RNA seq comparative analysis of XX, XY, and XXTet3-/- mutant mouse embryonic stem cells versus XX, XY, and XXTet3-/- mutant epiblast-like cells

In XXTet3-/- mESCs DNA methylation levels are higher than XX wildtype levels. We sought to determine if changes in cytosine modifications observed in XXTet3-/- mESCs impacted gene expression, we performed RNA-seq. 104 genes were up regulated in the mutant XX mESCs relative to wild type controls, and 86 were down regulated To ask whether the XX-specific nuclear enrichment of TET3 is necessary for a developmental transition, we differentiated WT XX and XXTet3-/- mESCs into epiblast-like cells (EpiLCs). Comparison of WT XX and XXTet3-/- EpiLC RNA-seq showed that 404 genes exhibited increased expression and 499 exhibited decreased expression in mutant cells. GO term analysis showed gene expression changes affecting several LIF and BMP signaling pathways. However, despite these changes in signaling pathway driven expression, the expression of mESC markers went down and mEpiLC markers went up comparably upon differentiation WT XX and XXTet3-/- mESCs, suggesting that many key transcriptional changes that characterize this transition can occur without TET3. Comparative RNA seq analysis to determine if TET3 is necessary for the developmental transition of mESC to EpiLCs