NSD1 PHD domains bind methylated H3K4 and H3K9 using interactions disrupted by point mutations in human sotos syndrome

Abstract

Sotos syndrome is a human developmental and cognitive disorder caused by happloinsufficiency of transcription factor NSD1. Similar phenotypes arise from NSD1 gene deletion or from point mutations in 9 of 13 NSD1 domains, including all 6 PHD domains, indicating that each NSD1 domain performs an essential role. To gain insight into the biochemical basis of Sotos syndrome, we tested the ability of each NSD1 PHD domain to bind histone H3 when methylated at regulatory sites Lys4, Lys9, Lys27, Lys36, and Lys79, and histone H4 at regulatory Lys20, and determined whether Sotos point mutations disrupted methylation site-specific binding. NSD1 PHD domains 1, 4, 5, and 6 bound histone H3 methylated at Lys4 or Lys9. Eleven of 12 Sotos mutations in PHD4, PHD5, and PHD6 disrupted binding to these methylated lysines, and 8 of 9 mutations in PHD4 and PHD6 severely compromised binding to transcription cofactor Nizp1. One mutation in PHD1 did not alter binding to specific methylated histone H3, and one mutation in PHD4 did not alter binding to either methylated histone or Nizp1. Our data suggests that Sotos point mutations in NSD1 PHD domains disrupt its transcriptional regulation by interfering with its ability to bind epigenetic marks and recruit cofactors.

NSD2 Is Recruited through Its PHD Domain to Oncogenic Gene Loci to Drive Multiple Myeloma

“…It has been shown that 11 of 12 Sotos mutations in PHD4-6 of NSD1 disrupted binding to H3K4me2 and H3K9me2, and 8 of 9 mutations in PHD4 and PHD6 severely compromised binding to transcription cofactor Nizp1 (21). Therefore, we generated single-point mutations on C720, C743, L749, and H762 in NSD2 PHD2 domain, corresponding to the Sotos mutations in NSD1 (Supplementary Fig.…”

“…Both PHD2 and PHD5-C5HCH are essential for clonogenic potential of NSD2, even though the latter has no impact on H3K36 dimethylation. Studies on other H3K36 methyltransferases such as Mes-4, NSD1, and NSD3 showed that PHD domains are important for binding to chromatin, interaction with methyl-lysines, and recruitment to target genes (19,21,22,42). The PHD5-6 domain of NSD1, corresponding to PHD5-C5HCH in NSD2, has also been implicated in interaction with adaptor protein Nizp1 (21,43).…”

“…The PWWP, HMG, and PHD domains have been shown to mediate chromatin interaction and recognition of histone marks (19)(20)(21)(22)(23). How different domains cross talk and contribute to the biological functions of NSD2 is not understood yet.…”

Histone H3 lysine methylation in cognition and intellectual disability disorders

“…The nuclear receptor-binding SET-domain protein 1 (NSD1, aka KMT3B) preferentially methylates H3K36 but also H4K20 (a label associated with gene repression), which suggests that NSD1 may act as co-repressor or coactivator of target genes depending on the context. NSD1 uses clues from H3K4 and H3K9 methylation for its local recruitment to DNA and these interactions were disrupted by the mutations in NSD1 found in 11 out of 12 patients with Sotos syndrome (Pasillas et al 2011). A recent study demonstrated that mice carrying a 1.5 Mb deletion similar to the one described for Sotos syndrome patients exhibit memory deficits in a social recognition task, although they lacked other phenotypic features associated with this syndrome (Migdalska et al 2012).…”

Examining the impact of gene variants on histone lysine methylation

“…Interestingly, eight out of nine mutations within PHD domains 4 and 6 reduced the binding to the transcription factor Nizp1 [95]. Nizp1 is responsible for recruitment of NSD1 to RNA polymerase II promoters, leading to transcriptional repression [96].…”