Researcher:
Steven Jones, head, Bioinformatics, Genome Sciences Center, British Columbia Cancer Research Center, Vancouver, BC, Canada
Project:
Mapping transcription-factor binding in interferon-gamma-stimulated and unstimulated human cells.
Problem:
Though the yeast genome fits on a single array, most mammalian genomes do not. How, then, does one analyze transcription-factor binding across the entire genome?
Solution:
Jones and his team took the DNA output from ChIP and sequenced it using an Illumina 1G Genome Analyzer, generating 47 million 27-bp reads, or about 1.27 GB of sequence data. Though others had tried sequencing ChIP'd DNA, using either Sanger sequencing or Roche's 454 technology, the depth of coverage was always limited, says Jones. The 1G yields shorter runs, but more of them. "That was the paradigm shift in our ability to map protein-DNA interactions in mammalian-sized genomes," he says.
Jones notes that ChIP is just an enrichment strategy; DNA that was not bound ...
