Isoform differences drive functional diversity of NHR-49.

The C. elegans nuclear hormone receptor, NHR-49 , is a critical regulator of lipid metabolism, which possesses five isoforms differing predominantly within their N-termini. Yet functional distinctions between these different isoforms remain largely unexplored. Using CRISPR-based N- and C-terminal epitope tagging with the biotin ligase, TurboID, we observed that the longest isoform displays a more dynamic subcellular localization, partitioning between nucleus and cytoplasm. Proximity labeling revealed differences in interactomes with N-terminally tagged long isoform of NHR-49 enriched for cytoplasmic proteins, including endocytic machinery like RAB-10 and RAB-11.1 , while C-terminal tags associated primarily with inner nuclear pore components and transcriptional regulators. These findings highlight isoform-specific differences for NHR-49 which dramatically impact its subcellular localization and interaction networks. Our study reveals a previously uncharacterized layer of regulatory complexity in nuclear receptor biology, which emphasize the importance of isoform preferences when interpreting functional genomics data in C. elegans and beyond.