Tet-dependent transcriptional programs during mESC differentiation. Mus musculus

Tet-family dioxygenases catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. Here, we show that Tet3 deficiency impairs neural differentiation of mouse ESCs, resulting in skewing towards cardiac mesoderm; conversely, ectopic expression of Tet3 enhances neural differentiation and limits cardiac mesoderm specification. To determine the effects of Tet3 gain and loss on global gene expression profiles during mESC differentiation, we performed whole transcriptome RNA-sequencing (RNA-seq) analysis of (i) WT and Tet3 KO mESCs differentiating into neuroectoderm under SFEB culture (days 6 and 10); and (ii) Control and Tet3-overexpressing mESCs in non-permissive neural differentiation conditions containing FBS (days 4 and 7). Genome-wide analyses showed that Tet3 mediates cell-fate decision by inhibiting Wnt signaling. Overall design: Total RNA obtained from ES cells under the following conditions: (i) WT and Tet3 KO mESCs differentiating into neuroectoderm under SFEB culture (days 6 and 10); and (ii) Control and Tet3-overexpressing mESCs in non-permissive neural differentiation conditions containing FBS (days 4 and 7). Multiplexed libraries were constructed using SOLiD Total RNA-seq kit. Libraries were sequenced on the SOLiD 5500 platforms according to the manufacturer's instructions.