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

Area of Science:

• Developmental Biology
• Genomics
• Molecular Biology

Background:

• Embryonic development requires precise gene expression control.
• Genomic topology, including opposite nested gene configurations, can influence gene regulation.
• Understanding these configurations is key to deciphering developmental gene expression patterns.

Purpose of the Study:

• To investigate the transcriptional effects of the opposite nested gene configuration during C. elegans development.
• To characterize the regulatory interactions between the nested gene ceh-10 and its host gene polq-1.
• To assess the prevalence and impact of opposite nested genes on host gene expression across C. elegans embryogenesis.

Main Methods:

• CRISPR genome engineering to create specific genetic configurations.
• Single molecule Fluorescence In Situ Hybridization (smFISH) to visualize gene expression.
• Single-cell RNA sequencing (scRNA-seq) to analyze gene expression patterns at single-cell resolution.
• Computational analysis of genomic data.

Main Results:

• The nested gene ceh-10 induced transcription of a shortened version of its host gene polq-1 in neurons.
• Coexpression between nested and host genes is common, especially in cells expressing the nested gene.
• Hundreds of protein-coding genes in C. elegans exist in opposite nested configurations.

Conclusions:

• The opposite nested gene configuration represents a significant mode of gene regulation during development.
• Nested genes can actively influence the expression of their host genes, impacting cellular function.
• This configuration provides a mechanism for generating transcript diversity and fine-tuning gene expression.