Methylation of lysine residues in histone tails is an intensively studied epigenetic signal that regulates transcription throughout development. Methylation of histone 3 lysine 4 (H3K4) is usually associated with promoters of actively transcribed genes whereas H3K27 or H3K9 methylation silences genes. Yeast possess only one H3K4 methyltransferase, Set1. In contrast, there are six enzymes capable of catalyzing this modification in mammals implying a certain specialization or division of labor. The present study examined the functions of the mouse H3K4 methyltransferase paralogs, Mixed Lineage Leukemia 1 (Mll1) and Mll2, during neural differentiation and reprogramming of neural stem (NS) cells to induced pluripotency. We could show that Mll2 is required for differentiation of embryonic stem (ES) cells to neural progenitors and identified Nuclear transport factor 2-like export factor 2 (Nxt2) as essential target gene. Mll2 trimethylated the Nxt2 promoter in ES cells in order to allow for transcriptional upregulation during subsequent neural differentiation. Additionally, Mll2 prevented apoptosis of differentiating cells by regulating B cell leukemia/lymphoma 2 (Bcl2) levels. Mll1 could replace Mll2 after the first steps of cell commitment towards epiblast stem (EpiS) cells. While Mll2 activity was only required briefly when ES cells started to differentiate, the influence of Mll1 seemed to increase with developmental progression. It stabilized the NS cell state by regulating expression of the neural transcription factor Orthodenticle homolog 2 (Otx2). Thereby, Mll1 impeded early steps of reprogramming to induced pluripotency and its inactivation increased the efficiency. Besides their specificity for certain target genes, both enzymes also differed in their activity. The major function of Mll1 was to prevent silencing by H3K27 methylation and possibly recruitment of transcription factors. In contrast, Mll2 conducted H3K4 trimethylation of its target genes. Importantly, once established in NS cells, the expression of Nxt2 became independent of promoter H3K4 methylation. Thus, Mll2 and its target gene Nxt2 represent an example for H3K4 methylation functioning as priming mechanism rather than for fine-tuning or maintenance of transcription levels.