Isolation of Homeodomain Engrailed Target Genes by UV Cross-Linking and Chromatin IP

Interactions between protein complexes and DNA are the heart of essential cellular processes such as transcription, cell division, metabolism, and development of organisms. Therefore, techniques are needed to identify DNA loci that interact in vivo with specific proteins. Only a few techniques are available to access sequences that are bound by transcription factors. These techniques have been developed in the last 10 years and are now very efficient for genome sequencing of different organisms (Ren et al. 2000; Iyer et al. 2001).

One interesting question concerns regulation by homeodomain proteins. These proteins all bind to the same TAAT motifs with slightly different affinities, but they still have a rather sharp effect on their targets (Carr and Biggin 1999). Therefore, it remains an open question as to understanding what controls the specificity of action of the different homeodomain proteins during development.