tion were labeled in heavy isotope medium. In this manner, we generated synchronous metabolically-labeled cell populations naturally passing from one phase to the next without the potentially confounding issue of harvesting cells from a strong checkpoint arrest. We confirmed cell cycle position by immunoblotting whole cell lysates for established cell cycle-regulated proteins. 11786503 For example, we confirmed that both the Cdc6 and geminin proteins, two targets of the Anaphase Promoting Complex/Cyclosome E3 ubiquitin ligase which is active from anaphase through late G1, were substantially more abundant in the S phase lysates than in the G1 lysates Dataset Comparison and GO Term Analysis The log2 transformed data from Whitfield et al. was downloaded from www.cyclebase.org. Based on the calculated pvalue of periodicity, mRNA data were separated according to mRNA peak time. These lists were compared to our lists of increased and decreased proteins, and p-values were calculated using Fisher’s exact test; a p-value less than 0.01 was considered significant. The same strategy was applied to comparisons to the ubiquitome, a published ATM/ATR substrate list, a published phosphoproteome, a Cyclin A/Cdk2 substrate list, and a dataset that determined the subcellular localization of proteins. GO term analysis was performed using the DAVID TG100 115 search engine. Analysis was performed on the individual lists, and the reported p-value was calculated using a modified Fisher’s exact test. When GO terms overlapped, terms were collapsed to the highest level. Immunoblot Validation Samples were subjected to SDS-PAGE on a 12% polyacrylamide gel and transferred to PVDF. Blots were probed with the following antibodies: anti-Cyclin 
B1, anti-Cyclin A, anti-Cdc6, anti-Cdt1, anti-Geminin, anti-SLBP, anti-atubulin, anti-RRM2, anti-MARCKSL1, anti-Palmdephin, anti-Prelamin A/C, anti-Tropomodulin-3, anti-MCM2, anti-Rbmx/hnRNPG, anti-hnRNPA1, anti-hnRNPA3, antihnRNPD0, antihnRNPL, and anti-b-actin. All HRP-conjugated secondary antibodies were purchased from Jackson Immunoresearch. Proteins were visualized following incubation with ECL prime reagent. Cell Cycle-Regulated Proteome: Splicing Proteins 4 Cell Cycle-Regulated Proteome: Splicing Proteins . In contrast to Cdc6 and geminin, the Cdt1 protein is targeted for degradation at the onset of S phase by the CRL4Cdt2 E3 ubiquitin ligase. As expected, we detected very little Cdt1 in the early-S phase cells compared to the G1 cells, but Cdt1 protein levels were high in the S phase cells treated with MG132. Moreover, we observed higher levels of Cdt1 in the G2 samples compared to the mid-S phase samples as expected because CRL4Cdt2 can only target Cdt1 during active DNA replication . Previously, we identified two proteins that are degraded at the end of S phase as a result of Cyclin A/Cdk1 activation. Their degradation is blocked by MG132 treatment. We detected not only the down-regulation of SLBP in G2 phase but also its stabilization in cells treated with MG132. Finally we confirmed that MG132 did not prevent 9346307 S phase entry or exit as determined by flow cytometry and immunoblot analysis of marker proteins Protein Abundance Changes at the G1/S and S/G2 Transitions portion of these proteins did not change by more than 1.5fold from S to G2 phase. Of the total quantifiable proteins, 15.3% either increased or decreased in their abundance. These protein lists are provided in Cell Cycle-Regulated Proteome: Splicing Proteins Frequent Discordanc
