Fig 2: The impact of DCP1a and DCP1b on the cellular proteome.(A) Lysates were collected from control, DCP1a KO, and DCP1b KO cells and subjected to SDS/PAGE. Proteins were stained, and bands were excised and analyzed by LC/MS/MS. PCA analysis is shown. (B, C) Volcano plot shows log2(Fold change) versus log10(P-value) in (B) DCP1a versus ctrl condition protein levels and (C) DCP1b versus ctrl condition of the 5,542 proteins identified. Vertical line indicates log2 fold change of 1 or −1. The horizontal line represents a P-value of 0.05. High-confidence proteins are shown in purple. (D) Ontology analysis of only significantly impacted proteins (which did not appear in DCP1b KO results) in DCP1a KO versus ctrl. GO terms with similar cellular roles are grouped. Only relevant GO terms with a P-value < 0.05 are shown. MF, Molecular Function; BP, Biological Process; CC, Cellular Compartment. (E) Ontology analysis of only significantly impacted proteins (which did not appear in DCP1a KO results) in DCP1b KO versus ctrl. Comparison of half-life of DCP1a-dependent mRNAs and log2 fold change in protein level and DCP1b-dependent mRNAs and log2 fold change in protein level.Source data are available for this figure.

Fig 3: DCP1a and DCP1b are found in chromatin bound and chromatin free cellular extracts.HCT116 cells were infected with viruses targeting either shLUC (L), shDCP1a (1a), or shDCP1b (1b). Cellular fractionation was performed.

Fig 4: DCP1b is a p53 target.(A) Chip-seq for p53 was performed in H1299 tet-on cells. DCP1a and DCP1b gene tracks are shown (Farkas, Hashimoto et al, 2021). (B) RE1-3 and RE1-15 are CRISPR clones (from parental HCT116) where the response element for p53 on DCP1b′s promoter was edited/mutated. Cells were treated with NUT (10 μM) or 5FU (100 μM) for 6 h and mRNA abundance was assessed by qRT-PCR. (C) H1299 tet-on cells were treated for the interval indicated with either tetracycline (tet), camptothecin (CPT) (1 µM), or both (TC). DMSO was used as a control treatment. The protein levels of DCP1b, p53, and GAPDH were assessed by WBs. RNA expression levels for DCP1b and BAX were evaluated by qRT-PCR.Source data are available for this figure.

Fig 5: RNase L inhibits SG but not PB assembly and promotes RLB assembly. A, Western blotting analysis of PKR and RNase L in parental (WT), RNase L–KO (RL-KO), PKR-KO, and RNase L/PKR double knockout (RL/PKR-KO) A549 cells. B, IF for G3BP1 (SG marker) and DCP1b (PB marker) in the indicated A549 cell lines transfected with or without poly(I·C). To calculate the percentage of cells with G3BP1+ foci (RLBs or SGs), 25–195 cells from between 3 and 15 fields of view were analyzed. C, histogram of the number of G3BP1-positive foci binned by area as represented in B. D, histogram of the number of DCP1b-positive foci binned by area as represented in B. E, similar to B but depicting RLB and PB association. F, IF for G3BP1 and FISH for poly(A)+ RNA in WT cells 4 h post-poly(I·C).