Researchers discover a simpler, more efficient strategy for creating high-resolution protein binding maps. Chromatin immunoprecipitation (ChIP), a common technique for generating such maps has various limitations that prevent scientists from collecting accurate data in their experiments. ChIP proves challenging on a large scale where model organisms are necessary. Small organisms also generate issues because genes are often expressed infrequently or for limited time. The ChIP method also lacks the ability to distinguish between different isoforms of the same protein, limiting research potential. New methods that have been introduced to eliminate the errors and inefficiency associated with ChIP are often difficult to implement, as they require complex bioinformatics.
The new strategy developed by scientists Peter Skene and Steven Henikoff at the Fred Hutchinson Cancer Research Center and Howard Hughes Medical Institute refines the process of analyzing protein-DNA interaction. Using micrococcal nuclease (MNase) that eliminates unnecessary DNA, this team of scientists was able to improve the precision and accuracy of the technique. This seemingly small tweak in the procedure could prove revolutionary to the future of biology. Getting more precise data can be extremely significant when dealing with nuanced protein behaviors that could be vital to determine the fate of cells and even the behavior of human diseases like cancer.
This refined process that eliminates unnecessary sequencing simplifies research, rendering it cost-effective. High-resolution ChIP-seq provides higher accuracy, precision, and cuts costs dramatically. For example, a protein 3’NT profile sequenced and analyzed using the old method required 150 million reads, while the refined method required only 7 million.
Oftentimes, the most revolutionary advancements in biology occur not as novel insights, but as modifications to previous methods that yield better results for researchers. Simplifying the complexities of analyzing protein-DNA relationships across the entire genome will ultimately help scientists better understand biology’s mysteries.
Article by Yael Lederman
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