Sequence and parent-of-origin dependent m6A contribute to allele-specific gene expression

Abstract Multiple regulatory layers influence allele-specific expression (ASE), particularly through sequence-dependent and parent-of-origin-dependent mechanisms at the transcriptional level. However, little is known about ASE regulation at the post-transcriptional level. The most prevalent post-transcriptional mRNA modification, N 6 -methyladenosine (m 6 A), plays important roles in regulating gene expression. Here, we conduct transcriptome-wide analysis of allele-specific m 6 A in mice. Using early postnatal tissues from reciprocal crosses of two divergent mouse strains, we measured allelic m 6 A differences at single-base resolution. Our study reveals widespread sequence-dependent allelic imbalance in m 6 A methylation, identifying thousands of allele-specific m 6 A (ASm 6 A) sites with statistically significant and reproducible allelic methylation differences. We find evidence of potential cis -regulatory variants within 50-nt flanking regions of ASm 6 As. Intriguingly, we detect parental effects on allelic methylation across m 6 As exhibiting parent-of-origin-dependent ASE. For both sequence- and parent-of-origin-dependent m 6 As, we observe opposing allelic preferences between methylation and expression, suggesting a potential role of ASm 6 A in regulating ASE through negative effects on gene expression. Overall, our findings reveal that both cis -acting and parent-of-origin effects influence ASm 6 A, offering new insights into post-transcriptional mechanisms of ASE regulation.