Histone lysine methylation modifiers controlled by protein stability

Abstract

Histone lysine methylation is pivotal in shaping the epigenetic landscape and is linked to cell physiology. Coordination of the activities of multiple histone lysine methylation modifiers, namely, methyltransferases and demethylases, modulates chromatin structure and dynamically alters the epigenetic landscape, orchestrating almost all DNA-templated processes, such as transcription, DNA replication, and DNA repair. The stability of modifier proteins, which is regulated by protein degradation, is crucial for their activity. Here, we review the current knowledge of modifier-protein degradation via specific pathways and its subsequent impact on cell physiology through epigenetic changes. By summarizing the functional links between the aberrant stability of modifier proteins and human diseases and highlighting efforts to target protein stability for therapeutic purposes, we aim to promote interest in defining novel pathways that regulate the degradation of modifiers and ultimately increase the potential for the development of novel therapeutic strategies.

Fig. 1. Histone lysine methylation modifiers.

Schematic representation of a nucleosome showing the principal lysine methylation sites on histones H3 and H4. The histone octamer composed of an H3-H4 tetramer combined with two H2A-H2B dimers, along with the DNA lesion surrounding them, collectively constitute the nucleosome, which is the main structural element of chromatin. The reported KMTs and KDMs for each type of lysine methylation are indicated. Modifiers whose protein stability is reported to be regulated by the UPS are highlighted in red.

Fig. 2. The UPS-mediated regulation of KMTs/KDMs.

Schematic representation of the UPS-mediated regulation of histone lysine methylation modifiers. Polyubiquitin chains are conjugated to KMTs/KDMs via E3 ubiquitin ligases. The resulting polyubiquitinated proteins are subsequently recognized by the proteasome and degraded into small peptides and amino acids. Conversely, polyubiquitin chains can be disassembled by DUBs, stabilizing the KMTs/KDMs. Various PTMs, including methylation, phosphorylation, acetylation, hydroxylation and poly(ADP-ribosyl)ation, affect the ubiquitination and deubiquitination of KMTs/KDMs. The dynamic regulation of KMT and KDM protein stability changes the status of histone methylation and thereby mediates diverse physiological effects.

Fig. 3. Oxygen-dependent regulation of SETDB1 and G9a.

Schematic illustration of the oxygen-dependent functional regulation of SETDB1 and G9a. Left: In normoxia, PHDs hydroxylate proline residues of SETDB1 and G9a, enabling their VHL-mediated polyubiquitination and subsequent proteasomal degradation. Middle: In hypoxia, unhydroxylated SETDB1 and G9a are stabilized and protected from VHL-mediated degradation. The resulting increases in the SETDB1 and G9a levels lead to increased SETDB1 occupancy at chromatin associated with TEs and subsequent strong repression of TEs through H3K9 methylation. They also result in increased G9a occupancy at chromatin associated with its target tumor suppressor genes in breast cancer cells, leading to increased cell growth and survival. Right: Loss of SETDB1 in hypoxia results in failure of TE silencing, thereby activating TE transcript-driven immune-inflammatory and DNA damage responses, followed by cell death. G9a loss in hypoxia derepresses the transcription of G9a target genes, inhibiting the growth and survival of breast cancer cells.

Fig. 4. Regulation of KMT/KDM protein stability in a cell cycle-dependent manner.

Schematic representation of histone lysine methylation modifiers regulated by cell cycle-dependent protein degradation. SET8 is degraded by SCF^Skp2 at the G1/S transition and is dynamically regulated by CRL4^Cdt2 during the S phase in a PCNA-dependent manner. PARP1-mediated poly(ADP-ribosyl)ation of SET8 promotes its UPS-dependent degradation. SET8 is also regulated in a phosphorylation-dependent manner during the G2/M phase by the CDK1/cyclin B complex, while the dephosphorylation of SET8 by CDC14 in the late M phase leads to its degradation by the APC/C^Cdh1 complex. SCF^Fbxl4-dependent proteasomal degradation accounts for the decrease in the KDM4A level in the S phase. PHF8 is regulated by the APC/C^Cdc20 complex in the G2/M phase. MLL1 degradation is mediated by the E3 ligase complex SCF^Skp2 in the S phase of the cell cycle and by the APC/C^Cdc20 complex in the late M phase. In response to genotoxic stress during the S phase, the DNA replication checkpoint kinase ATR phosphorylates MLL1 and inhibits its degradation mediated by SCF^Skp2. The different colors of the histone methylation modifiers indicate specific targets of the modifiers.

Fig. 5. Regulation of KMT/KDM protein stability in response to cellular stress.

Schematic representation of histone lysine methylation modifiers regulated in response to stress-dependent protein degradation. a DNA damage-induced degradation of histone methylation modifiers. In response to genotoxic stress, the DNA replication checkpoint kinase ATR phosphorylates MLL1. Phosphorylated MLL1 loses its physical interaction with SCF^Skp2 and is thereby stabilized and accumulates H3K4 methylation at late replication origins, which inhibits CDC45 loading to delay DNA replication. DNA damage activates the APC/C^Cdh1 E3 complex, enabling the binding of G9a as well as GLP. This binding triggers the proteasomal degradation of G9a and GLP, causing a global decrease in H3K9me2 and subsequently upregulating senescence-associated gene expression. Radiation-induced DNA damage promotes USP7-mediated stabilization of PHF8. The USP7-PHF8 axis promotes the cell cycle by decreasing the H3K9me1 levels on genes involved in the cell cycle. In addition, PHF8 accumulation at DNA damage sites promotes DSB repair. Upon DNA damage stress, the CRL4^Cdt2 complex ubiquitinates and degrades SET8 in a PCNA-dependent manner. This leads to a decrease in H4K20 methylation to modulate the chromatin structure, promoting cell cycle progression. KDM4A is degraded by RNF8 and RNF168 in response to DNA damage, facilitating 53BP1 recruitment to DNA damage sites. The different colors of the histone methylation modifiers indicate specific targets of the modifiers. b Hypotonic stress-mediated stability of the SUV420H2 protein. The antisense RNA PAPAS mediates rDNA silencing via distinct mechanisms in cells exposed to different stresses. In quiescent cells, PAPAS is upregulated and guides the histone methyltransferase SUV420H2 to rDNA, leading to H4K20me3 and chromatin compaction. rRNA synthesis is subsequently attenuated. In contrast, in proliferating cells exposed to hypotonic stress, the SUV420H2 protein is degraded by the E3 ligase NEDD4. The resulting depletion of SUV420H2 facilitates the interaction of PAPAS with CHD4, a subunit of the NuRD complex, rather than with SUV420H2. Recruitment of the NuRD complex to rDNA through PAPAS modifies the promoter-bound nucleosome into a transcriptionally repressive state, thereby attenuating rRNA synthesis.