Translational profiling through biotinylation of tagged ribosomes in zebrafish

Phenotypic heterogeneity within a population of cells of the same cell type is a common theme in metazoan development. Apprehending complex developmental and physiological processes critically relies on our ability to probe the expression profile of these genetically defined cell sub-populations. Current strategies rely on cell enrichment based on tandem or simultaneous evaluation of multiple intersecting markers starting from a heterogeneous cellular suspension. The extensive tissue manipulations required for single-cell suspension generation, as well as the complexity of the required equipment, inherently complicates these approaches. Here, we propose an alternative methodology based on a genetically encoded system in the model organism Danio rerio (zebrafish). In transgenic fish, we take advantage of the combinatorial biotin transfer system where polysome-associated mRNAs are selectively recovered from cells expressing both a tagged ribosomal subunit, Rpl10a and the bacterial biotin ligase, BirA. We have applied this technique to skeletal muscle development, identifying genes with novel regulation and have developed tools for highly specific gene expression profiling during vertebrate development. Translational profiling of zebrafish skeletal muscle during 4 time points (21, 24, 27, 34 hours post fertilization)