Identification and Characterization of Novel SET Domain-Containing Histone Lysine Methyltransferase and Implications of Histone Methylation in Acute Leukemia.

Evolutionally conserved SET domains, which methylate histone lysine residues, and thereby methylation of histones have been implicated in diverse malignancies including leukemias or multiple myelomas. Here we describe novel SET domain-containing proteins with histone methyltransferase (HMTase) activity and their characteristics. Using bioinformatics for homology screening, SET-domain containing proteins named WHISTLE, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, and RE-IIBP, interleukin-5 response element II binding protein, were identified. By mass spectrometric and immunoblot analysis, we demonstrated that WHISTLE dimethylates H9K4 and di-, and tri-methylates H3K27, while RE-IIBP methylates only H9K27. WHISTLE and RE-IIBP repressed transcription of the SV40 and IL-5 promoter activity and they recruited histone deacetylase. Chromatin immunoprecipitation analysis revealed that shRNA-mediated knockdown of RE-IIBP reduces histone methylation on the IL-5 promoter. Both proteins induce apoptosis in leukemic cells via caspase-3 activation. In acute lymphoblastic leukemia patients, the expression of RE-IIBP and WHISTLE was increased, which was accompanied with increase in the methylation histone 3. These data illustrate the important regulatory role of novel SET domain proteins with HMTase activity in transcriptional regulation and apoptosis, thereby pointing to the critical role in leukemogenesis.