CRL4(Cdt2)-mediated destruction of the histone methyltransferase Set8 prevents premature chromatin compaction in S phase

Abstract

The proper coordination between DNA replication and mitosis during cell-cycle progression is crucial for genomic stability. During G2 and mitosis, Set8 catalyzes monomethylation of histone H4 on lysine 20 (H4K20me1), which promotes chromatin compaction. Set8 levels decline in S phase, but why and how this occurs is unclear. Here, we show that Set8 is targeted for proteolysis in S phase and in response to DNA damage by the E3 ubiquitin ligase, CRL4(Cdt2). Set8 ubiquitylation occurs on chromatin and is coupled to DNA replication via a specific degron in Set8 that binds PCNA. Inactivation of CRL4(Cdt2) leads to Set8 stabilization and aberrant H4K20me1 accumulation in replicating cells. Transient S phase expression of a Set8 mutant lacking the degron promotes premature H4K20me1 accumulation and chromatin compaction, and triggers a checkpoint-mediated G2 arrest. Thus, CRL4(Cdt2)-dependent destruction of Set8 in S phase preserves genome stability by preventing aberrant chromatin compaction during DNA synthesis.

Figure 1

Set8 is degraded by CRL4^Cdt2 in response to DNA damage. (A) Sequence alignment of the PIP degrons of human Cdt1, p21, and Set8 from different species. Ψ is any moderately hydrophobic amino acid L, V, I, or M. ϑ is an aromatic residue, Y or F. B is a positively charged residue, R or K. Red residues are conserved in the PIP boxes, and the blue residues are only conserved in the PIP degrons. (B) UV-induced Set8 degradation is 26S proteasome-dependent. U2OS cells were treated with 50J/m² UV, and the levels of endogenous Set8, Cdt1, and tubulin were monitored at the indicated times by Western blotting. Where indicated, 10 μM MG132 was added to cells 5 hr prior to irradiation. (C) UV-induced Set8 degradation is independent of ATM, ATR, and Chk1. U2OS cells were treated with 1 μM UCN-01 (Chk1 inhibitor) or 100 μM wortmannin (PI3KK inhibitor) for 1 hr prior to UV irradiation. Inhibition of Chk1 phosphorylation serves as a positive control for wortmannin activity. Note that UCN-01 does not inhibit the phosphorylation of Chk1 by ATR, but prevents the mobility change of Chk1 indicative of Chk1 autophosphorylation. (D) CRL4^Cdt2 down regulates Set8 protein levels. U2OS cells were transfected with control siRNA or siRNAs targeting Ddb1, Cdt2 and Cul4A. The levels of the indicated proteins were monitored by Western blotting. (E) UV-induced Set8 degradation is Cdt2-dependent. U2OS cells transfected with Cdt2 siRNA or control siRNA were treated with UV followed by 100 μg/ml cycloheximide. The levels of the indicated proteins were analyzed in a time course. In all panels, * labels non-specific bands recognized by the indicated antibodies.

Figure 2

UV-induced Set8 degradation is dependent on its PIP degron. (A) The Set8^ΔPIP mutant lacks the two conserved aromatic residues in the putative PIP degron. (B) The Set8^ΔPIP mutant is defective in binding to PCNA and Cdt2. Flag-tagged Set8^WT and Set8^ΔPIP were transiently expressed in U2OS cells and immunoprecipitated with anti-Flag antibody. The Set8, PCNA, and Cdt2 proteins in the immunoprecipitates and input extracts (2%) were analyzed by Western blotting. (C) Set8 ubiquitylation is induced by UV. HeLa cells stably expressing His/biotin-tagged ubiquitin and control HeLa cells were treated with UV or left untreated. Ubiquitylated proteins were captured with streptavidin beads under denaturing condition. Ubiquitylated Set8 was detected with Set8 antibody. * Nonspecific proteins bound to streptavidin beads and cross-reacted with Set8 antibody. (D) UV-induced Set8 ubiquitylation requires the PIP degron. Cells expressing Flag-tagged Set8^WT or Set8^ΔPIP were synchronized in G1, pretreated with MG132 for 3 hr, and irradiated with UV. The Set8 proteins were analyzed with anti-Flag antibody 2 hr post UV treatment. (E) The Set8^ΔPIP mutant is more stable than Set8^WT after UV damage. U2OS cells with induced Flag-tagged Set8^WT or Set8^ΔPIP were treated with UV, and cultured in cycloheximide-containing media for the indicated times. The levels of Flag-Set8 and tubulin were analyzed by Western blotting.

Figure 3

CRL4 ^Cdt2-dependent and DNA damage-induced Set8 degradation in Xenopus egg extracts. (A) DNA damage and proteasome dependent destruction of Set8 in Xenopus egg extract. HSS was supplemented with human 50 nM GST-FLAG-Set8, as well as buffer (no DNA), undamaged plasmid, MMS-damaged plasmid, and MG132, as indicated, and at different times, samples were blotted for GST (top panel) or Cdt1 (bottom panel). (B) 50 nM recombinant GST-FLAG-tagged human Set8 was added to mock-depleted or PCNA-depleted HSS that was optionally supplemented with 5 μM recombinant human PCNA. At the different times, samples were blotted for GST. (C) 50 nM recombinant GST-Flag-tagged human Set8 was added to mock-depleted or Cdt2-depleted HSS that was optionally supplemented with 25 nM recombinant human Cdt2, as indicated. At different times, samples were blotted for GST. (D) HSS was supplemented with MMS-treated plasmid, as well as buffer, 50 nM GST-Flag-tagged Set8^WT, or Set8^ΔPIP. At different times, samples were blotted for the indicated proteins. (E) HSS was supplemented with 1 mg/ml Myc-Ubiquitin and MG132, as well as buffer or 50 nM GST-Flag-tagged Set8^WT, as indicated. Immobilized, 1 kb MMS DNA was added and after 10 min, chromatin was recovered from the extract. Chromatin-bound proteins were denatured to release them from chromatin then diluted and immunoprecipitated with Flag antibody. The isolated material was blotted for Set8 (bottom panel), Ubiquitin (middle panel), or Myc (top panel). (F) Immobilized, 1 kb MMS DNA was isolated from mock-depleted or Cdt2-depleted HSS, each of which was supplemented with 2 mg/ml methyl-ubiquitin and 50 nM GST-Flag-tagged Set8 and incubated for 10 min. Samples were blotted for Cdt2, Set8, and PCNA. (G) Methyl-ubiquitin, GST-Flag-tagged Set8^WT or Set8^ΔPIP, and 5 ng/μl MMS plasmid DNA was added to HSS. Set8^WT, Set8^ΔPIP, and their associating proteins were immunoprecipitated from total extract with Flag antibody, and the indicated proteins were analyzed by Western blotting. * A protein nonspecifically recognized by PCNA antibody.

Figure 4

PIP degron-mediated Set8 degradation during DNA replication. (A) Set8 is actively degraded by the proteasome in replicating cells. Cells harboring inducible Flag-Set8 were synchronized in S phase with 1 mM HU for 24 hr. During the last 4 hr of HU treatment, Flag-Set8 was induced, and 10 μM MG132 was added when indicated. Subsequently, cells were released into HU-free and cycloheximide-containing media with or without MG132. Set8 levels were analyzed in a time course by Western blotting. (B) Endogenous Set8 is stabilized by knockdown of Cdt2, but not Ddb2. Cells transfected with siRNAs targeting Cdt2 or Ddb2 and cells mock transfected were synchronized with thymidine and released into cycloheximide-containing media. The levels of endogenous Set8 were analyzed at the indicated time points by Western blotting. (C) Set8 is degraded in Xenopus egg extracts in a replication- and PIP degron-dependent manner. Sperm chromatin was incubated with HSS for 30 min to promote replication licensing. Subsequently, a highly concentrated nucleoplasmic extract (Walter et al., 1998) containing GST-Flag-tagged Set8^WT or Set8^ΔPIP was added, which stimulated efficient replication initiation (data not shown). At different times after NPE addition, the reactions were stopped and samples were blotted for GST and Cdt1. In lanes 1–3, HSS was incubated with 200 nM Geminin before addition of sperm chromatin.

Figure 5

Forced expression of Set8 interferes with the cell cycle. (A) Forced Set8 expression slows cell proliferation. U2OS cells harboring inducible Flag-tagged Set8^WT, Set8^ΔPIP, Set8^ΔPIP,CD, or the parental cell line were cultured in the absence or presence of 0.1 μg/ml tetracycline (Tet). The total cell numbers at the indicated time points were plotted. Error bars indicate the standard deviation of three independent experiments. (B) Constitutive Set8 expression leads to reduced DNA synthesis and accumulation of cells in G2/M. Cells were cultured for 48 hr with or without Set8 induction. Cell cycle profiles (left panel) and BrdU incorporation (right panel) were analyzed by FACS. (C) Constitutive expression of Set8 elicits the ATR checkpoint. Cells were cultured for 48 hr with or without Set8 induction. The levels of Set8, phospho-Chk1 (Ser345), Chk1, and phospho-H3 (Ser10) were analyzed by Western blotting. (D–E) Overexpression of Set8 prior to S phase inhibits mitotic entry. Cells were synchronized in mitosis with 100 ng/ml nocodazole and then released into media containing 2 mM thymidine. Where indicated, Set8 was induced after the release from nocodazole. Cells synchronized at G1/S were then released from thymidine in the absence of Tet. Cell cycle profiles are shown in D, and protein levels of Flag-Set8, phospho-H3, and tubulin were analyzed by Western blotting in E.

Figure 6

Expression of the Set8^ΔPIP mutant induces premature H4K20me1 accumulation. (A) Constitutive expression of the Set8^ΔPIP mutant leads to a dramatic loss of S-phase cells and accumulation of G2/M cells. Cell cycle profiles and BrdU incorporation of cells expressing Set8^WT or Set8^ΔPIP for 48 hr. (B–D) Expression of the ΔPIP mutant prevents mitotic entry after release from HU arrest. In B, cells harboring inducible Set8^WT or Set8^ΔPIP were synchronized in S phase with HU for 24 hr. During the last 4 hr in HU, expression of Set8^WT or Set8^ΔPIP was induced. Subsequently, cells were released from HU in the absence of Tet, and the levels of the indicated proteins in whole-cell extracts were analyzed by Western blotting. In C, Set8^ΔPIP,CD cells were included. Experiment was performed as in B, except that cells were released into media containing nocodazole to trap mitotic cells. Where indicated, caffeine was added at 5 mM to bypass ATM/ATR-mediated checkpoint response. Twenty-four hr after HU release, phospho-H3-positive mitotic cells were scored by FACS. Error bars indicate standard deviation and * indicates p < 0.005 by student’s t-test. In D, experiment was performed as in B, except that 4 hr after HU release, chromatin-bound histones were extracted with acid and analyzed by Western blotting.

Figure 7

The Set8^ΔPIP mutant induces aberrant chromatin compaction in replicating cells. (A) Transient expression of the ΔPIP mutant in S-phase cells leads to aberrant co-staining of PCNA and H4K20me1. Cells were arrested in S phase with HU for 24 hr, and Set8^WT or Set8^ΔPIP was transiently induced during the last 4 hr. Cells were subsequently released from HU, and were stained with antibodies to PCNA and H4K20me1 4 hr after HU release. (B) Co-localization of PCNA and H4K20me1 in the replicating cells that express Set8^ΔPIP. (C) Knockdown of Cdt2, but not Ddb2, leads to accumulation of H4K20me1 in PCNA-positive cells. Cells were transfected with siRNAs targeting Cdt2 and Ddb2, or mock treated. The levels of H4K20me1 and PCNA were analyzed by immunostaining. (D–E) The Set8^ΔPIP mutant reduces the distance between two loci on chromosome 16 in replicating cells. Cells were synchronized and induced to express Set8^WT, Set8^ΔPIP, or Set8^ΔPIP,CD as in A, and released for 6 hours. Dual colored FISH probes were used to visualize 16q22 and 16p13. Representative images of the two loci are shown in D. The distance between the two loci in the indicated cell populations were measured using confocal microscopy (see Materials and Methods). Distances were normalized to the uninduced population of the same cell line, and the average of three independent experiments is plotted in E. Error bars indicate standard deviation. * indicates p < 0.05 and ** indicates p < 0.001 by student’s t-test. (F) The Set8^ΔPIP mutant promotes premature binding of condensin II to chromatin in S phase. Cells expressing Set8^WT or Set8^ΔPIP were synchronized and released as in A, and were subjected to chromatin fractionation 6 hr after HU release. The levels of CAP-D3, CAP-G2, Set8, and PCNA in chromatin fractions were analyzed by Western blotting.