Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types, as well as robust methods for tissue-specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies, we have developed a tissue-specific binary in vivo biotinylation system in zebrafish termed "biotagging", a versatile methodology that uses genetically-encoded components to biotinylate target proteins, enabling in-depth genome-wide analyses of their molecular interactions. Using tissue-specific transgenic drivers and individual cell compartment effector lines from our "biotagging" toolkit, we demonstrate the specificity of our approach at the biochemical, cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments (ribosomes and nucleus), we identify a comprehensive network of protein-coding and non-coding RNAs and uncover cis-regulatory modules and regulatory logic conferring cell-specific identity, embedded in the complexity of the non-coding nuclear transcriptomes. Our study demonstrates that "biotagging" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution. Overall design: Examination of RNA-seq and ATAC-seq using in vivo biotinylated nuclei and polysomes.