An optimized translating ribosome affinity purification protocol for low-abundance Drosophila tissues

Localized protein translation enables spatially restricted cellular dynamics, particularly in neurons, where specific mRNAs are translated in axons and dendrites far from the cell body. Translating ribosome affinity purification (TRAP) has been used to study axonal translation in rodents and cell-type-specific translation in Drosophila, but existing protocols are not optimized for axons, where material is extremely limited. Here, we present a highly sensitive TRAP protocol for isolating ribosome-bound mRNAs from low-input samples, enabling recovery of axonal mRNAs from Drosophila larval and adult (leg) motor neurons. RNA-seq identified axonally translated transcripts, including mRNAs encoding ribosomal and mitochondrial proteins, similar to those reported in axons of other species, indicating conservation of axonal translation in Drosophila. This low-input method enables analysis of local translation with Drosophila genetics across developmental stages, genetic backgrounds, and disease models, and can be adapted for rare genotypes, other tissues and model systems requiring high sensitivity.