The multi-domain protein Np95 connects DNA methylation and histone modification

Abstract

DNA methylation and histone modifications play a central role in the epigenetic regulation of gene expression and cell differentiation. Recently, Np95 (also known as UHRF1 or ICBP90) has been found to interact with Dnmt1 and to bind hemimethylated DNA, indicating together with genetic studies a central role in the maintenance of DNA methylation. Using in vitro binding assays we observed a weak preference of Np95 and its SRA (SET- and Ring-associated) domain for hemimethylated CpG sites. However, the binding kinetics of Np95 in living cells was not affected by the complete loss of genomic methylation. Investigating further links with heterochromatin, we could show that Np95 preferentially binds histone H3 N-terminal tails with trimethylated (H3K9me3) but not acetylated lysine 9 via a tandem Tudor domain. This domain contains three highly conserved aromatic amino acids that form an aromatic cage similar to the one binding H3K9me3 in the chromodomain of HP1ß. Mutations targeting the aromatic cage of the Np95 tandem Tudor domain (Y188A and Y191A) abolished specific H3 histone tail binding. These multiple interactions of the multi-domain protein Np95 with hemimethylated DNA and repressive histone marks as well as with DNA and histone methyltransferases integrate the two major epigenetic silencing pathways.

Crystal structure of PHD domain of UHRF1 and insights into recognition of unmodified histone H3 arginine residue 2

“…The ITC results show that Tudor UHRF1 , which mainly recognizes H3K9me3 [9], had significantly less affinity for the unmodified H3 (Kd = 35.8 µM). The SRA domain, which binds hemimethylated DNA, had no detectable binding to histone H3 (Supplementary information, Figure S2 and Table S2).…”

“…The PHD of UHRF1 has been reported to be involved in large-scale reorganization of PCH [8], and together with the SRA domain, define the binding affinity to H3K9me3 [3]. However, recent studies show that H3K9me3 binding is mediated by the tandem Tudor domain [9,10]. Thus, what PHD domain binds to remains unclear.…”

Epigenetic Mechanisms in Inflammation

“…The NP95 protein, which contains SET-, Ring-, and Tudor domains, is responsible for linking DNMT1 with DNA and histone H3 methylation (H3K9me3). Therefore, NP95 coordinates two major epigenetic silencing pathways, DNA methylation and histone methylation (Rottach et al, 2010).…”

Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1

“…1A). The isolated PHD finger and TTD recognize the methylation states of Arg-2 (H3-R2) and Lys-9 (H3-K9) in the H3 tail, respectively (19)(20)(21)(22)(23). Stable isotope labeling by amino acids in cell culture (SILAC)-based proteomics analysis indicated that UHRF1 binds to nucleosomes containing trimethylated H3-K9 (H3-K9me3) (24).…”