As eIF3a is an important m
6A reader, we investigated the regulatory mechanism of eIF3a in immunity by identifying its target genes with m
6A modifications. For this purpose, we first used a colorimetric assay to quantify m
6A levels in the spleen of our mice and found that the total m
6A modification was significantly lower in the
eIF3afl/fl mice compared to the control mice (
Fig. 3A). This finding suggests that eIF3a may regulate m
6A modification directly or indirectly. Subsequently, we devised a methylated RNA immunoprecipitation sequencing (MeRIP-seq) to investigate the regulation of m
6A by eIF3a in sepsis. Consequently, the
eIF3afl/– and control mice were treated with tamoxifen for 5 days and 10 days after tamoxifen treatment, injected with LPS (
Fig. 3B). Splenic RNA was then extracted at 12 h after LPS induction of sepsis and the differential m
6A modification was discovered by MeRIP-seq and validated by MeRIP-qPCR. After MeRIP-seq data processing and data quality control process, the Pearson's correlation test and Uniform Manifold Approximation and Projection(UMAP) plot revealed significant disparities between the control and
eIF3afl/– groups, while the intra-group differences were relatively minor (Supporting Information Fig. S6A–S6D), suggesting that the data quality is satisfactory. The m
6A-modified fragments were identified as the detected “peaks” in the analysis. There were no significant differences in the count and average enrichment between the two groups (Fig. S6E and S6F). The distribution of m
6A peaks on mRNA was found to be concentrated in the coding sequence (CDS) region and highest near termination codons (STOP) across all samples, which is consistent with previous reports
25 (
Fig. 3C), indicating the reliability of our data. The average proportions of m
6A peaks located in the CDS relative to total m
6A modifications in the control and
eIF3afl/– mice were 50.63% and 47.18%, respectively (
Fig. 3D). However, there is no change in the relative m
6A modifications in other regions. Thus, reduction in eIF3a expression may lead to decreased m
6A modification in the CDS but not other regions including 5′- or 3′-UTRs. A specific “RRACH” motif for m
6A modification was identified in both
eIF3afl/– and control mice. The “RRACH” motif is a well-recognized consensus sequence for m
6A modification. The breakdown of this motif is as follows: R = purine (adenine (A) or guanine (G)), R = purine (adenine (A) or guanine (G)), A = adenine (A), CH = any base (A, C, G or T/U). “RRACH” enriching indicates that the peaks analyzed in the data were m
6A-modified fragments, confirming the accuracy of the results (Fig. S6G). We also identified motifs “GCAG”, which were more enriched in the control than the
eIF3afl/– mice (
Fig. 3E and F), suggesting that these motifs may be specific to eIF3a regulation. To investigate whether m
6A modification affects mRNA expression, we examined the correlation between expression with peak intensity and regions. As shown in Fig. S6H–S6J, the reduction of eIF3a in
eIF3afl/– mice did not lead to changes in mRNA level through altered m
6A modification. Next, we calculated the overlapping peaks of m
6A between the two groups and their differences. There were 2429 overlapping peaks between the two groups, among which 2312 showed no significant difference. Of the remaining mRNAs, 70 were up-regulated and 47 were down-regulated in
eIF3afl/– mice (
Fig. 3G).