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 mA levels than their cognate protein-coding genes, associated with de novo mA peaks and motifs in human cells. Furthermore, pseudogenes have rapidly accumulated mA motifs during evolution. The mA sites of pseudogenes are evolutionarily younger than neutral sites and their mA levels are increasing, supporting the idea that mA on the RNAs of pseudogenes is under positive selection. We then find that the mA 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 mA 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 mA of DSTNP2 regulation of DSTN is partially dependent on the miRNA miR-362-5p.

CONCLUSIONS

Our discovery reveals a novel evolutionary role of mA RNA modification in cleaning up the unnecessary processed pseudogene transcripts to attenuate their interference with the regulatory network of protein-coding genes.