High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS)

Highly replicated experiments studying complex genotypes using nested DNA barcodes

Many biological experiments involve studying the differences caused by genetic modifications, including genotypes composed of modifications at more than one locus. However, as the number and complexity of the genotypes increases, independently generating and tracking the necessary number of biological replicate samples becomes a major challenge. We developed a barcode-based method to track large numbers of independent replicates of combinatorial genotypes in a pooled format, enabling robust detection of subtle phenotypic differences. To construct a plasmid library of combinatorial genotypes, we utilized a nested serial cloning process to combine gene variants of interest that have associated DNA barcodes. The final plasmids each contain variants of multiple genes of interest, and a combined barcode that specifies the genotype of all the genes while also encoding a random sequence for tracking individual replicates. Sequencing of the pool of barcodes by next-generation sequencing allows the whole population to be studied in a single flask, enabling a high degree of replication even for complex genotypes. Using this approach, we tested the functionality of combinations of yeast, human, and null orthologs of the nucleotide excision repair factor I (NEF-1) complex and found that cells expressing all three yeast NEF-1 subunits had superior growth in DNA-damaging conditions. We also assessed the sensitivity of our method by simulating downsampling of barcodes across different degrees of phenotypic differentiation. Our results demonstrate the utility of NICR barcodes for high-throughput combinatorial genetic screens and provide a scalable framework for exploring complex genotype-phenotype relationships.

Expansion of the split hygromycin toolkit for transgene insertion in Caenorhabditis elegans

Engineered sites for genetic transformation have simplified transgene insertion in Caenorhabditis elegans . These strategies include our split hygromycin system ​(Stevenson et al. 2020)​ which allows for integration-specific selection of transgenes. Here we have expanded the split hygromycin selection system to include two additional chromosomal locations, both of which are permissive for germline expression, as well as engineered landing pads in three additional natural isolates. Corresponding guide and empty repair template plasmids are also available for each of these sites.