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.