Role for the nuclear receptor-binding SET domain protein 1 (NSD1) methyltransferase in coordinating lysine 36 methylation at histone 3 with RNA polymerase II function

Abstract

The NSD (nuclear receptor-binding SET domain protein) family encodes methyltransferases that are important in multiple aspects of development and disease. Perturbations in NSD family members can lead to Sotos syndrome and Wolf-Hirschhorn syndrome as well as cancers such as acute myeloid leukemia. Previous studies have implicated NSD1 (KMT3B) in transcription and methylation of histone H3 at lysine 36 (H3-K36), but its molecular mechanism in these processes remains largely unknown. Here we describe an NSD1 regulatory network in human cells. We show that NSD1 binds near various promoter elements and regulates multiple genes that appear to have a concerted role in various processes, such as cell growth/cancer, keratin biology, and bone morphogenesis. In particular, we show that NSD1 binding is concentrated upstream of gene targets such as the bone morphogenetic protein 4 (BMP4) and zinc finger protein 36 C3H type-like 1 (ZFP36L1/TPP). NSD1 regulates the levels of the various forms of methylation at H3-K36 primarily, but not exclusively, within the promoter proximal region occupied by NSD1. At BMP4 we find that this reduces the levels of RNAP II recruited to the promoter, suggesting a role for NSD1-dependent methylation in initiation. Interestingly, we also observe that the RNAP II molecules that lie within BMP4 have inappropriate persistence of serine-5 phosphorylation and reduced levels of serine-2 phosphorylation within the C-terminal domain (CTD) of the large subunit of RNAP II. Our findings indicate that NSD1 regulates RNAP II recruitment to BMP4, and failure to do so leads to reduced gene expression and abrogated levels of H3K36Me and CTD phosphorylation.elongation | initiation | C-terminal domain | histone code | ChIP on chip

The Methyltransferase NSD3 Has Chromatin-binding Motifs, PHD5-C5HCH, That Are Distinct from Other NSD (Nuclear Receptor SET Domain) Family Members in Their Histone H3 Recognition

“…S1). PHD5-C5HCH NSD3 showed no or very weak binding to other histone peptides such as H3 (7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26), H3 (16 -35), H3 (26 -45), H4 (1-19), H2A (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19), and H2B (1-19) irrespective of their modification states (Fig. 1C).…”

“…Several reports have revealed that NSD family members are possibly recruited to specific gene loci. NSD1 binds upstream of the bone morphogenetic protein 4 promoter, enforces H3K36 methylation levels within this region, and thus promotes bone morphogenetic protein 4 transcription (19). NSD3, LSD2 (an H3K4-specific demethylase, lysine demethylase 2, also known as KDM1B), and G9a (an H3K9-specific methyltransferase, also known as EHMT2) form complexes in vivo, predominantly localize to the gene bodies of actively transcribed genes and may coordinate modifications at H3K4, H3K9, and H3K36 during elongation for optimal transcription (20).…”

Histone H2A Ubiquitination Inhibits the Enzymatic Activity of H3 Lysine 36 Methyltransferases

“…In budding yeast, Set2 is the sole H3K36-specific methyltransferase (9). In higher eukaryotes, several enzymes have been reported to be H3K36-specific methyltransferases (7), including HYPB, which is the primary H3K36-specific trimethylase (10 -12), and NSD1, NSD2, NSD3, and ASH1L, which are best characterized as H3K36-specific dimethylases (13)(14)(15)(16)(17)(18)(19).…”

In vitro histone lysine methylation by NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L

“…H3K9 (a.a. 5-11) peptide is stabilized by hydrogen bonds with Phe1997, Thr2001, Arg2018, Met2020, Met1999, Tyr2059, Glu2062, Cys2063, Leu2064 and Asn2066 in NSD1, with Asp1112, Met1118, Thr1120, Arg1137, Met1139, Leu1183 and Asn1185 in NSD2, and with Met1200, Met1221, Asn1267, Asn1197, Phe1198, and Thr1270 in NSD3. H3K27 (a.a. [23][24][25][26][27][28][29] peptide is stabilized by hydrogen bonds with Thr1995, Phe1997, Met1999, Arg2018, Met2020, Asn2021, Cys2063, Asn2066 and Thr2069 in NSD1, with Tyr1091, Asp1112, Thr1114, Phe1116, Thr1120, Arg1137, Met1139, Tyr1178, Asp1181, Leu1183, Asn1185 and Thr1188 in NSD2, and, with Thr1196, Phe1198, Met1200, Arg1219, Met1221, Asp1263, Cys1264, Leu1265, Asn1267, Arg1269 and Thr1270 in NSD3. H3K36 (a.a. 32-38) peptide is stabilized by hydrogen bonds with Asp1193, Phe1997, Met1999, Arg2018, Met2020, Asn2021, Glu2062 and Asn2066 in NSD1, with Thr1114, Phe1116, Arg1137, Met1139, Leu1180, Cys1182, Gly1184, Asn1185 and Glu1186 in NSD2, and, with Thr1270, Thr1196, Phe1198, Met1200, Arg1219, Met1221, Asp1263 and Cys1264 in NSD3.…”

“…The amplification of NSD1 has been reported in multiple myeloma, lung cancer, neuroblastoma and glioblastoma. The amplification of either NSD1 or NSD2 triggers cellular transformation [21][22][23][24][25][26][27][28]. NSD2 is associated with tumor aggressiveness or prognosis in most types of cancers, including prostate cancer and multiple myeloma and is overexpressed in at least 15 different cancers [9,10,17,18,20,21,25,[29][30][31][32][33].…”