Fig. 2: TurboID combined with CLIP and MS reveals compartment-specific changes of RNAs and proteins in resting and KCl-depolarized neurons.
From: Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding
a, Comparison of PL-CLIP with other dendritic RNA-seq datasets (Methods; FDR < 0.05). b, GSEA on PL-CLIP-enriched transcripts in resting neurons (FDR < 0.05). c, Examples of PL-CLIP-enriched RNAs in resting and KCl-depolarized neurons. Expression (cpm) is plotted as log2 (n = 4 biologically independent samples, values from PL-CLIP). Colors: salmon (resting); burgundy (depolarized). Significance was calculated using the two-tailed, paired Student’s t-test. P values: NS (not significant) >0.05; * <0.05; ** <0.01; *** <0.001; **** <0.0001. P values: Shank1 (rest = 0.0033, dep = 0.42), Rpl24 (rest = 0.0061, dep = 0.0047), Map1b (rest = 0.0035, dep = 0.18), Syn1 (rest = 0.027, dep = 0.18), Tamm41 (rest = 0.0064, dep = 0.24), Uqcrc1 (rest = 0.0024, dep = 0.019) and Frmd6 (rest = 0.019, dep = 0.00081). d, GSEA on dendritically enriched RNAs upon depolarization (differential PL-CLIP: depolarized minus resting) (FDR < 0.05). e, Volcano plots showing proteins enriched and de-enriched (by log2 fold change (FC)) in dendrites according to resting (449 enriched; 835 de-enriched), depolarized (658 enriched; 594 de-enriched) and differential (depolarized minus resting) (808 enriched; 609 de-enriched) PL-MS (n = 5 biologically independent samples). Significance was calculated using the two-tailed, paired (resting and depolarized) and unpaired (differential) Student’s t-test. Multiple testing correction was performed using the Benjamini–Hochberg method (a,b,d). NES, normalized enrichment score.
