ABSTRACT
Histone methylation by histone methyltransferases (HMTases) has a key role in transcriptional regulation. Discrepancies between the known HMTases and the histone lysine methylome suggest that HMTases remain to be identified. Here we report the discovery, characterization, and crystal structure of Schizosaccharomyces pombe Set7, an HMTase methylating the uncharted histone H3 lysine 37 (H3K37) mark. Set7 forms a dimer with its substrate-binding site structurally specific to K37, not the neighboring well-studied K36 mark. We also discovered that H3K37 methylation levels dramatically increase during gametogenesis. Set7 deletion mutant cells show defects in gametogenesis and produce the abnormal number of spores with aberrant morphology. S. pombe gametogenesis shares similarities with mammalian spermatogenesis. These findings extend our understanding of epigenetic regulation during gametogenesis and support a link between Set7, the epigenetic H3K37 methyl mark, and proper gametogenesis.
Subject(s)
Gametogenesis/genetics , Histone-Lysine N-Methyltransferase/genetics , Histones/metabolism , Protein Processing, Post-Translational , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces/genetics , Amino Acid Sequence , Epigenesis, Genetic , Histone-Lysine N-Methyltransferase/metabolism , Histones/genetics , Methylation , Models, Molecular , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Schizosaccharomyces/growth & development , Schizosaccharomyces/metabolism , Schizosaccharomyces/ultrastructure , Schizosaccharomyces pombe Proteins/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Spores, Fungal/genetics , Spores, Fungal/growth & development , Spores, Fungal/metabolism , Spores, Fungal/ultrastructureABSTRACT
The NSD family (NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1) are histone lysine methyltransferases (HMTases) essential for chromatin regulation. The NSDs are oncoproteins, drivers of a number of tumors and are considered important drug-targets but the lack of potent and selective inhibitors hampers further therapeutic development and limits exploration of their biology. In particular, MMSET/NSD2 selective inhibition is being pursued for therapeutic interventions against multiple myeloma (MM) cases, especially in multiple myeloma t(4;14)(p16.3;q32) translocation that is associated with a significantly worse prognosis than other MM subgroups. Multiple myeloma is the second most common hematological malignancy, after non-Hodgkin lymphoma and remains an incurable malignancy. Here we report the discovery of LEM-14, an NSD2 specific inhibitor with an in vitro IC50 of 132⯵M and that is inactive against the closely related NSD1 and NSD3. LEM-14-1189, a LEM-14 derivative, differentially inhibits the NSDs with in vitro IC50 of 418⯵M (NSD1), IC50 of 111⯵M (NSD2) and IC50 of 60⯵M (NSD3). We propose LEM-14 and derivative LEM-14-1189 as tools for studying the biology of the NSDs and constitute meaningful steps toward potent NSDs therapeutic inhibitors.
Subject(s)
Enzyme Inhibitors/pharmacology , Histone-Lysine N-Methyltransferase/antagonists & inhibitors , Oncogene Proteins/antagonists & inhibitors , Repressor Proteins/antagonists & inhibitors , Catalytic Domain , Drug Design , Drug Discovery , Drug Evaluation, Preclinical , Enzyme Inhibitors/chemistry , Histone-Lysine N-Methyltransferase/chemistry , Histone-Lysine N-Methyltransferase/genetics , Humans , Kinetics , Models, Molecular , Molecular Docking Simulation , Molecular Structure , Protein Conformation , Repressor Proteins/chemistry , Repressor Proteins/genetics , User-Computer InterfaceABSTRACT
Dysfunction of histone-modifying enzymes affects chromatin regulation and is involved in carcinogenesis, tumour progression and other diseases. Histone methyltransferases are a family of key histone-modifying enzymes, but their structures, functions and mechanisms are incompletely understood, thus constraining drug-design efforts. Here, preliminary steps towards structure-function studies of Schizosaccharomyces pombe Set7, a putative histone methyltransferase and the first yeast full-length SET-domain-containing protein to be studied using X-ray crystallography, are reported. The methods from cloning to X-ray diffraction and phasing are discussed and the results will aid in prospective studies of histone-modifying enzymes.
