Extended Data Fig. 8: YTHDF1 binding sites and m6A sites in the hippocampus of adult mice, and YTHDF1-mediated effects of m6A on hippocampal transcriptome and proteome.
From: m6A facilitates hippocampus-dependent learning and memory through YTHDF1
a, Peak overlap among three biological replicates of YTHDF1-CLIP-seq. b, Validation of immunoprecipitation efficiency for YTHDF1-CLIP-seq. The position of the gel slice cut during the step of protein–RNA complex size selection is indicated in red (see Methods). c, Consensus motif and its P value generated by HOMER40 of the three sets of hippocampal m6A sites from biological replicates of m6A-CLIP-seq. d, e, Distribution of m6A-CLIP peaks along the different regions of transcripts (d) and genome (e). f, Functional annotation of m6A-modified transcripts in the adult mouse hippocampus (number of mutations in m6A-CLIP-seq ≥ 5, n = 2,922). g, Peak overlap between high-confidence YTHDF1-CLIP peaks and high-confidence m6A-CLIP peaks. The percentage of YTHDF1-CLIP peaks overlapped is indicated. h, Integrative Genomics Viewer (IGV) screenshots of the piled mutated reads for the each of the biological triplicates of YTHDF1-CLIP-seq (red) and m6A-CLIP-seq (blue). Three examples of synaptic plasticity transcripts were presented; the overlapped peak regions are highlighted in orange. i, j, Box-plots of mRNA abundance (i) and protein abundance (j) log2 fold changes (Δ) between Ythdf1-KO hippocampus and wild-type control for all expressed genes (black), non-YTHDF1-CLIP transcripts (grey), YTHDF1-CLIP targets (red), transcripts with overlapped YTHDF1-CLIP peaks and m6A-CLIP peaks (pink), and m6A-modified transcripts (blue). Box-plot elements: centre line, median; box limits, upper and lower quartiles, whiskers, 1–99%; P values, two-sided unpaired Kolmogorov–Smirnov test; number of genes and 95% confidence interval of mean are indicated for each box (i, j).
