SET8 prevents excessive DNA methylation by methylation-mediated degradation of UHRF1 and DNMT1

Abstract

Faithful inheritance of DNA methylation across cell division requires DNMT1 and its accessory factor UHRF1. However, how this axis is regulated to ensure DNA methylation homeostasis remains poorly understood. Here we show that SET8, a cell-cycle-regulated protein methyltransferase, controls protein stability of both UHRF1 and DNMT1 through methylation-mediated, ubiquitin-dependent degradation and consequently prevents excessive DNA methylation. SET8 methylates UHRF1 at lysine 385 and this modification leads to ubiquitination and degradation of UHRF1. In contrast, LSD1 stabilizes both UHRF1 and DNMT1 by demethylation. Importantly, SET8 and LSD1 oppositely regulate global DNA methylation and do so most likely through regulating the level of UHRF1 than DNMT1. Finally, we show that UHRF1 downregulation in G2/M by SET8 has a role in suppressing DNMT1-mediated methylation on post-replicated DNA. Altogether, our study reveals a novel role of SET8 in promoting DNA methylation homeostasis and identifies UHRF1 as the hub for tuning DNA methylation through dynamic protein methylation.

H4K20 monomethylation inhibition causes loss of genomic integrity in mouse preimplantation embryos

“…SETD8 methylates not only H4K20, but also non-histone proteins [ 21 , 22 , 23 , 24 ]. To determine whether developmental arrest by inhibition of SETD8 was due to a decrease in the level of H4K20me1, mRNA encoding wild-type histone H4 (H4K20WT) with a FLAG tag or a mutated histone H4 in which the 20 th lysine was replaced by methionine (H4K20M), also with a FLAG tag, was overexpressed in embryos ( Fig.…”

“…The reason why SETD8-inhibited embryos were arrested at an earlier stage than Setd8 -null embryos [ 13 ] is likely that the activity of maternally derived SETD8 is also blocked in SETD8-inhibited embryos, or that the effect of SETD8 inhibition varies depending on mouse strain [ 34 ]. However, SETD8 methylates not only histone H4K20 but also many non-histone proteins, including p53 and PCNA [ 21 , 22 , 23 , 24 ]; thus, it is difficult to determine from conventional methyltransferase inhibition experiments which SETD8-catalyzed methylation is important for preimplantation development. To analyze the function of H4K20me1 from a different point of view, we carried out dominant-negative experiments using histone lysine–methionine substituents.…”

“…Setd8 -null embryos derived from Setd8 +/− intercrosses are arrested by the eight-cell stage, emphasizing the importance of SETD8 in preimplantation development; however, its function remains unknown [ 13 ]. In addition, SETD8 methylates not only a lysine (Lys) residue of H4K20 but also Lys residues of non-histone proteins such as Lys382 of p53, Lys158 and Lys163 of NUMB, Lys248 of PCNA, and Lys385 of UHRF1 [ 21 , 22 , 23 , 24 ]. This is the main reason why the importance of H4K20me1 during preimplantation development remains largely unclear.…”

microRNA‐related single‐nucleotide polymorphisms and breast cancer

“…SET8 (also called SETD8, KMT5A, and PR‐SET7) catalyzes the histone H4 K20 monomethylation as well as nonhistone proteins such as p53 (Fang et al, 2002; Shi et al, 2007). The expression of SET8 protein is regulated over cell cycle; degradation of SET8 is achieved at G1/S transition by proteasome (H. Zhang et al, 2019). Accordingly, in G1 and G2/M, SET8 expression is high; SET8 depletion causes early chromatin compaction, failing in repair of DNA damage as well as G2/M arrest (Abbas et al, 2010; Centore et al, 2010).…”

“…The expression of SET8 protein is regulated over cell cycle; degradation of SET8 is achieved at G1/S transition by proteasome (H Zhang et al, 2019)…”