Predicted m6A and m5C marks in honeybee larval transcriptomes imply functional differences in caste development

Female (diploid) honeybee (Apis mellifera) larvae are developmentally plastic and may become either queens or workers, depending on the nutritional stimuli received during the larval stages. Caste-specific diets activate distinct regulatory networks, leading to differential expression of coding and non-protein-coding genes, splicing variants, differences in the chromatin structures, and DNA methylation patterns, as well as variations in proteomic landscapes and the activity of key signaling pathways. Previous studies have reported the involvement of RNA epigenetics in honeybee caste fate. To further explore this and gain new insights on RNA modifications in caste diphenism, we predicted m⁶A and m⁵C RNA methylation sites in differentially expressed transcriptomes of the fourth instar larvae (L4) of queens and workers. We showed enriched functions among upregulated transcripts in L4 workers with predicted m⁶A and m⁵C sites, such as the metabolism of macromolecules and juvenile hormone synthesis. In L4 queens, these sites were predicted in upregulated transcripts that participate in mitochondrial energy metabolism, cytoskeletal organization, transport, and localization of molecules. Our findings add relevant information and novel perspectives on the potential role of the epitranscriptomic layer in the complex molecular interactions that guide the process of caste differentiation.