HNF4a, a human nuclear receptor transcription factor that is involved in diabetes, governs the expression of a wide range of metabolic genes in different tissues. The C.elegans homolog of HNF4a is NHR-49 which has been demonstrated to coordinate fatty acid beta-oxidation and desaturation. In a gene expression analysis, we found that NHR-49 is also essential for repressing the expression of genes predicted to participate in sphingolipid processing and lipid remodeling. Thus, NHR-49 coordinately influences several genes in multiple fat metabolism pathways, through both activation and repression. This differential regulation of NHR-49 modules led us to propose a model whereby NHR-49 controls its different sectors of lipid metabolism by interacting with specific transcriptional cofactors. We evaluated potential NHR-49 interacting proteins (ref: Brock, T and Watts, J et al. and Taubert, S et al.) for their impact on global NHR-49 gene activation or repression. We found 4 potential co-factors that controlled distinct NHR-49 target genes: NHR-66, NHR-80, NHR-13 and MDT-15. Notably, we found that knockout of
nhr-66 specifically abrogated NHR-49 repression of sphingolipid and lipid remodeling targets. In contrast, deletion of
nhr-66 did not impact NHR-49''s activation of beta-oxidation and desaturase genes. Our findings thus support a model whereby NHR-49 collaborates with NHR-66 to regulate a system of genes involved in modulating the glycosphingolipid and phospholipid membrane composition. In addition, we found that knockout of
nhr-80 and
nhr-13 affected the expression of NHR-49-regulated fatty acid desaturase genes, but had no impact on any of its other gene targets. Thus, NHR-49 partners with NHR-80 and NHR-13 to regulate the ratio of saturated and unsaturated fat in lipid membranes. Therefore, in characterizing NHR-49''s transcriptional network, we found that the control of distinct NHR-49 regulatory modules is based on NHR-49''s association with distinct interacting partner proteins.