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| Status |
Public on Aug 20, 2024 |
| Title |
ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The primed epiblast acts as a transitional stage between the relatively homogeneous naïve epiblast and the gastrulating embryo. Its formation entails coordinated changes in regulatory circuits driven by strict epigenetic mechanisms. Using a multi-omic approach in human embryonic stem cell models across the spectrum of peri-implantation development, we demonstrate that the transcription factors ZIC2 and ZIC3 have overlapping but essential roles in opening primed-specific enhancers. Together they are essential to facilitate progression to and maintain primed pluripotency. ZIC2/3 achieve their function by recruiting SWI/SNF to chromatin and loss of ZIC2/3 or degradation of SWI/SNF both prevent enhancer activation. Loss of ZIC2/3 results in transcriptome changes consistent with perturbed Polycomb activity and a shift towards the expression of genes linked to mesendoderm differentiation. Additionally, we find an intriguing dependency on the transcriptional machinery for sustained recruitment of ZIC2/3 over a subset of primed-hESC specific enhancers. Taken together, ZIC2 and ZIC3 regulate highly dynamic lineage-specific enhancers and collectively act as key regulators of human primed pluripotency.
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| Overall design |
Profiling of genome-wide chromatin occupancy dynamics of ZIC2 and ZIC3 in primed hPSCs, and the effect on BRG1 and H3K27me3 occupancy upon loss of ZIC2 and ZIC3 or upon gain of ZIC2 in primed hESCs and naïve hESCs respectively.
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| Contributor(s) |
Hossain I, Pastor WA |
| Citation missing |
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| Submission date |
Jun 25, 2024 |
| Last update date |
Aug 20, 2024 |
| Contact name |
William A. Pastor |
| E-mail(s) |
william.pastor@mcgill.ca
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| Phone |
5143988962
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| Organization name |
McGill University
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| Department |
Biochemistry
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| Street address |
3655 Promenade Sir-William-Osler
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3G1Y6 |
| Country |
Canada |
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| Platforms (4)
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| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL20795 |
HiSeq X Ten (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL34281 |
Illumina NovaSeq X (Homo sapiens) |
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| Samples (107)
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| GSM8351849 |
UCLA1 primed hESC, ZIC2 ChIP-seq, rep1 |
| GSM8351850 |
UCLA1 primed hESC, IgG ChIP-seq, rep1 |
| GSM8351851 |
UCLA1 primed hESC, Input, rep1 |
| GSM8351852 |
UCLA1 primed hESC, ZIC2 ChIP-seq, rep2 |
| GSM8351853 |
UCLA1 primed hESC, IgG ChIP-seq, rep2 |
| GSM8351854 |
UCLA1 primed hESC, Input, rep2 |
| GSM8351855 |
UCLA1 primed hESC, ZIC2 ChIP-seq, rep3 (technical rep 1) |
| GSM8351856 |
UCLA1 primed hESC, IgG ChIP-seq, rep3 |
| GSM8351857 |
UCLA1 primed hESC, ZIC2 ChIP-seq, rep3 (technical rep 2) |
| GSM8351858 |
UCLA1 primed hESC, Input, rep3 |
| GSM8351859 |
UCLA1 primed hESC, IgG ChIP-seq, rep4 |
| GSM8351860 |
UCLA1 primed hESC, ZIC2 ChIP-seq, rep4 |
| GSM8351861 |
UCLA1 primed hESC, Input, rep4 |
| GSM8351862 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, Flag ChIP-seq |
| GSM8351863 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, H3K27me3 ChIP-seq, rep1 |
| GSM8351864 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, Input, rep1 |
| GSM8351865 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, H3K27me3 ChIP-seq, rep2 |
| GSM8351866 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, Input, rep2 |
| GSM8351867 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 24h, Flag ChIP-seq |
| GSM8351868 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 24h, H3K27me3 ChIP-seq, rep1 |
| GSM8351869 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 24h, Input, rep1 |
| GSM8351870 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 24h, H3K27me3 ChIP-seq, rep2 |
| GSM8351871 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 24h, Input, rep2 |
| GSM8351872 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 72h, Flag ChIP-seq |
| GSM8351873 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 72h, H3K27me3 ChIP-seq |
| GSM8351874 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 72h, Input (control for H3K27me3 ChIP) |
| GSM8351875 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 72h, Input (control for Flag ChIP) |
| GSM8351876 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 8h, Flag ChIP-seq |
| GSM8351877 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 8h, H3K27me3 ChIP-seq, rep1 |
| GSM8351878 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 8h, Input, rep1 |
| GSM8351879 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 8h, H3K27me3 ChIP-seq, rep2 |
| GSM8351880 |
UCLA1 naïve hESC, Inducible ZIC2 DOX 8h, Input, rep2 |
| GSM8351881 |
UCLA1 primed hESC, ZIC2-/-, H3K27me3 ChIP-seq, rep1 |
| GSM8351882 |
UCLA1 primed hESC, ZIC2-/-, Input, rep1 |
| GSM8351883 |
UCLA1 primed hESC, ZIC2-/-, H3K27me3 ChIP-seq, rep2 |
| GSM8351884 |
UCLA1 primed hESC, ZIC2-/-, Input, rep2 |
| GSM8351885 |
UCLA1 primed hESC, ZIC2-/-, H3K27me3 ChIP-seq, rep3 |
| GSM8351886 |
UCLA1 primed hESC, ZIC2-/-, Input, rep3 |
| GSM8351887 |
UCLA1 primed hESC, H2AK119ub ChIP-seq, rep1 |
| GSM8351888 |
UCLA1 primed hESC, NT control, H3K27me3 ChIP-seq, rep1 |
| GSM8351889 |
UCLA1 primed hESC, NT control, Input, rep1 |
| GSM8351890 |
UCLA1 primed hESC, NT control, H3K27me3 ChIP-seq, rep3 |
| GSM8351891 |
UCLA1 primed hESC, NT control, Input, rep3 |
| GSM8351892 |
UCLA1 primed hESC, H2AK119ub ChIP-seq, rep2 |
| GSM8351893 |
UCLA1 primed hESC, NT control, H3K27me3 ChIP-seq, rep2 |
| GSM8351894 |
UCLA1 primed hESC, NT control, Input, rep2 |
| GSM8351895 |
UCLA1 primed hESC, NT control, H3K27me3 ChIP-seq, rep4 |
| GSM8351896 |
UCLA1 primed hESC, NT control, Input, rep4 |
| GSM8351897 |
UCLA1 PXGL naïve hESC, Inducible ZIC2 DOX 16h, Flag ChIP-seq, rep1 |
| GSM8351898 |
UCLA1 PXGL naïve hESC, Inducible ZIC2 DOX 16h, Input, rep1 |
| GSM8351899 |
UCLA1 PXGL naïve hESC, Inducible ZIC2 DOX 16h, Flag ChIP-seq, rep2 |
| GSM8351900 |
UCLA1 PXGL naïve hESC, Inducible ZIC2 DOX 16h, Input, rep2 |
| GSM8351901 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, H3K27me3 ChIP-seq, rep1 |
| GSM8351902 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, H3K27me3 ChIP-seq, rep1 |
| GSM8351903 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, H3K27me3 ChIP-seq, rep2 |
| GSM8351904 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, H3K27me3 ChIP-seq, rep2 |
| GSM8351905 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, Input, rep1 |
| GSM8351906 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, Input, rep1 |
| GSM8351907 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, Input, rep2 |
| GSM8351908 |
UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, Input, rep2 |
| GSM8351909 |
UCLA1 primed hESC, WT +sgNT, H2AK119ub ChIP-seq, rep1 |
| GSM8351910 |
UCLA1 primed hESC, WT +sgNT, H2AK119ub ChIP-seq, rep2 |
| GSM8351911 |
UCLA1 primed hESC, WT +sgNT, Input, rep1 |
| GSM8351912 |
UCLA1 primed hESC, WT +sgNT, Input, rep2 |
| GSM8351913 |
UCLA1 primed hESC, ZIC2-/- +sgZIC3, H2AK119ub ChIP-seq, rep1 |
| GSM8351914 |
UCLA1 primed hESC, ZIC2-/- +sgZIC3, H2AK119ub ChIP-seq, rep2 |
| GSM8351915 |
UCLA1 primed hESC, ZIC2-/- +sgZIC3, Input, rep1 |
| GSM8351916 |
UCLA1 primed hESC, ZIC2-/- +sgZIC3, Input, rep2 |
| GSM8351917 |
UCLA1 primed hESC, DMSO 1h, Input |
| GSM8351918 |
UCLA1 primed hESC, DMSO 1h, ZIC2 ChIP-seq |
| GSM8351919 |
UCLA1 primed hESC, TRP 1h, Input |
| GSM8351920 |
UCLA1 primed hESC, TRP 1h, ZIC2 ChIP-seq |
| GSM8351921 |
UCLA1 primed hESC, DMSO, Input, rep1 |
| GSM8351922 |
UCLA1 primed hESC, DMSO, ZIC2 ChIP-seq, rep1 |
| GSM8351923 |
UCLA1 primed hESC, FLV 4h, Input, rep1 |
| GSM8351924 |
UCLA1 primed hESC, FLV 4h, ZIC2 ChIP-seq, rep1 |
| GSM8351925 |
UCLA1 primed hESC, STM2457 24h, Input, rep1 |
| GSM8351926 |
UCLA1 primed hESC, STM2457 24h, ZIC2 ChIP-seq, rep1 |
| GSM8351927 |
UCLA1 primed hESC, DMSO, Input, rep2 |
| GSM8351928 |
UCLA1 primed hESC, DMSO, ZIC2 ChIP-seq, rep2 |
| GSM8351929 |
UCLA1 primed hESC, FLV 4h, Input, rep2 |
| GSM8351930 |
UCLA1 primed hESC, FLV 4h, ZIC2 ChIP-seq, rep2 |
| GSM8351931 |
UCLA1 primed hESC, STM2457 24h, Input, rep2 |
| GSM8351932 |
UCLA1 primed hESC, STM2457 24h, ZIC2 ChIP-seq, rep2 |
| GSM8351933 |
UCLA1 primed hESC, TRP 4h, Input, rep1 |
| GSM8351934 |
UCLA1 primed hESC, TRP 4h, ZIC2 ChIP-seq, rep1 |
| GSM8351935 |
UCLA1 primed hESC, DMSO, Input (control for TRP 4h), rep1 |
| GSM8351936 |
UCLA1 primed hESC, DMSO, ZIC2 ChIP-seq (control for TRP 4h), rep1 |
| GSM8351937 |
UCLA1 primed hESC, TRP 4h, Input, rep2 |
| GSM8351938 |
UCLA1 primed hESC, TRP 4h, ZIC2 ChIP-seq, rep2 |
| GSM8351939 |
UCLA1 primed hESC, DMSO, Input (control for TRP 4h), rep2 |
| GSM8351940 |
UCLA1 primed hESC, DMSO, ZIC2 ChIP-seq (control for TRP 4h), rep2 |
| GSM8351941 |
UCLA1 primed hESC, ZIC2 ChIP-seq, rep5 |
| GSM8351942 |
UCLA1 primed hESC, Input, rep5 |
| GSM8351943 |
UCLA1 primed hESC, Inducible ZIC2 DOX 16h, Flag ChIP-seq |
| GSM8351944 |
UCLA1 primed hESC, Inducible ZIC2 DOX 16h, Input |
| GSM8351945 |
UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgNT, Input, rep2 |
| GSM8351946 |
UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgNT, ZIC3 ChIP-seq, rep2 |
| GSM8351947 |
UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgNT, Input, rep1 |
| GSM8351948 |
UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgNT, ZIC3 ChIP-seq, rep1 |
| GSM8351949 |
UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgZIC3, ZIC3 ChIP-seq |
| GSM8351950 |
UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgZIC3, Input |
| GSM8351951 |
UCLA1 primed hESC, Inducible ZIC3 DOX 16h, Flag ChIP-seq |
| GSM8351952 |
UCLA1 primed hESC, Inducible ZIC3 DOX 16h, Input |
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| This SubSeries is part of SuperSeries: |
| GSE270787 |
ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency |
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| Relations |
| BioProject |
PRJNA1128168 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE270784_RAW.tar |
19.4 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
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