Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes

BACKGROUND: Canonical nonsense-mediated decay (NMD) is an important splicing-dependent process for mRNA surveillance in mammals. However, processed pseudogenes are not able to trigger NMD due to their lack of introns. It is largely unknown whether they have evolved other surveillance mechanisms. RESULTS: Here, we find that the RNAs of pseudogenes, especially processed pseudogenes, have dramatically higher m(6)A levels than their cognate protein-coding genes, associated with de novo m(6)A peaks and motifs in human cells. Furthermore, pseudogenes have rapidly accumulated m(6)A motifs during evolution. The m(6)A sites of pseudogenes are evolutionarily younger than neutral sites and their m(6)A levels are increasing, supporting the idea that m(6)A on the RNAs of pseudogenes is under positive selection. We then find that the m(6)A RNA modification of processed, rather than unprocessed, pseudogenes promotes cytosolic RNA degradation and attenuates interference with the RNAs of their cognate protein-coding genes. We experimentally validate the m(6)A RNA modification of two processed pseudogenes, DSTNP2 and NAP1L4P1, which promotes the RNA degradation of both pseudogenes and their cognate protein-coding genes DSTN and NAP1L4. In addition, the m(6)A of DSTNP2 regulation of DSTN is partially dependent on the miRNA miR-362-5p. CONCLUSIONS: Our discovery reveals a novel evolutionary role of m(6)A RNA modification in cleaning up the unnecessary processed pseudogene transcripts to attenuate their interference with the regulatory network of protein-coding genes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02402-2.