Bulk RNA sequencing of different brain regions from MBP29 mice after PLX5622 administration. A, Heat maps of DEGs in the cortex, corpus callosum, and striatum of PLX5622- and control-fed MBP29 and WT mice. B, Scatter plot represents relative gene expression of RNA transcripts and (C) resulting GO terms in the corpus callosum of control-fed WT compared with MBP29 mice. D, Log2 fold change of DEGs associated with ECM organization upregulated in control-fed MBP29 compared with WT mice and downregulated in MBP29 mice on PLX5622 administration. E, Scatter plot represents relative gene expression of RNA transcripts in the corpus callosum of mice fed with PLX5622 compared with control. GO term analysis of DEGs is depicted for the (F) corpus callosum, (G) cortex, and (H) striatum of control- compared with PLX5622-fed MBP29 animals. I, Venn diagram with genes associated with synapse pruning in respective brain regions and a list of the shared genes among the three regions. J, Selected DEGs associated with synapses in the corpus callosum relevant for signal release, regulation of transsynaptic signaling, and synapse pruning depicted in a Venn diagram. Right boxes, Top 10 DEGs for each pathway. K, DEGs related to synaptic function and neuronal survival in the striatum. J, K, Arrows (↑) indicate upregulation.