The nuclear oncoprotein SET is necessary for MLL/KMT2A binding and transcriptional elongation.

Abstract

The nuclear oncoprotein SET (patient "SE" translocation) has been implicated in the etiology of MLL/KMT2A-fusion induced leukemia. Here we examine the details of this dependency in murine, primary hematopoietic cells. Experiments demonstrated Set as downstream target of HoxA9 and a direct interactor of Mll/Kmt2A. Mll/Kmt2A and Set globally co-bound promoter regions. Impairing Set expression induced a metabolic shift towards oxidative phosphorylation phenocopying a knockdown of Mll/Kmt2A fusion targets. Set acted predominantly as transcriptional activator driving a pro-proliferative gene expression program with features indicative for Mll/Kmt2A involvement. Molecularly, Set depletion caused dissociation of Mll/Kmt2A from chromatin accompanied by a selective loss of elongating RNA PolymeraseII Ser2-P. Concomitant with a function of Set as inhibitor of protein phosphatase 2A (PP2A), specific recruitment of PP2A to the Meis1 promoter, a known Mll/Kmt2A target, inhibited transcription in reporter assays and in a natural chromatin environment. We identified Mitogen and stress induced kinase 1 (Msk1) as potential substrate protected by Set from dephosphorylation. Active and phosphorylated Msk1-P colocalized with Mll and disappeared from chromatin upon Set depletion. Biochemically, Msk-1 bound directly to Mll/Kmt2A as well as to menin, a known Mll/Kmt2a tethering factor. Loss of Set/Mll/Msk1 selectively affected H3K14 acetylation at promoters and this could be partially attributed to the reduced presence of the histone acetyltransferase Moz/Kat6a. Finally, we show that kinase and menin inhibitors cooperate in leukemia cells indicating that the relay function of Mll/Kmt2A, allowing control of hematopoiesis by cellular signaling, is retained in MLL-fusion proteins.