Fig. 1

a RNA-seq analysis comparing nlrc3l mutants over heterozygous and wild-type siblings at the 4-dpf larval stage show significant upregulation of inflammatory and immune response genes, and downregulation of metabolic and microglia genes in whole larvae. b Whole mount in situ hybridization of macrophage activation marker irg1/acod1 mRNAs in the 2.5 dpf zebrafish larvae show specific and robust induction of irg1 expression in nlrc3l mutants but no expression in wild-type or heterozygous siblings. c Top, schematic of the macrophage rescue construct used to generate the stable mpeg1-nlrc3l transgenic line to restore wild-type macrophages in nlrc3l mutants using the Tol2 transposon system. Bottom, qPCR analysis demonstrates efficacy of the stable macrophage rescue transgene to reverse increased expressions of pro-inflammatory and neutrophil genes in nlrc3l mutants, thereby abrogating systemic inflammation. Dotted line marks no change relative to control siblings at a fold difference of 1. Error bars show sem; **p-value < 0.01; *p < 0.05. qPCR was conducted using three technical replicates and a minimum of three biological replicates. Fold difference is determined relative to average sibling level either with or without the macrophage rescue construct. d Characterization of macrophage-rescued nlrc3l mutants demonstrates restoration of microglia in all mutants analyzed carrying the mpeg1-nlrc3l transgene (+GH) but not in mutants without the macrophage rescue construct (no GH). Left, neutral red staining marks microglial cells in red (arrows). Right, cartoons showing status of microglia and peripheral macrophages; dotted box shows region depicted in the neutral red images on the left.