Induction of host genes by nested genes during C. elegans development
Fabien Soulavie,
Carole Couillault,
Matéo Melki,
Khulganaa Buyannemekh,
Antoine Barrière,
Paul Villoutreix,
Vincent Bertrand
Affiliations
Fabien Soulavie
Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
Carole Couillault
Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
Matéo Melki
Aix Marseille University, Université de Toulon, CNRS, LIS, Turing Centre for Living Systems, Marseille, France; Aix Marseille University, INSERM, MMG, Turing Centre for Living systems, Marseille, France
Khulganaa Buyannemekh
Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France; Aix Marseille University, Université de Toulon, CNRS, LIS, Turing Centre for Living Systems, Marseille, France; Aix Marseille University, INSERM, MMG, Turing Centre for Living systems, Marseille, France
Antoine Barrière
Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
Paul Villoutreix
Aix Marseille University, Université de Toulon, CNRS, LIS, Turing Centre for Living Systems, Marseille, France; Aix Marseille University, INSERM, MMG, Turing Centre for Living systems, Marseille, France
Vincent Bertrand
Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France; Corresponding author
Summary: Embryonic development relies on tightly controlled gene expression. In this study, we analyzed the transcriptional effect during C. elegans 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 ceh-10, a transcription factor involved in neuronal specification, and its host polq-1, 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 C. elegans 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.
