Induction of host genes by nested genes during C. elegans development

Embryonic development relies on tightly controlled gene expression. In this study, we analyzed the transcriptional effect during <i>C. elegans</i> development of a striking genomic topology, the opposite nested configuration, where a gene is located in an intron of a host gene in the opposite direction. Using CRISPR genome engineering and single molecule FISH, we characterized the regulatory interactions between <i>ceh-10</i>, a transcription factor involved in neuronal specification, and its host <i>polq-1</i>, a DNA repair enzyme, showing that the nested gene induces transcription of a short version of its host in neurons. Extending our analysis to the hundreds of protein coding genes in opposite nested configuration and using single-cell RNA-seq data covering <i>C. elegans</i> embryogenesis, we observed that coexpression between nested and host genes is relatively common especially in cells positive for the nested gene. Our study illustrates how the presence of a nested gene can influence expression of its host.