Fig. 3: Plasmid Pull-down Mass Spectrometry (PP-MS) reveals proteasome and PAR-dependent E3 ubiquitin ligase recruitments.
A Overview of reaction conditions for PP-MS analysis. B Heatmap showing the mean of the z-scored log2 label-free quantitation (LFQ) intensity (i.e., protein abundance) from four biochemical replicates of pCTRL and pMHssDNA incubated in SPRTN-RFWD3-depleted HSS in the presence of the indicated inhibitors. Dynamic proteins, responsive to PARGi and/or PARPi treatment, were selected. C pMHssDNA was incubated in SPRTN-RFWD3-depleted HSS, which was then additionally mock-depleted, PARP1-depleted, or PARP1-depleted and supplemented with recombinant PARP1 (Input, left WB). Plasmids were recovered via plasmid pull-down and protein recruitment to the plasmid was monitored with the indicated antibodies. D pMHssDNA was incubated in SPRTN-RFWD3-depleted HSS, which was further mock-depleted, PSA1-depleted, DDI2-depleted, or PSA1- and DDI2-depleted. Samples were recovered by DPC pull-down and immunoblotted against M.HpaII. Source data are provided as a Source Data file.
