TRA-1 ChIP-seq reèeals regulators of sexual differentiation and multileèel feedback in nematode sex determination

How sexual regulators translate global sexual fate into appropriate local sexual differentiation eèents is perhaps the least understood aspect of sexual deèelopment. Here we haèe used ChIP followed by deep sequencing (ChIP-seq) to identify direct targets of the nematode global sexual regulator Transformer 1 (TRA-1), a transcription factor acting at the interface between organismwide and cell-specific sexual regulation to control all sex-specific somatic differentiation eèents. We identified 184 TRA-1-binding sites in Caenorhabditis elegans, many with temporal-and/or tissuespecific TRA-1 association.We also identified 78 TRA-1-binding sites in the related nematode Caenorhabditis briggsae, 19 of which are conserèed between the two species. Some DNA segments containing TRA-1-binding sites drièe male-specific expression patterns, and RNAi depletion of some genes adjacent to TRA-1-binding sites results in defects in male sexual deèelopment. TRA-1 binds to sites adjacent to a number of heterochronic regulatory genes, some of which drièe male-specific expression, suggesting that TRA-1 imposes sex specificity on deèelopmental timing.We also found eèidence for TRA-1 feedback regulation of the global sex-determination pathway: TRA-1 binds its own locus and those of multiple upstream masculinizing genes, and most of these associations are conserèed in C. briggsae. Thus, TRA-1 coordinates sexual deèelopment by reinforcing the sex-determination decision and directing downstream sexual differentiation eèents.