CUT&Tag: a higher resolution, lower cost way to map chromatin
CUT&Tag improves upon CUT&RUN. Both methods grew out of the team’s dissatisfaction with the standard method for mapping epigenetic factors, known as ChIP (Chromatin Immunoprecipitation). ChIP takes days to perform, requires many passes to ensure DNA sequence accuracy and can’t be used on small samples or single cells.
In contrast to ChIP, CUT&Tag and CUT&RUN don’t require cells to be cracked open and their DNA and chromatin to be broken into pieces. Instead, cells stay intact, making the approach applicable to single-cell analyses, including projects like the Human Cell Atlas.
Henikoff Lab postdoctoral fellow Dr. Hatice Kaya-Okur — another lead scientist on the team — worked with Henikoff and Ahmad to improve CUT&Tag so that it compresses the DNA-processing from two steps into one. This makes it possible to produce sequencing-ready DNA snippets in a single day. In contrast, ChIP and CUT&RUN take a few days to get to that step. The team also automated most of the process to speed it even further.
The satisfaction of making an impact
Now that CUT&Tag has been developed, the team is looking forward to applying it to their own projects.
They’re also working to share the method with the scientific community, having already sent CUT&Tag materials to more than 300 laboratories around the world that study the epigenome’s role from human health to essential cellular biology. The response has been very positive, Ahmad said.
Many “are people who used ChIP-seq for many years. They can directly compare CUT&RUN. And then they’re coming back and saying, ‘We want the newer one, CUT&Tag,'” he said.
Like the researchers examining the hemoglobin switch, cancer researchers are asking fundamental questions about cancer cell biology that can’t be answered with a low-resolution map. They need to know exactly where epigenetic changes occur, and how. CUT&Tag will accelerate their search for answers, as well as support scientists seeking to understand basic cell biology.
“It’s satisfying to think it can have this kind of general impact,” Henikoff said.