Chromatin state shapes site-specific A-to-I RNA editing

Abstract

Adenosine-to-inosine (A-to-I) RNA editing is a widespread post-transcriptional mechanism that diversifies the transcriptome. While ADAR enzymes catalyze this reaction, the upstream mechanisms that determine why individual adenosines are edited at markedly different efficiencies remain poorly understood. Here, we integrated multi-omics datasets from human cell lines and mouse embryonic tissues and developed machine learning models that distinguish high-and low-frequency editing sites based on local epigenetic features. Across species, tissues, and developmental stages, H3K36me3 consistently emerges as the strongest negative predictor of editing frequency, whereas the histone variant H2A.Z.1 shows a positive association. Functional validations in H2AFZ-knockdown cells reveal that H2A.Z.1 preferentially facilitates editing at high-frequency sites (76.3% of sites decreased, mean {Delta} =-0.07), whereas SETD2-knockout-mediated loss of H3K36me3 selectively derepresses editing at low-frequency sites (86.9% upregulated, [~]2.7-fold increase). These findings establish chromatin state as an upstream regulatory layer that modulates RNA editing independently of editing enzyme abundance and reveal opposing roles for H3K36me3 and H2A.Z.1 in shaping RNA editing landscapes. Together, our study provides a conceptual framework linking epigenetic regulation to post-transcriptional RNA modification, suggesting that chromatin-mediated regulation contributes to the establishment of site-specific RNA editing programs across mammalian genomes.