Construction and analysis of a developmental RNA editome in adipose tissue of Ningxiang pigs

The Ningxiang pig, a renowned indigenous Chinese breed characterized by exceptional fat deposition, is an ideal model for studying the role of RNA editing in adipose tissue development.

In this study, we constructed a dynamic landscape of RNA editing in subcutaneous adipose tissue across four developmental stages (30, 90, 150, and 210 days) using whole-genome resequencing and transcriptome sequencing data. A total of 86,540 RNA editing sites were identified, with A-to-G conversions being the predominant type (95.73%). These sites were primarily located in intronic regions (80.35%) and highly enriched within the pig-specific SINE retrotransposon PRE-1 (63.08% of all sites). Differential editing analysis revealed 2,023 differentially edited sites (DESs), corresponding to 956 genes, which were significantly enriched in lipid metabolism, insulin signaling, and PI3K-Akt pathway. Temporal clustering analysis identified nine distinct editing patterns, demonstrating stage-specific functional dynamics: early-stage (30 days) events were predominantly involved in catabolic processes; mid-stage events shifted toward PPAR and PI3K-Akt signaling; and late-stage (210 days) events were mainly associated with autophagy and focal adhesion pathways-indicating functional reprogramming of RNA editing during adipogenesis. Integrated protein-protein interaction (PPI) and weighted gene co-expression network analysis (WGCNA) identified hub genes including FOXO3, MAPK1, and PPP2CA, and revealed stage-specific co-editing modules-MEgreen associated with early proliferation and MEturquoise with late-stage maturation.

This study provides a comprehensive RNA editing atlas of adipose development in the Ningxiang pig, revealing its potential role in regulating fat deposition and offering new insights into post-transcriptional regulatory mechanisms in swine.