Data from: α-Ketoglutarate inhibits the pluripotent-to-totipotent state transition
Data files
Feb 03, 2025 version files 2.08 MB
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README.md
3.43 KB
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Supplementary_Table_.xlsx
2.07 MB
Abstract
In early mouse embryogenesis, the distinct enrichment of α-ketoglutarate (αKG) in blastocysts and L-2-hydroxyglutarate (L-2HG) in 2-cell (2C) embryos serves as a key metabolic signature. While elevated L-2HG levels inhibit the resolution of totipotency during the transition from the 2C stage to the blastocyst, the role of αKG remains elusive. Mouse embryonic stem cells (mESCs) cultured in vitro naturally harbor a subpopulation that transitions dynamically into a 2C-like totipotent state, providing a convenient model to investigate the role of αKG in totipotency reprogramming. This study demonstrates that αKG significantly inhibits the pluripotency to totipotency transition through upregulating ten-eleven translocation (TET) DNA hydroxylases. We further show that reducing endogenous αKG levels via glutamine withdrawal or inhibiting αKG-dependent dioxygenases by blocking succinate dehydrogenase (SDH) markedly enhances the induction of 2C-like cells (2CLCs). Finally, leveraging the potent SDH inhibitor dimethyl malonate (DMM), we have developed a highly efficient protocol for 2CLC induction, producing cells that transcriptionally resemble mid-to-late 2C embryos. Our findings deepen the understanding of the metabolic regulation of totipotency and provide a previously undescribed approach for capturing totipotent-like stem cells in vitro.
README: README: Supplementary Data Description
General Information
This README file provides details about the supplementary tables included in the dataset. These tables contain shRNA sequence information, primer details, RNA sequencing, and scRNA sequencing data related to MERVL-GFP cell line under different experimental conditions.
File Description
The provided Excel file consists of the following supplementary tables:
Supplementary Table 1: shRNA Sequences
- This table contains the sequences of short hairpin RNAs (shRNAs) used in the study.
- Column descriptions:
- Gene: Gene targeted by the shRNA
- Target Sequence: Nucleotide sequence of the shRNA
Supplementary Table 2: Primer Sequences for RT-qPCR
- This table lists the primer sequences used for reverse transcription quantitative PCR (RT-qPCR).
- Column descriptions:
- Gene: Target gene for qPCR
- Forward Primer (5'→3'): Forward primer sequence
- Reverse Primer (5'→3'): Reverse primer sequence
Supplementary Table 3: MERVL-GFP Bulk RNA Sequencing Data
- This table reports bulk RNA sequencing data for MERVL-GFP-expressing cells.
- Includes differential expression analysis for the following comparison:
- DMM 30 mM treated cells vs. Control cells
- Column descriptions:
- Gene symbol: Official gene symbol corresponding to the differentially expressed gene.
- Ensembl ID: Unique Ensembl identifier for the gene.
- D30 Log2 FC: Log2 fold change in gene expression for DMM 30 mM vs. SL (Control).
- D30 padj: Adjusted p-value for the differential expression analysis of DMM 30 mM vs. SL (Control).
- VTD Log2 FC: Log2 fold change in gene expression for VTD-treated vs. SL (Control).
- VTD padj: Adjusted p-value for the differential expression analysis of VTD-treated vs. SL (Control).
Supplementary Table 4: Single-Cell RNA Sequencing Data of MERVL-GFP cell line (VTD Treatment)
- This table reports single-cell RNA sequencing data for MERVL-GFP cell line.
- Includes differential expression analysis for the following comparison:
- VTD treated cells vs. Control cells
- Column descriptions:
- Gene symbol: Official gene symbol corresponding to the differentially expressed gene.
- Ensembl ID: Unique Ensembl identifier for the gene.
- VTD Log2 FC: Log2 fold change in gene expression for VTD-treated vs. SL (Control).
- VTD padj: Adjusted p-value for the differential expression analysis of VTD-treated vs. SL (Control).
Supplementary Table 5: Single-Cell RNA Sequencing Data of Selected MERVL-GFP Cells (VTD Treatment)
- This table reports single-cell RNA sequencing data for MERVL-GFP cell line.
- Includes differential expression analysis for the following comparison:
- VTD-2CLC cells (top 200 VTD-treated cells selected based on totipotency gene expression) vs. Control cells (randomly selected 200 Control cells)
- Column descriptions:
- Gene symbol: Official gene symbol corresponding to the differentially expressed gene.
- Ensembl ID: Unique Ensembl identifier for the gene.
- VTD-2CLC Log2 FC: Log2 fold change in gene expression for VTD-2CLC vs. SL cells (Control).
- VTD-2CLC padj: Adjusted p-value for the differential expression analysis of for VTD-2CLC vs. SL cells (Control).
Notes
- Data are provided in standard tabular format (.xlsx).