Allele-specific gene regulation beyond transcription though translational control and RNA modification

Allele-specific expression (ASE) reflects preferential expression of one allele over the other and arises from genetic variation and epigenetic asymmetry established in the nucleus. While ASE has been extensively studied at the transcriptional level, its consequences for translational regulation remain poorly understood. We previously discovered that genes exhibiting ASE show unexpectedly low translational efficiency (TE) during early mouse development. However, the molecular basis underlying this relationship between ASE and reduced translation has remained unclear. To investigate this phenomenon, we analyzed reciprocal crosses between C57BL/6J and CAST/EiJ mice and performed matched single-embryo RNA-seq and ribosome profiling. We found that genes with both sequence-dependent and parent-of-origin–dependent ASE exhibit markedly reduced TE at the 8-cell stage. A similar pattern was observed in hybrid mouse embryonic stem cells, indicating that reduced translation of ASE genes extends beyond early embryogenesis. One potential mechanistic link between ASE and translation is RNA modification. N6-methyladenosine (m6A) is a co-transcriptionally deposited RNA modification known to influence mRNA stability and translational regulation, yet its allele-specific regulation and functional consequences remain insufficiently explored. Leveraging long-read direct RNA sequencing, we simultaneously assigned allelic origin and detected m6A modifications at single-molecule resolution in human and mouse cells. Using a supervised machine learning framework, we identified allele-specific m6A (ASM) events, including cases not directly explained by nearby genetic variants. Together, these findings support a model in which allelic differences established at the transcriptional level may extend to RNA chemical modification and ultimately influence translational output. By integrating allele-resolved analyses of transcription, translation, and RNA modification, this work provides insight into how genetic and epigenetic asymmetry between alleles can shape gene expression beyond transcription during development.