The Replication-initiation determinant protein (RepID) modulates replication by recruiting CUL4 to chromatin

Cell cycle progression in mammals is modulated by two ubiquitin ligase complexes, CRL4 and SCF, which facilitate degradation of chromatin substrates involved in the regulation of DNA replication. One member of the CRL4 complex, RepID (DCAF14/PHIP), is a WD40-containing protein that selectively binds and activates a group of replication origins. We found that RepID recruits the CRL4 complex to chromatin prior to DNA synthesis, thus playing a crucial architectural role in the proper licensing of chromosomes for replication. In the absence of RepID, cells rely on the alternative ubiquitin ligase, SKP2-containing SCF, to progress through the cell cycle. RepID depletion markedly increases cellular sensitivity to SKP2 inhibitors, which triggered massive genome re-replication. Both RepID and SKP2 interact with distinct, non-overlapping groups of replication origins, suggesting that selective interactions of replication origins with specific CRL components execute the DNA replication program and maintain genomic stability by preventing re-initiation of DNA replication. Nascent strands were purified with the lambda exonuclease methods from U2OS RepID WT or HCT116 RepID KO cells. Chromatin from unsynchronized untreated cultures of U2OS RepID WT cells was subjected to ChIP-Seq with antibody directed against CUL4A, H3K4me3 and H3K9me3. Chromatin from unsynchronized untreated cultures of U2OS FLAG-RepID-FL overexpressed stable cells was subjected to ChIP-Seq with antibody directed against CDT2. Chromatin from unsynchronized untreated cultures of HCT116 RepID WT or RepID KO cells was subjected to ChIP-Seq with antibody directed against SKP2.