Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naïve state
- School of Life Sciences and Technology, Tongji University, China
Figures
Figure 1 with 1 supplement
Establishment of the secondary naïve iPSC induction system.
(A) Representative bright field images of hiF-Ts, niPSC-Ts and reprogramming cells at the indicated time points during reprogramming. Scale bar, 100 μm. (B) Phase and OCT4-ΔPE-GFP images of niPSC-Ts …
Figure 1—figure supplement 1
Optimization of secondary human naïve iPSCs reprogramming system.
(A) Schematic overview of secondary naïve reprogramming strategy to generate human naïve iPSCs. 1° HEF, primary human embryonic fibroblasts; 1° piPSCs, primary primed iPSCs; 2° hiF, inducible …
Figure 2 with 2 supplements
Transcriptional profiling of cells during naïve reprogramming.
(A) Schematic representation of reprogramming intermediate collection at different time points, as indicated. hiF-T cells were first cultured in conventional hESM with dox for 6 days and then …
Figure 2—figure supplement 1
Transcriptional profiling of naïve pluripotency reprogramming cells.
(A) Correlation analysis (left panel) ad cell clustering analysis (right panel) of transcriptional profiles at different time points during naïve reprograming. (B) Bar plot showing dynamic changes …
Figure 2—figure supplement 2
Expression dynamics of gene clusters in Figure 2C.
Detailed description of Figure 2D gene clusters with specific expression patterns. Line plot and heatmap (left panels) showing expression patterns of each cluster during naïve reprograming. Grey …
Figure 3 with 2 supplements
Transient activation of transcripts with 8C-stage-like signatures during naïve reprogramming.
(A) Line plot showing expression dynamics of 8C-stage-specific genes during human embryonic development. Gray shades represent a 95% confidence interval around the mean value. (B) Line plot showing …
Figure 3—figure supplement 1
Dynamics of 8C-genes during naïve reprogramming.
(A) Bar plot showing the p-value of 8C-gene enrichments in each cluster measuring with Fisher’ exact test. (B) Line plot showing expression patterns of selected genes during human pre-implantation …
Figure 3—figure supplement 2
Dynamics of TEs during naïve reprogramming.
(A) Pie charts of genomic distribution of top 100 8C-TEs distribution (upper panel) and all TEs (lower panel), showing significant enrichment (Fisher’s exact test p-value=0.00408) in LTRs. (B) …
Figure 4 with 1 supplement
Changes in DNA methylation during naïve reprogramming.
(A) Bar plot showing changes in average DNA methylation ratios of all covered C sites during naïve and primed reprogramming. Error bars represent a 95% confidence interval around the mean value. (B) …
Figure 4—figure supplement 1
Dynamics of DNA methylation in naïve reprogramming.
(A) Histograms showing the distribution of methylation levels (%) across all CpGs at indicated time points during naïve reprogramming. a, average methylation level. (B) 5mC dynamics across naïve and …
Figure 5 with 1 supplement
Histone modification profiles during naïve reprogramming.
(A) Alluvial plots showing the global dynamics of genes covered by different chromatin states during naïve reprogramming. Each line represents a gene. Red bar represents genes with promoter that …
Figure 5—figure supplement 1
Dynamics of histone modifications in naïve reprogramming.
(A) Alluvial plots showing the global dynamics of genes covered by different chromatin states during naïve reprogramming. Each line represents a gene. Red bar represents genes with promoter that …
Figure 6 with 1 supplement
Integrative analysis of transcriptional and epigenetic dynamics during naïve reprogramming.
(A) Transcriptional dynamics of genes with different patterns are closely correlated with epigenetic modifications at promoter regions during naïve reprogramming. Black lines in the heatmaps …
Figure 6—figure supplement 1
Epigenetic changes of representative genes during naïve reprogramming path.
(A) Base-level visualization of DNA methylation and histone modifications in the promoter regions of representative genes. (B) Classification of genes by the CG ratio in their promoter. (C) …
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Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| gene () | NA | NA | ||
| strain, strain background () | NA | NA | ||
| genetic reagent () | NA | NA | ||
| cell line () | Human embryonic fibroblasts (HEFs); Primary primed iPSC lines; hiF-T cell lines; Secondary primed iPSC lines; Secondary naïve iPSC lines | This paper; Cacchiarelli, D., Trapnell, C., Ziller, M.J., Soumillon, M., Cesana, M., Karnik, R., Donaghey, J., Smith, Z.D., Ratanasirintrawoot, S., Zhang, X., et al. (2015). Cell. 2015 Jul 16;162(2):412–424. doi: 10.1016/j.cell.2015.06.016. Yan, L., Yang, M., Guo, H., Yang, L., Wu, J., Li, R., Liu, P., Lian, Y., Zheng, X., Yan, J., et al. (2013). Nat Struct Mol Biol. 2013 Sep;20(9):1131–9. doi: 10.1038/nsmb.2660. Epub 2013 Aug 11. | ||
| transfected construct () | dox-inducible, polycistronic OKMS lentiviral vector | Addgene 51543. Cacchiarelli, D., Trapnell, C., Ziller, M.J., Soumillon, M., Cesana, M., Karnik, R., Donaghey, J., Smith, Z.D., Ratanasirintrawoot, S., Zhang, X., et al. (2015).Cell. 2015 Jul 16;162(2):412–424. doi: 10.1016/j.cell.2015.06.016. | ||
| biological sample () | hiF-T/0d/2d/6d/8d/12d/14d/20d/ 24d+dox/24d-dox/niPSC-T; Oocyte/Zygote/2 cell/4 cell/8 cell/ Morula/MTE/PTE/EPI/PE/hESC0/hESC10; hiF-T/2d/6d/8d/14d/20d/24d+ dox/24d-dox/piPSC-T; | this paper; | ||
| antibody | anti-SSEA3, SSEA4, TRA-1–60, UTF1, DPPA3, ZSCNA4, MBD3L2 | Millipore MAB4304, Millipore MAB4360, Abcam ab24273, Santa Cruz sc- 67249, Millipore AB4340, Abcam ab174802 | ||
| recombinant DNA reagent | NA | NA | ||
| sequence-based reagent | KAPA Stranded mRNA-Seq Kit; KAPA DNA Library Preparation Kits | KAPA KK8401; KAPA KK8234 | ||
| peptide, recombinant protein | human LIF recombinant protein; bFGF recombinant protein | Peprotech 300–05; Peprotech 450–33 | ||
| commercial assay or kit | bowtie; TopHat; Cufflinks; edgeR; MACS2; | KAPA KK8401; KAPA KK8234 | ||
| chemical compound, drug | Activin A; PD0325901; IM-12; SB590885; WH-4–023; Y-27632; | Peprotech 120–14; Stemgent 04–0012; Enzo BML-WN102; R and D systems 2650; A Chemtek 0104–002013; Stemgent 04–0012; | ||
| software, algorithm | bowtie; TopHat; Cufflinks; edgeR; MACS2; | PMID: 22388286; PMID: 19289445; PMID: 22383036; PMID: 24743990; PMID: 18798982; | RRID:SCR_005476; RRID:SCR_013035; RRID:SCR_014597; RRID:SCR_012802; RRID:SCR_013291 | NA |
| other |
Additional files
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Source data 1
Source Data for Figures 2–6 and Figure Supplements.
The Source Data files include the source R code for Figures 2–6. The R scripts use the data in the ‘Expression Data’ folder with the relative path. The ‘Expression Data’ folder contains the non-redundant related gene expression, methylation and histone modification tables for the main figures and figure supplements.
- https://doi.org/10.7554/eLife.29518.016
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Transparent reporting form
- https://doi.org/10.7554/eLife.29518.017
