Factor tracker

Thomas Splettstoesser / wikimedia.org

C.-L. Wei et al., "A global map of p53 transcription-factor binding sites in the human genome," Cell, 124:207-19, 2006. (Cited in 184 papers)

Yijun Ruan, of the Genome Institute of Singapore, and colleagues wanted a better way to study where transcription factors (TFs) bind to DNA. They developed a genome-wide technique using chromatin immunoprecipitation (ChIP), which isolates DNA bound to proteins such as transcription factors. They then sequenced the DNA using a novel paired end ditag (PET) method which tags both 3' and 5' end of the DNA.

Using the tool called ChIP-PET, on p53, Ruan et al. identified 542 binding sites, 98 of which were located on previously unidentified genes.

Since 2006, ChIP-sequencing methods, like ChIP-PET, have become commonly used, says Mark Biggin, at the Ernest Orlando Lawrence Berkeley National Laboratory, for studying whole genome binding of TFs controlling development, speech, and language. Other researchers have gone on to show that only 160 of the 542 sites in this study are actual p53 binding sites that control 122 genes (Nat Rev Mol Cell Biol, 9:402-12, 2008).

To examine the remaining 382 binding sites not associated with genes, called distal binding sites, Ruan's group developed a method called ChIA-PET, short for chromatin interaction analysis. By capturing the distal TF binding sites that loop around to interact with other regions of DNA, Ruan hopes to uncover whether these sites are merely parking spaces for inactive TFs or act on DNA directly.