(A) Whole-cell CA1 FMRP targets fall into three functional clusters. Functional module detection was performed for CA1 FMRP targets by the HumanBase software. (B) Top GO terms for the three largest functional modules of CA1 FMRP targets. Q-values for enrichment of terms were determined by the HumanBase software. (C) Dendritic FMRP targets are enriched in functionally distinct modules of CA1 FMRP targets. CA1 genes were ranked according to FMRP dendritic and cell bodies FMRP-CLIP scores, and gene set enrichment analysis (GSEA) was performed using the FMRP functional clusters (from A) as gene sets. Circles are colored according to normalized enrichment scores (NES) and sized according to false discovery rate (FDR) from the GSEA. NES values are shown, and asterisks indicate significance (**FDR <0.001, ****FDR<0.00001). (D) Dendritic FMRP targets are enriched in a functional module of autism candidate genes. GSEA was performed as shown in (C), with functional modules of autism candidate genes (SFARI) clustered according to the HumanBase software. (E) Localization of FM2/3 FMRP targets is largely unchanged in compartment-specific bulk RNA-seq of FMRP KO animals, but increased in TRAP. Left: neuropil localization (log2 fold change [LFC]/standard error [SE] of CA1 neuropil bulk RNA-seq vs. cell bodies bulk RNA-seq) was assessed in FMRP KO vs. WT animals. Cumulative distribution plots are shown. Shifts to the right indicate more localization in the FMRP KO animals, and shifts to the left indicate more localization in WT animals. All CA1-expressed genes, all CA1 FMRP targets and dendritic FMRP targets are shown. Right: localized ribosome association in TRAP-seq on FMRP KO vs. WT animals, with subsets including the FM1/2/3 groups of CA1 FMRP targets as described in (A). (F) Distinct, compartment-specific FMRP regulation of functionally distinct subsets of mRNAs in CA1 cell bodies and dendrites. Localization of mRNA to the dendrites does not appear to be FMRP-dependent in CA1 neurons, but likely depends on other factors (e.g., other RNA-binding proteins or mRNA characteristics such as GC content, length, or secondary structure) that target mRNAs to the dendrite or compartments within the neuronal soma. In dendrites, the absence of FMRP increases the ribosome association of its targets; this finding is consistent with a model in which FMRP inhibits ribosomal elongation and thereby translation (Darnell et al., 2011). In resting neurons, the translation of FMRP-bound mRNAs encoding synaptic regulators (FM2 and FM3 mRNAs) is repressed. When FMRP is not functioning, due to either genetic alteration (FMRP KO or FXS) or neuronal activity-dependent regulation (e.g., FMRP calcium-dependent dephosphorylation; Lee et al., 2011; Bear et al., 2004), ribosome association and translation of targets are increased. In cell bodies, FMRP binds mRNAs that encode for chromatin regulators (the FM1 cluster of FMRP targets), as well as FM2/3 mRNAs (consistent with synapses forming on the cell soma). FM1 targets show patterns of mRNA regulation similar to what our group observed in bulk CA1 neurons: FMRP target abundance is decreased in FMRP KO cells, perhaps due to loss of FMRP-mediated block of degradation of mRNAs with stalled ribosomes (Sawicka et al., 2019; Darnell, 2020). This does not preclude the observation that FMRP also inhibits translation of chromatin regulators (Korb et al., 2017).