New method quickly, precisely maps epigenome in single cells

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New method quickly, precisely maps epigenome in single cells

CUT&Tag speeds process of precisely locating molecules that turn genes on or off

April 29, 2019
Dr. Hatice Kaya-Okur operates an automated experimental system.

Henikoff Lab postdoctoral fellow Dr. Hatice Kaya-Okur, who developed CUT&Tag with Drs. Steve Henikoff and Kami Ahmad, demonstrates the new tool.

Photo by Robert Hood / Fred Hutch News Service

Scientists at Fred Hutchinson Cancer Research Center have published a new method that allows investigators to map chromatin — the DNA modifications, packaging proteins and molecular factors that work together to turn genes on or off — precisely, quickly, at low cost and in single cells. The CUT&Tag (Cleavage Under Targets & Tagmentation) approach, which the team hopes will make it possible for scientists to rapidly make high-resolution, low-cost epigenetic maps, was published today in Nature Communications.

“Our method replaces one of the most widely used methods in science,” said Fred Hutch geneticist Dr. Steven Henikoff, who co-led the work with Hutch colleague Dr. Kami Ahmad. They also co-authored a blog post on the new method for technical readers. “We are confident that this is going to improve the way chromatin mapping is generally done.”

Dr. Steve Henikoff

Dr. Steve Henikoff

Photo by Robert Hood / Fred Hutch News Service

The epigenome: the cell’s software program

The Human Genome Project, the collective push to map the human genome — the sequence of all the DNA in a human cell — provided scientists with an incredible wealth of information about our genetic blueprint. But knowing our DNA sequence is just the first step to understanding our cells and how they work.

“Basically what the Human Genome Project provided was the hardware [of the cell],” explained Henikoff. “But that DNA is in all of our cells. The question is, what makes one cell different from another?”

What distinguishes an infection-fighting white blood cell from, say, a kidney cell? It’s chromatin, the molecules and chemical modifications that alter which genes are turned on and off. Chromatin can be thought of as a cellular version of a software program. Different cells have different software programs, which are also known as the epigenome.

More and more, scientists are discovering that variation in the epigenome has profound implications for fundamental cellular biology, as well as for human health and diseases such as cancer. Often the epigenetic variation underlies a fundamental biological process. For example, our blood cells switch from one version of the hemoglobin gene to another shortly after birth. A shift in the location of a specific epigenetic factor controls this switch.

In some cases of cancer, a change in a gene’s expression, not its DNA sequence, drives cancer development. With their software programs rewritten, cancer cells stop following normal rules of growth and behavior. Several drugs that block this epigenetic rewriting, called histone deacetylase or HDAC inhibitors, are being tested in clinical trials against certain forms of cancer. One, known as vorinostat, is already approved to treat cutaneous T-cell lymphoma.

Scientists are also eagerly seeking to better understand how the many cells of the body perform their varying functions, and what goes wrong in disease. The Human Cell Atlas is a large collaborative project aimed at creating a comprehensive reference map of all human cells.

A deeper understanding of how epigenetic changes underlie cell identity in health and disease requires a tool that pinpoints the location of various chromatin components. It’s been known for decades that our red blood cells switch their hemoglobin genes, but scientists couldn’t identify the switch until they used a precise mapping tool called CUT&RUN (Cleavage Under Target & Release Using Nuclease), previously developed by Henikoff’s group.

Dr. Kami Ahmad

Dr. Kami Ahmad

Fred Hutch file photo

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.

Sabrina Richards, a staff writer at Fred Hutchinson Cancer Research Center, has written about scientific research and the environment for The Scientist and OnEarth Magazine. She has a Ph.D. in immunology from the University of Washington, an M.A. in journalism and an advanced certificate from the Science, Health and Environmental Reporting Program at New York University. Reach her at srichar2@fredhutch.org.

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