To understand how genes are regulated, researchers create genome-wide maps that connect regulatory proteins to their target sites on the DNA. This analysis is typically performed using “chromatin immunoprecipitation followed by sequencing” (ChIP-seq). With this method, the cell’s chromosomes are cut into small pieces, and an antibody is used to fish out those DNA fragments that are bound by the regulatory protein of interest. Unfortunately, ChIP-seq is a relatively complex protocol that requires a lot of cells, which makes it difficult to analyze some of the most interesting cell types – for example stem cells and cancer initiating cells.
Researchers in Christoph Bock’s group at CeMM have developed a new and very efficient alternative to ChIP-seq that addresses these limitations. Their approach, which is called “ChIPmentation”, combines the creation and enrichment of antibody-bound DNA fragments in a single-step reaction, making it much faster and more efficient for rare and difficult cell types. Their new paper was published in Nature Methods, which is the leading journal for new methods in biology and biomedicine, and the method is expected to substantially reduce the burden of large-scale studies on gene regulation. At CeMM, ChIPmentation will be used to dissect the role of epigenetic marks in the development and treatment of cancer.
Christian Schmidl*, André F. Rendeiro*, Nathan C. Sheffield and Christoph Bock. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nature Methods, 17 August 2015, DOI: 10.1038/nmeth.3542 (*shared first authors)
This work was supported by the European Commission (BLUEPRINT), the Austrian Science Fund (CINOCA), the Alexander von Humboldt Foundation, the Human Frontier Science Program, and the New Frontiers Programme of the Austrian Academy of Sciences.