Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases

Abstract

The NSD family histone methyltransferases, including NSD1, NSD2 and NSD3, play crucial roles in chromatin regulation and are implicated in oncogenesis 1 , 2 . NSD enzymes exhibit an auto-inhibitory state that is relieved by nucleosome engagement, allowing for H3K36 di-methylation catalysis 3 – 7 . However, the molecular basis underlying this mechanism is largely unknown. Here, we have solved the cryo-EM structures of NSD2 and NSD3 bound to mononucleosomes at atomic resolution. We find that NSD2/3 mononucleosome engagement causes DNA near the linker region to unwrap, which facilitates insertion of their catalytic core in-between the histone octamer and the unwrapped segment of DNA. A network of DNA- and histone-specific contacts between the nucleosome and NSD2/3 precisely define the enzymes’ position on the nucleosome, explaining the methylation specificity for H3K36. Further, NSD-nucleosome intermolecular contacts are altered by several recurrent cancer-associated NSD2/3 mutations. NSDs harboring these mutations are catalytically hyperactive in vitro and in cells, and their ectopic expression promotes cancer cell proliferation and xenograft tumor growth. Together, our research provides molecular insights into the nucleosome-based recognition and modification mechanisms of NSD2 and NSD3, which should uncover strategies for therapeutic targeting of the NSD family of proteins.

Allosteric regulation of histone lysine methyltransferases: from context-specific regulation to selective drugs

“…The NSD family exhibits higher enzymatic activity and H3K36 selectivity with nucleosome substrate compared with the histone substrates [ 79 , 91 , 92 ]. Consistent with these observations, NSD2 and NSD3 undergo conformational changes in the autoinhibitory loop region upon nucleosome binding [ 93 , 94 ]. In the absence of nucleosome binding, the autoinhibitory loop is stabilised in the active site of NSD2 or NSD3 through inhibitory interactions with the SET domain [ 93 , 94 ].…”

“…In the absence of nucleosome binding, the autoinhibitory loop is stabilised in the active site of NSD2 or NSD3 through inhibitory interactions with the SET domain [93,94]. Upon nucleosome binding, the SET domain interacts with the histones and the nucleosomal DNA to replace the interaction with the autoinhibitory loop [93,94]. Consequently, the autoinhibitory loop is pushed away from the active site, making the substrate-binding site accessible.…”

An epigenetic tipping point in cancer comes under the microscope

“…One way in which genes are controlled is through the addition of various chemical marks to DNA and DNA-associated proteins. Writing in Nature, Yuan et al 1 and Li et al 2 show that one of the enzymes that deposit such marks, NSD3, is mutated and hyperactive in some human cancers -a finding that suggests new avenues for treating people with the diseases.…”

“…Figure 1 | Deregulation of histone methylation in human cancer.The enzyme NSD3 is a histone methyltransferase -it dimethylates (adds two methyl groups to) histone H3 proteins, around which DNA is packaged. Yuan et al1 have found that NSD3 is dysregulated in human squamous cell lung carcinoma, and Li et al2 have unravelled the structural mechanism involved. a, In 'NSD3-addicted cancers', the enzymatic activity of NSD3 is increased through an increase in the number of copies of the NSD3 gene, or through mutations that cause hyperactive enzyme activity (not shown).…”

The H3K36me2 writer-reader dependency in H3K27M-DIPG

“…However, extensive efforts to target the SET domains of NSD proteins with potent inhibitors have proven unsuccessful at the nano-molar scale. In this regard, a recent Cryo-EM study revealed that a series of residues within and flanking the SET domain are crucial for unwrapping the linker and nucleosomal DNA such that an autoinhibitory state inherent to NSD proteins is converted to an active conformation 35,36 . Understanding these unique features of NSDs could further facilitate the structurally-assisted design of new inhibitors.…”