A technique to sequence small quantities of DNA is published online this week in Nature Methods. This method, which uses 100-fold less starting material than standard methods, will allow insights into chromatin structure and gene regulation in small cell populations, such as small tumor biopsies.
Chromatin immunoprecipitation, known as ChIP, is based on the isolation of chromatin proteins associated with DNA. The subsequent analysis of this DNA yields information about the interaction between the DNA and the proteins that turn gene expression on or off. Standard ChIP procedures involve a multistep protocol that can lead to sampling bias and require millions of cells as starting material. Bradley Bernstein and colleagues now present an alternative analysis approach based on single-molecule sequencing of chromatin-immunoprecipitated DNA on the Heliscope sequencer.
The scientists show that analysis of as little as 50 picograms of input DNA, the equivalent of about 25,000 cells, yields reproducible and robust results. Making do with fewer cells will enable researchers to analyze chromatin structure, and thus DNA regulation, from cell populations that have hitherto been inaccessible to this analysis.