Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

Area of Science:

• Genomics
• Molecular Biology
• Developmental Biology

Background:

• Long intergenic RNAs (lincRNAs) are crucial in eukaryotic cells, but systematic phenotypic analysis in animals is limited.
• Understanding the functional roles of lincRNAs is essential for deciphering gene regulation and cellular processes.

Purpose of the Study:

• To systematically analyze the phenotypes of Caenorhabditis elegans long intergenic RNAs (lincRNAs).
• To generate a resource of lincRNA knockout strains for future research.
• To elucidate the functional mechanisms and regulatory roles of identified lincRNAs.

Main Methods:

• CRISPR/cas9 technology was employed to generate knockout strains for 155 C. elegans lincRNAs.
• Phenotypic analysis was conducted across 6 different traits for the generated mutant strains.
• Gene expression patterns and potential functional mechanisms, including cis and trans roles, were investigated.

Main Results:

• 155 C. elegans lincRNA knockout strains were successfully generated, representing a significant resource.
• Mutants of 23 lincRNAs exhibited observable phenotypes across the 6 analyzed traits.
• Identified lincRNAs demonstrated cis-regulatory roles on neighboring genes and trans-regulatory roles as competing endogenous RNAs (ceRNAs).
• The study detailed the regulatory pathway of linc-73 expression by transcription factors UNC-30 and UNC-55, and its cis function on the unc-104 gene impacting locomotion.

Conclusions:

• CRISPR/cas9 technology provides a powerful tool for generating lincRNA knockout resources.
• The study provides valuable biological insights into the functions of 23 C. elegans lincRNAs.
• This work establishes a foundation for further investigation into lincRNA functions in vivo.