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

TL;DR

This study shows how nested genes in C. elegans can influence the expression of their host genes during development.

Contribution

The study reveals that nested genes can induce host gene transcription and that coexpression is common during development.

Findings

The nested gene ceh-10 induces transcription of a short version of its host gene polq-1 in neurons.

Coexpression between nested and host genes is relatively common, especially in cells expressing the nested gene.

polq-1 transcription in neurons is regulated by ceh-10 cis- and trans-regulators.

Abstract

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.

•The host gene polq-1 is coexpressed with its nested gene ceh-10 in neurons•polq-1 transcription in neurons starts internally at the level of the ceh-10 gene•polq-1 transcription in neurons is regulated by ceh-10 cis- and trans-regulators•Coexpression of nested and host genes is relatively common during development

The host gene polq-1 is coexpressed with its nested gene ceh-10 in neurons

polq-1 transcription in neurons starts internally at the level of the ceh-10 gene

polq-1 transcription in neurons is regulated by ceh-10 cis- and trans-regulators

Coexpression of nested and host genes is relatively common during development

Genes; Developmental genetics; Developmental biology

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