |
(ftp)(http) |
TSV |
| GSE139430_SCNT_mESC_ctrl_H3K9me3_rep1_100bp_rpkm.tsv.gz |
42.5 Mb |
(ftp)(http) |
TSV |
| GSE139430_mESC_SMC3_100bp_rpkm.tsv.gz |
31.5 Mb |
(ftp)(http) |
TSV |
| GSE139430_mouse_SCNT_PCC_1C_Late2C_8C_fpkm.txt.gz |
861.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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