RNA sequencing analysis to demonstrate Erk dependent and independent functions of Mek.

Mek inhibition and Erk knockout (KO) have quite distinct effects on pluripotency maintenance in mouse embryonic stem cells (ESCs). To test whether there is an Erk-independent function of Mek, RNA-sequencing (RNA-seq) is carried out on six samples, WT KH2 ESCs treated with or without PD0325901 (PD) for 48 h (KH2_PD and KH2, respectively), iErk1; Erk KO ESCs cultured in the presence of Dox (P0), 48 and 96 h after Dox withdrawal (P1 and P2, respectively), and iErk1; Erk KO ESCs cultured without Dox for 96 h, and treated with PD in the last 48 h (P2_PD). These RNA-seq data demonstrate that Mek inhibition has quite different effect on the transcriptional profile of mouse ESCs, compared to Erk KO. Moreover, a significant fraction of genes is regulated by Mek inhibition, regardless of the presence or absence of Erk, indicating an Erk-independent function of Mek. RNA-seq data are deposited in Gene Expression Omnibus (GEO) datasets under accession number GSE70304.