Fig. 5. EJCs and RNPS1 protect proximal RNA regions from aberrant mRNA processing.

(A) Differentially methylated regions upon RNPS1 KD in HeLa cells (FDR < 0.1, |log₂FC| > 1), three biological replicates. Gray and red dots indicate differentially methylated regions that overlap and do not overlap with m⁶A peaks in the control KD cells, respectively. (B) Metagenes of significantly m⁶A hypermethylated regions (and top quartile) upon RNPS1 KD in HeLa cells in comparison with that of all m⁶A peaks in control cells. (C) Input and m⁶A-IP read coverage at CDH24 and NRAS upon RNPS1 KD and EIF4A3 KD, respectively, as well as corresponding controls in HeLa cells. (D) Enrichment of suppressed m⁶A sites (identified from MPm⁶A) at EIF4A3-suppressed splice sites (left) and enrichment of EIF4A3 KD hypermethylated regions at EIF4A3-suppressed splice sites (right). Fisher’s exact test, dot and bar represent odds ratio and 95% confidence interval. (E) Input and m⁶A-IP read coverage at SENP3 and HNRNPH1 in EIF4A3 KD and control HeLa cells. (F) Schematic model depicting that EJCs and RNPS1 (and potentially other EJC-associated proteins) protect exon junction-proximal RNA from m⁶A deposition through local mRNA packaging. For (C) and (E), red bracket indicates EIF4A3-suppressed splice variant, with ends of bracket indicating the suppressed splice junctions.