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Fig. 5 | Genome Biology

Fig. 5

From: Spatiotemporal variation of mammalian protein complex stoichiometries

Fig. 5

The NuRD complex undergoes a paralog switch of its members MBD2 and MBD3 across HeLa and HEK293 cells. a We directly compared the abundance of NuRD components between HeLa and HEK293 cells and identified a paralog switch involving MBD2 and MBD3. This suggests a different equilibrium between the MBD2- and the MBD3-containing NuRD variants in these two cell lines. Variable components are depicted as colored circles while core components are represented as gray circles. A double orange line connects the co-regulated paralog pair. b Nuclear extracts from HEK293 and HeLa cells were separated by size-exclusion chromatography and NuRD complex members were quantified by targeted proteomics (Additional file 8, Methods). As predicted by the computational analysis, MBD3 is more abundant in HEK293 cells. Since MBD2 and MBD3 are mutually exclusive in NuRD, this suggests a different equilibrium between the two variants of the complex in these cell lines. c Barplot showing the quantification of NuRD components upon induction of the miRNA targeting MBD3. mRNA levels and protein abundances were compared by qPCR and targeted proteomics upon induction of the miRNA targeting MBD3 or a scrambled miRNA control (n = 3 for each sample group). Significant protein changes (adjusted p value <0.01) are highlighted with an asterisk. The cartoon summarizes the concept that the abundances of the mutually exclusive NuRD components MBD2 and MBD3 are co-regulated: the depletion of MBD3 causes an increased abundance of its paralog MBD2 at the protein level. Gray circles represent core NuRD components

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