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Series GSE139430 Query DataSets for GSE139430
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
Genome binding/occupancy profiling by high throughput sequencing
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.
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.
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
Organization name Tsinghua university
Department School of Life Sciences
Lab Wei Xie
Street address Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100084
Country China
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (75)
GSM4141596 RNA_PCC_rep1
GSM4141597 RNA_PCC_rep2
GSM4141598 RNA_PPN1_rep1
BioProject PRJNA579764
SRA SRP227097

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Series Matrix File(s) TXTHelp

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
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