The epigenome’s many obfuscations may soon “come out with the wash,” thanks to a microfluidics-based technique that can improve the collection of high-quality ChIP-enriched DNA. The new technique, which is called microfluidic oscillatory washing–based chromatin immunoprecipitation (MOWChIP-seq), is so good at removing nonspecifically binding chromatin that it allows analysis of epigenomic modifications with as few as 100 cells.
Chromatin immunoprecipitation (ChIP) combined with deep sequencing, or ChIP-seq, is the technique of choice for genome-wide chromatin analysis. But ChIP-seq has lacked sensitivity. In fact, with conventional ChIP-seq protocols, as many as 10 million cells may be required for an individual test, all but eliminating ChIP-seq as a potential clinical tool. In recent years, modified ChIP-seq protocols have improved ChIP collection efficiency, bringing the number of cells needed down to as few as 5,000. In general, however, these modified approaches are most useful for studying specific loci. They are less useful for genome-wide analyses because they must contend with a haze of nonspecific adsorption.
The MOWChIP-seq technique is different. It can work with a small number of cells because it combines two capabilities: high-efficiency collection of ChIP DNA and the suppression of nonspecific adsorption.
The technique, which was developed by researchers at Virginia Tech and the University of Iowa, appeared July 27 in Nature Methods, in an article entitled, “A microfluidic device for epigenomic profiling using 100 cells.” MOWChIP-seq, the article explained, obtains high yields of highly enriched DNA by combining the use of a packed bed of beads for ChIP and effective oscillatory washing for removing nonspecific adsorption.
“Using this technology, we uncovered many new enhancers and super enhancers in hematopoietic stem and progenitor cells from mouse fetal liver,” wrote the authors, “suggesting that enhancer activity is highly dynamic during early hematopoiesis.”
The authors noted that the entire MOWChIP process takes about 90 minutes as opposed to the many hours that conventional ChIP assays took.
“The use of a packed bed of beads for ChIP allowed us to collect the chromatin fragments with a very high efficiency. At the same time, effective washing for removing undesired molecules and debris guarantees the purity of the collected molecules. These two factors constitute a successful strategy for epigenomic analysis with extremely high sensitivity” said Chang Lu, a professor of chemical engineering at Virginia Tech.
“Little is known about the dynamics of the epigenome during embryonic hematopoiesis, largely due to the difficulty in isolating sufficient quantities of these cells from developing embyros,” added Kai Tan, a systems biologist and associate professor of internal medicine at the University of Iowa. “This technology is the perfect tool for tackling this problem.”