Who Needs Arrays?
Bradley Bernstein, of the Broad Institute of Harvard and MIT, has developed a genomewide screening approach for histone modifications that eliminates DNA arrays. “ChIP-Seq” combines chromatin immunoprecipitation (ChIP) and Illumina’s next-generation sequencing technology, acquired from Solexa. Like ChIP-on-chip, which reads ChIP data using whole-genome microarrays, ChIP-Seq provides a genomewide view of chromatin changes. The difference, says Bernstein, is that ChIP-on-chip measures fluorescence intensity, while ChIP-Seq counts the absolute number of times a particular genomic fragment is detected. “ChIP-on-chip is an analog readout, whereas sequencing is a digital readout,” he explains. This past August, Bernstein coauthored a study that used ChIP-Seq to map several histone modifications across the genome in mouse embryonic stem cells, neural progenitors, and embryonic fibroblasts. The data shed light on the cells’ transcriptional past, present, and future, Bernstein said. “It is a wa
