Understanding animal behavior and development requires visualization and analysis of their synaptic connectivity, but existing methods are laborious or may not depend on trans-synaptic interactions. Here we describe a transgenic approach for in vivo labeling of specific connections in Caenorhabditis elegans, which we term iBLINC. The method is based on BLINC (Biotin Labeling of INtercellular Contacts) and involves trans-synaptic enzymatic transfer of biotin by the Escherichia coli biotin ligase BirA onto an acceptor peptide. A BirA fusion with the presynaptic cell adhesion molecule NRX-1/neurexin is expressed presynaptically, whereas a fusion between the acceptor peptide and the postsynaptic protein NLG-1/neuroligin is expressed postsynaptically. The biotinylated acceptor peptide::NLG-1/neuroligin fusion is detected by a monomeric streptavidin::fluorescent protein fusion transgenically secreted into the extracellular space. Physical contact between neurons is insufficient to create a fluorescent signal, suggesting that synapse formation is required. The labeling approach appears to capture the directionality of synaptic connections, and quantitative analyses of synapse patterns display excellent concordance with electron micrograph reconstructions. Experiments using photoconvertible fluorescent proteins suggest that the method can be utilized for studies of protein dynamics at the synapse. Applying this technique, we find connectivity patterns of defined connections to vary across a population of wild-type animals. In aging animals, specific segments of synaptic connections are more susceptible to decline than others, consistent with dedicated mechanisms of synaptic maintenance. Collectively, we have developed an enzyme-based, trans-synaptic labeling method that allows high-resolution analyses of synaptic connectivity as well as protein dynamics at specific synapses of live animals. KEYWORDS biotin; circuit; connectome; labeling; synapse U NDERSTANDING animal behavior requires the determination and analysis of their precise neural connectivity, i.e., their connectome. Historically, this has been accomplished through reconstruction of serial sections of electron micrographs (White et al. 1986;Jarrell et al. 2012). Pioneered in the nematode Caenorhabditis elegans with its defined and invariant nervous system, partial circuits from Drosophila and the mouse retina have now also been reconstructed (Helmstaedter et al. 2013;Takemura et al. 2013). However, both the experimental effort and the static nature of the connectome at the time of analysis render investigations into the variability of synaptic connections between individuals, during development, or in different genotypes laborious at best. Live-imaging techniques to visualize synaptic connectivity have been developed such as GFP Reconstitution Across Synaptic Partners (GRASP) in C. elegans and, more recently, Synaptic Tagging with Recombination (STaR) in flies (Feinberg et al. 2008;Chen et al. 2014). GRASP takes advantage of the strong molecular intera...