Fig. 3: One-carbon metabolism related RNAs increasingly bind to RRP1 in IL-1β mediated inflammation.
From: The RNA-binding protein RRP1 brakes macrophage one-carbon metabolism to suppress autoinflammation
a Volcano plot showing of RNA molecules that differentially bind to RRP1 in BMDMs between 0 h and 12 h of IL-1β stimulation. b Heatmap showing metabolites in BMDMs stimulated by IL-1β for 12 h or not (n = 6). c KEGG analysis of metabolic pathway-related gene sets of RIP-seq identified RNAs that increasingly binding to RRP1 following IL-1β treatment. d Schematic of 1C-metabolism, including the folate cycle and the downstream methionine cycle. Met methionine, SAM S-adenosyl methionine, SAH S-adenosyl homocysteine, Hcy homocysteine, VB12 vitamin B12, THF tetrahydrofolate, 5, 10-mTHF N5,10-methylene- tetrahydrofolate, 5-mTHF N5-methyltetrahydrofolate, DHF dihydrofolate, DHFR dihydrofolate reductase, TYMS thymidylate synthetase. e Enrichment of 1C-metabolic-related gene sets of RIP-seq identified mRNAs that differentially binding to RRP1 following IL-1β treatment. f RIP-qPCR detects RRP1 binding to the Tyms mRNA, as assessed by two pairs of primers in BMDMs stimulated by IL-1β for indicated hours. g Western blot detects the Flag tagged full-length RRP1 (FL), Nop52 and C terminal (Cter) expression in NIH/3T3 cells as long as the immunoprecipitation (IP) effect by using the anti-Flag beads. The data were quantified with Image J. h RIP-qPCR detects the Flag tagged full-length RRP1 (FL), Nop52 and C-terminal (Cter) binding to Tyms mRNA in NIH/3T3 cells followed with IL-1β treatment for indicated hours. The cells transfected with empty Vector were used as controls. The data were normalized as (2^-ΔCt RIP RNA / 2^-ΔCt Input RNA) / (integrated density IP protein / integrated density Input protein). RIP-seq data are presented with normalized FPKM values of technical replicates (n = 3) from three independent experiments (a, e). Metabolomics data are presented with normalized response peak area values (z-score) (b). KEGG enrichment are used by hypergeometric test (one-tailed) with FDR correction (Q-values) (c). Western blotting data is representative of three independent experiments. RT-qPCR data are presented as means ± SD of (f, h, n = 3) biologically replicates from three independent experiments with student’s t test (two-tailed unpaired). Source data are provided as a Source Data file.
