Cut and paste, or just cut

Ah, the redolence of root beer, peanuts and pretzels ... so familiar, so comfortable. My friend, Slamdunk Callahan, was sitting at his corner table, as usual, holding forth to some newcomers. No problem. I ordered a root beer, grabbed a bowl of peanuts and walked over to the table.

“Yes,” Slamdunk was saying, “after all these years, finally, cattlemen have put some real money into across-breed expected progeny differences (EPDs) … lots of professors and breed experts at meetings from Oregon to Maryland.

Even if some folks use the terminology EBVs (estimated breeding values) instead of EPDs, the technology is the same, and there’s nothing better for selecting cattle.”

I had to interject, “Uh, Slamdunk ... maybe there is. Those EPDs may fade in importance sooner than you think.”

Suddenly, the room became very quiet.

But Slamdunk was not rattled. “There you go again,” he said. “Another bombshell, just to interrupt and spout importance. Last time it was about the polymerase chain reaction and the time before that was about George Washington’s sheep breeding program of the Arlington Long Wools. What obscure corner of genetics are you touting tonight?”

I must admit, that was a very coherent discourse from Slamdunk. But we’re pretty good friends, so I rolled on. “Well, it’s a technique called CRISPR, which is pronounced ‘crisper’ but it has nothing to do with crisp cookies. Very simply, it’s causing a revolution in genetics.”

(Clustered regularly interspaced short palindromic repeats = CRISPR, but don’t let that term discourage you. Read on.)

“Funny. OK, you have my attention.”

“You’re familiar, of course, with the cell nucleus and its DNA. And that all cells have an effective mechanism for repairing breaks and damages to their DNA.”

“Of course – everyone knows that. Otherwise, we and our cattle would soon die off from endless small mutations from damaged chromosomes.”

“Exactly. Hold that thought for a moment.”

I continued, “The 1990s and early 2000s saw major genetic research programs to map entire chromosomes, like the cattle genome project and the human genome project. We compiled huge genomic databases of DNA sequences, in species from humans to cattle to insects and worms and all sorts of microbes like bacteria and viruses.

We also developed extremely rapid techniques for mapping the DNA of new species as we found them.”

“This is common knowledge,” said Slamdunk.

I took some peanuts and sipped my root beer. “In 2007, some dairy scientists working for the Danisco company had a problem with their yogurt. It seems that some of their yogurt batches had an off taste.

After studying the bacteria that ferments the milk, they found that when those bacteria were infected by viruses, the yogurt had weird flavors.”

“When they mapped the bacterial genome, they saw regions that contained short DNA sequences were repeated quite frequently. Interspersed between these sequences were spacer segments of DNA, and each spacer was different from the others. This, actually, was not new.

Scientists had known about repeating segments in bacteria for a couple of years and had named them “clustered regularly interspaced short palindromic repeats” or CRISPR.

"Sure, it’s kind of a tongue twister, but maybe they chose it because the acronym is so cool and they liked crisper cookies. In any case, researchers originally thought the duplicate DNA sections were like backup sequences, you know, in case things went wrong.”

“But in 2007,” I continued, “those Danisco scientists found something very strange. They discovered the spacer segments were actually DNA sequences of viruses, not the host bacteria. And through some excellent deductive logic, they concluded the bacteria used this chromosome region as a library of viral DNA and also that these sequences were part of some type of bacterial immune defense system against those viruses."

"This really made sense when they discovered a bacterial enzyme that killed viruses. The enzyme would use the viral DNA as a search sequence, and when it found a corresponding DNA sequence inside the cell, which had to be the invading virus, the enzyme would cut that DNA and thus destroy the virus.”

“This was fascinating information, but the folks mainly interested in it were scientists who studied viral infections of bacteria. Not a very large field. And that’s where our story lay for a few years.”

Slamdunk was watching me intently. “OK, I’ll bite,” he said. “This clearly is leading to something more than viral infections of bacteria. Go on.”

I continued, “Jump to the summer of 2012. Scientists from two widely separated labs – the University of California in Berkeley and Umea University in Sweden – worked together on the properties of a very special enzyme called Cas9. This is one of the powerful cutting enzymes in the CRISPR system.

Even though Cas9 is a bacterial enzyme, these researchers found they could insert this enzyme into the nucleus of mammalian cells so it could work on mammalian DNA. These cells also have sophisticated DNA repair mechanisms, like I mentioned earlier.

“These researchers found that if they preloaded the Cas9 enzyme with a guide-RNA, the enzyme would search for the corresponding sequence in the chromosomal DNA and cut the DNA at that point. The cell would try to repair the DNA, but it may not repair it properly."

"Thus cutting the DNA would effectively silence that gene. And by strategically choosing an appropriate guide-RNA sequence, they could program the Cas9 enzyme to cut DNA at nearly any specific point in the chromosome."

"They had essentially discovered chromosomal scissors. And by using the vast amount of DNA information in modern genomic databases, they could identify a specific gene along a chromosome, use the Cas9 enzyme, and effectively silence that gene. This had never been previously accomplished so elegantly and precisely.”

“In addition, researchers found they could use the CRISPR-Cas9 technique in all sorts of living cells – mammals, birds, insects, worms, even plants. It had nearly universal application across species.”

“Knockouts!” Slamdunk suddenly cried. “That’s what they are. The Cas9 enzyme gave researchers a tool to do knockouts, like in shearing when we would knock out every other tooth of a 13-tooth comb to make a seven-tooth comb."

"Which means scientists could knock out a single gene and see what happens next. That’s a fantastically powerful research tool! Especially when you know exactly which gene you knock out.”

“Yes, just like that,” I responded. “But then researchers discovered one more thing – the thing that really made CRISPR the game-changer. They found that if they loaded the DNA repair enzymes with a new DNA sequence, the repair enzymes would then insert that new DNA in place of the old sequence.”

“You mean ….” Slamdunk started.

“Yes, Slamdunk,” I interrupted, because, after all, this was my moment, “the CRISPR system allows scientists to replace a DNA sequence with a different sequence of their choosing, with extreme precision. Basically, CRISPR is a technique for editing genes.”

Slamdunk could hardly contain himself. “In other words, cut-and-paste! I see it clearly now. CRISPR does to genes what a word processing program does to sentences. It can cut out a word or phrase completely, or it can cut a word and replace it with a different word of your choice.” Then he paused for a second, “Maybe using a better word.”

That was an impressive metaphor. I added another thought, “And if the CRISPR technique were applied to eggs or sperm or embryos, the genetic change would be permanent; the organism would carry that new genetics in all its cells and pass the new DNA sequence to its progeny.”

“And one more thing,” I added, “This CRISPR technology is incredibly cheap. A lab equipped for genetic research could use CRISPR to change a DNA sequence for less than $200."

"So there’s been an explosion in gene-editing research. As we speak, laboratories around the world are aggressively using the CRISPR technique to manipulate and edit genes in every species imaginable.”

Around the table, everyone was stunned. The genetic possibilities were ... staggering – as were the ethical and legal implications.

Genetics, as we know it, would never be the same. Now that we can easily edit genes, our genetic knowledge would increase exponentially. We could knock out genetic faults or silence the genes that cause disease susceptibility.

As more information comes in, genomic databases could identify the precise genetic codes that control productive traits in cattle like weight gain, milk production and feed efficiency. Down the road, people would think of concepts like heritability and EBVs as “quaint but crude” statistical approximations compared to the precision of CRISPR.

How long would it be before we could fix genetic problems or swap genetic sequences until we developed super animals? Or super humans?

Everyone in the room was pondering these ramifications. Even Slamdunk was quiet. Confused Chromosome Club indeed. I ordered a round of root beers for the entire table.

ILLUSTRATION: Illustration by Kristen Phillips.

Woody Lane, Ph.D., is a livestock nutritionist and forage specialist in Roseburg, Oregon. He operates an independent consulting business and teaches workshops across the U.S. and Canada. His book, From The Feed Trough: Essays and Insights on Livestock Nutrition in a Complex World, is available through Lane Livestock Services.