A TCER-1-siRNA Regulatory Axis Suppresses Innate Immunity in C. elegans

Non-coding small RNAs (sRNAs) are important regulators of gene expression with well-established roles in development and anti-viral defense. However, their role in antibacterial immunity is not well understood. Here, we identify a role for an endogenous small interfering RNA (siRNA) pathway in repressing innate immunity in Caenorhabditis elegans. We show that genes required for the biogenesis or function of WAGO Argonaute-associated siRNAs, called 22G-RNAs, function in a common genetic pathway with the immune-suppressive transcription elongation and splicing factor TCER-1. Loss of tcer-1 leads to reduced levels of 22G-RNAs from a subset of WAGO targets, while mutations in several WAGO 22G-RNA pathway genes phenocopies the enhanced immune-resistance of tcer-1 mutants, indicating that TCER-1 and the WAGO 22G-RNA pathway function within a shared regulatory module to limit antibacterial immunity. However, rather than mediating widespread gene silencing, this regulatory module targets a restricted set of potential immune-relevant effectors, including scrm-4, encoding a phospholipid translocase that promotes antibacterial resistance. Overall design: High-throughput small RNA and mRNA sequencing was performed on wild-type and tcer-1 mutant strains. RNA was extracted from cell lysates from C. elegans cultured at 20°C and libraries were prepared using NEB kits. Small RNA data was analyzed using the tinyRNA pipeline. mRNA data was analyzed using a custom pipeline of fastp, RSEM, STAR, and DESeq2.