Animal mRNAs are regulated by hundreds of RNA binding proteins (RBPs). The 
identification of RBP targets is crucial for understanding their function. A 
recent method, PAR-CLIP, uses photoreactive nucleosides to crosslink RBPs to 
target RNAs in cells prior to immunoprecipitation. Here, we establish iPAR-CLIP 
(in vivo PAR-CLIP) to determine, at nucleotide resolution, transcriptome-wide 
binding sites of GLD-1, a conserved, germline-specific translational repressor 
in C. elegans. We identified 439 reproducible target mRNAs and demonstrate an 
excellent dynamic range of target detection by iPAR-CLIP. Upon GLD-1 knockdown, 
protein but not mRNA expression of the 439 targets was specifically upregulated, 
demonstrating functionality. Finally, we discovered strongly conserved GLD-1 
binding sites near the start codon of target genes. These sites are functional 
in vitro and likely confer strong repression in vivo. We propose that GLD-1 
interacts with the translation machinery near the start codon, a so-far-unknown 
mode of gene regulation in eukaryotes.