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| Status |
Public on Oct 03, 2023 |
| Title |
Epigenetic dynamics during capacitation of naïve human pluripotent stem cells [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Human pluripotent stem cells (hPSCs) are of fundamental relevance in regenerative medicine and the primary source for many novel cellular therapies. The development of naïve culture conditions has led to the expectation that these naïve hPSCs could overcome some of the limitations found in conventional (primed) hPSCs culture conditions, including recurrent epigenetic anomalies. Recent work has shown that transition to the primed state (or capacitation) is necessary for naïve hPSCs to acquire multi-lineage differentiation competence. This pluripotent state transition may recapitulate essential features of human peri-implantation development. Here we studied epigenetic changes during the transition between naïve and primed pluripotency, examining global genomic redistribution of histone modifications, chromatin accessibility, and DNA methylation, and correlating these with gene expression. We identify CpG islands, enhancers, and retrotransposons as hotspots of epigenetic dynamics between pluripotency states. Our results further reveal that hPSC resetting and subsequent capacitation rescue X chromosome-linked epigenetic erosion and reduce the ectoderm-biased gene expression of conventional primed hPSCs.
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| Overall design |
2 lines of human naïve pluripotent stem cells (embryo-derived HNES1 and chemically reset cR-H9-EOS) were cultured in N2B27 and 2uM XAV939 for 10 days. After that the cells were split into two conditions: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF), or E8 medium, for extended maintenance. The experiment was performed with the cells on day 0 and 10, when the cells were cultured in XAV939; and one time point after transfer to maintenance conditions, at not less than 22 days of culture from the start of the experiment. Conventional hPSC cell line H9-EOS, which was a parental line for the chemically reset cR-H9-EOS was used as a control.
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| Contributor(s) |
Agostinho de Sousa J, Rostovskaya M, Wong C, Reik W, Smith A, von Meyenn F |
| Citation(s) |
37774033 |
| Submission date |
Nov 21, 2022 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Laura Biggins |
| E-mail(s) |
laura.biggins@babraham.ac.uk
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| Organization name |
The Babraham Institute
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| Department |
Bioinformatics
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| Street address |
Babraham Research Campus
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| City |
Cambridge |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (70)
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| GSM6749147 |
HNES1_d0_rep2, H3K4me1 |
| GSM6749148 |
cR_H9_EOS_d10_rep1, H3K4me1 |
| GSM6749149 |
cR_H9_EOS_d10_rep2, H3K4me1 |
| GSM6749150 |
HNES1_d10_rep1, H3K4me1 |
| GSM6749151 |
HNES1_d10_rep2, H3K4me1 |
| GSM6749152 |
cR_H9_EOS_d20E_rep1, H3K4me1 |
| GSM6749153 |
cR_H9_EOS_d20E_rep2, H3K4me1 |
| GSM6749154 |
cR_H9_EOS_d20X_rep1, H3K4me1 |
| GSM6749155 |
cR_H9_EOS_d20X_rep2, H3K4me1 |
| GSM6749156 |
H9_EOS_rep1, H3K4me1 |
| GSM6749157 |
H9_EOS_rep2, H3K4me1 |
| GSM6749158 |
cR_H9_EOS_d0_rep1, H3K4me3 |
| GSM6749159 |
cR_H9_EOS_d0_rep2, H3K4me3 |
| GSM6749160 |
cR_H9_EOS_d10_rep1, H3K4me3 |
| GSM6749161 |
cR_H9_EOS_d10_rep2, H3K4me3 |
| GSM6749162 |
cR_H9_EOS_d20E_rep1, H3K4me3 |
| GSM6749163 |
cR_H9_EOS_d20E_rep2, H3K4me3 |
| GSM6749164 |
cR_H9_EOS_d20X_rep1, H3K4me3 |
| GSM6749165 |
cR_H9_EOS_d20X_rep2, H3K4me3 |
| GSM6749166 |
H9_EOS_rep1, H3K4me3 |
| GSM6749167 |
H9_EOS_rep2, H3K4me3 |
| GSM6749168 |
HNES1_d0_rep1, H3K4me3 |
| GSM6749169 |
HNES1_d0_rep2, H3K4me3 |
| GSM6749170 |
HNES1_d10_rep1, H3K4me3 |
| GSM6749171 |
HNES1_d10_rep2, H3K4me3 |
| GSM6749172 |
cR_H9_EOS_d0_rep1, H3K9me3 |
| GSM6749173 |
cR_H9_EOS_d0_rep2, H3K9me3 |
| GSM6749174 |
cR_H9_EOS_d10_rep1, H3K9me3 |
| GSM6749175 |
cR_H9_EOS_d10_rep2, H3K9me3 |
| GSM6749176 |
cR_H9_EOS_d20E_rep1, H3K9me3 |
| GSM6749177 |
cR_H9_EOS_d20E_rep2, H3K9me3 |
| GSM6749178 |
cR_H9_EOS_d20X_rep1, H3K9me3 |
| GSM6749179 |
cR_H9_EOS_d20X_rep2, H3K9me3 |
| GSM6749180 |
H9_EOS_rep1, H3K9me3 |
| GSM6749181 |
H9_EOS_rep2, H3K9me3 |
| GSM6749182 |
HNES1_d0_rep1, H3K9me3 |
| GSM6749183 |
HNES1_d0_rep2, H3K9me3 |
| GSM6749184 |
HNES1_d10_rep1, H3K9me3 |
| GSM6749185 |
HNES1_d10_rep2, H3K9me3 |
| GSM6749186 |
cR_H9_EOS_d0_rep1, H3K27ac |
| GSM6749187 |
cR_H9_EOS_d0_rep2, H3K27ac |
| GSM6749188 |
cR_H9_EOS_d10_rep1, H3K27ac |
| GSM6749189 |
cR_H9_EOS_d10_rep2, H3K27ac |
| GSM6749190 |
cR_H9_EOS_d20E_rep1, H3K27ac |
| GSM6749191 |
cR_H9_EOS_d20E_rep2, H3K27ac |
| GSM6749192 |
cR_H9_EOS_d20X_rep1, H3K27ac |
| GSM6749193 |
cR_H9_EOS_d20X_rep2, H3K27ac |
| GSM6749194 |
H9_EOS_rep2, H3K27ac |
| GSM6749195 |
H9_EOS_rep1, H3K27ac |
| GSM6749196 |
HNES1_d0_rep1, H3K27ac |
| GSM6749197 |
HNES1_d0_rep2, H3K27ac |
| GSM6749198 |
HNES1_d10_rep1, H3K27ac |
| GSM6749199 |
HNES1_d10_rep2, H3K27ac |
| GSM6749200 |
cR_H9_EOS_d0_rep1, H3K27me3 |
| GSM6749201 |
cR_H9_EOS_d0_rep2, H3K27me3 |
| GSM6749202 |
cR_H9_EOS_d10_rep1, H3K27me3 |
| GSM6749203 |
cR_H9_EOS_d10_rep2, H3K27me3 |
| GSM6749204 |
cR_H9_EOS_d20E_rep1, H3K27me3 |
| GSM6749205 |
cR_H9_EOS_d20E_rep2, H3K27me3 |
| GSM6749206 |
cR_H9_EOS_d20X_rep1, H3K27me3 |
| GSM6749207 |
cR_H9_EOS_d20X_rep2, H3K27me3 |
| GSM6749208 |
H9_EOS_rep1, H3K27me3 |
| GSM6749209 |
H9_EOS_rep2, H3K27me3 |
| GSM6749210 |
HNES1_d0_rep1, H3K27me3 |
| GSM6749211 |
HNES1_d0_rep2, H3K27me3 |
| GSM6749212 |
HNES1_d10_rep1, H3K27me3 |
| GSM6749213 |
HNES1_d10_rep2, H3K27me3 |
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| This SubSeries is part of SuperSeries: |
| GSE218512 |
Epigenetic dynamics during capacitation of naïve human pluripotent stem cells |
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| Relations |
| BioProject |
PRJNA904046 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE218510_H3K27ac.tar.gz |
3.0 Gb |
(ftp)(http) |
TAR |
| GSE218510_H3K27me3.tar.gz |
1.7 Gb |
(ftp)(http) |
TAR |
| GSE218510_H3K4me1.tar.gz |
3.1 Gb |
(ftp)(http) |
TAR |
| GSE218510_H3K4me3.tar.gz |
2.3 Gb |
(ftp)(http) |
TAR |
| GSE218510_H3K9me3.tar.gz |
2.0 Gb |
(ftp)(http) |
TAR |
| GSE218510_peaks.tar.gz |
100.0 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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