SF3B4 “reads” RNA that is methylated by METTL16

Using this approach, we identified the spliceosomal protein SF3B4 as a potential m6A reader. RNA pull-down assays using m6A-modified RNA probes demonstrated selective enrichment of endogenous SF3B4, supporting its ability to recognize m6A RNA.

To define the RNA targets of SF3B4, we performed SF3B4 RIP-seq alongside m6A RIP-seq, followed by RIP-qPCR validation of overlapping targets. Motif analysis revealed that SF3B4 preferentially associates with the conserved GRAGRA (R=A/G) motif, consistent with the RNA sequence recognized by the METTL16 methyltransferase. Notably, transcripts of the BCR and MET oncogenes were identified as shared targets of SF3B4 and METTL16.