Gene-Centered Regulatory Network Mapping - Caenorhabditis Elegans: Molecular Genetics and Development - page 274

Fig. 3 Both TF-centered and gene-centered methods can be used for the identification of TF-target
gene interactions.
a single gene (or a set of genes) and wants to identify the TFs that contribute to its
(their) regulation. This is because all 940 TFs would have to be tested and under all
relevant developmental and physiological conditions. Detailed discussion and pro-
tocols for ChIP in worms are provided elsewhere ( Mukhopadhyay et al., 2008 ).
3. Gene-Centered Methods: Y1H Assays
Y1H assays provide a genetic method for the gene-centered identification of TF-
target gene interactions. The Y1H system is conceptually similar to yeast two-hybrid
(Y2H) assays that have been used extensively to map C. elegans protein-protein
interaction networks ( Li et al., 2004 ; Walhout et al., 2000a, 2002 ). Here, I will
discuss the principles of the Y1H system. Detailed Y1H protocols are available
elsewhere ( Deplancke et al., 2006b ).