Concept


Although DNA transmits genetic information through time, it basically has a passive role. Proteins encoded by DNA actually carry out the myriad cellular reactions that constitute "life." Now that the Human Genome Project has provided us with a catalog of tens of thousands of genes, we are left with the question: "What do proteins made by these genes actually do?" Scientists have always looked to mutant organisms to provide clues about protein function. Now, specific mutants can be created at will by inserting an altered or non-functioning copy of a gene back into a living organism, then looking for changes in behavior or development. Since mice breed quickly and share about 99% of their genes with humans, they have become the animal model of choice for large-scale functional studies. However, doing a single transgenic experiment is several orders of magnitude more difficult than sequencing the gene itself. The real work of understanding the human genome still lies ahead.

Animation


Hi, I'm Mario Capecchi. I came up with a method that is being used to analyze the functions of proteins. This will help us make sense of the tens of thousands of genes discovered by the Human Genome Project. Some call this new field of large-scale studies of protein structure and function "proteomics." This amounts to carrying Beadle and Tatum's "one gene-one protein" experiments to a massive scale. A particularly good way to study the function of a human protein is to manipulate its homologous protein in mice. Our chromosomes are highly similar in structure. . . . . . and it is estimated that mouse genes are about 99% identical to humans. In the mid-1980s, biologists began to insert new genes into mouse embryonic stem (ES) cells. These cells, which are derived from the inner cell mass of a developing blastocyst, can be grown in culture, like bacteria or yeast. However, they retain the ability to develop and differentiate like normal embryonic tissue. A plasmid carrying a gene to be transferred, or transgene, is cut once with a restriction enzyme. Then, the linearized plasmid is added to the culture. Upon exposure to a short pulse of electrical current, about 10% of the cells take up the new gene. This method of DNA uptake is called electroporation. Blastocysts are then harvested from a pregnant mouse. A number of electroporated ES cells are injected into a host blastocyst. The chimeric blastocyst is then inserted into a surrogate mother, where the transgenic ES cells develop along with the host blastocyst cells. The chimeric pup is, in fact, derived from four parents and visibly shows its mixed heritage. The ES cells are usually derived from mating black parents, and the blastocyst is from a mating of two albino parents. So the transgenic offspring has black and white patches. Initially, there was no way to predict where the transgene incorporated in the host genome. In some cases, it might insert harmlessly into an intergenic region. In other cases, it might disrupt a functioning gene. In rare cases, it recombines with its homologous sequence. My method precisely "targets" a transgene to a particular position on a chromosome by homologous recombination. In one early experiment, I "knocked out" the int-2 gene, which produces a growth factor involved in early mouse development. First, I constructed a "targeting vector" from the first three exons of the int-2 gene. I inserted a neomycin-resistance gene into one of the coding exons, disabling the int-2 gene. I also added a nonhomologous DNA sequence and the thymidine kinase (tk) gene from the herpes simplex virus (HSV). Then I used electroporation to introduce the targeting vector into cultured ES cells. One of two scenarios occurs during integration of the targeting vector in the mouse chromosome. In the first scenario, during homologous recombination, int-2 sequences on the targeting vector and the host chromosome align and exchange. Because its sequences are different, the thymidine kinase gene is excluded during the exchange. However, if random integration occurs, the entire targeting vector is inserted, including the thymidine kinase gene. Because of the way the targeting vector was constructed, we can easily distinguish between the two scenarios. First, neomycin selection kills any cells that have not integrated the transgene. Then, gancyclovir, an antiviral drug, kills cells that have integrated the thymidine kinase gene during nonhomologous recombination. Only cells that have homologously integrated the targeted transgene survive the double selection and reproduce on the culture plate. These cells are inserted into a blastocyst, and the blastocyst is integrated into a surrogate mother that will carry the chimeric embryo to term. Producing a chimeric pup is only the first step of creating a gene knockout. Some of the chimeric pups have sex cells derived from the ES cells. These are from black mice and so will have a gene encoding black coat color. Breeding the chimeras to albino mice produces some black mice with the ES genome in their germ plasm. Because the chimeric mouse produces two types of sex cells with the black coat gene – one with the transgene and one without – black mice are then screened to show which carry the neomycin gene insert. Although I used Southern blots in my original experiment, PCR is more widely used today. PCR primers are made so that in mice with the integrated transgene, PCR yields a 400-base pair fragment. In wild-type mice, PCR would not produce a fragment because the neo gene isn't present. When the results are run on a gel, the mice with the targeted mutation show one band, represented by +. Those without a band are represented by -. Now, back to Mendelian genetics. Each of the positive mice is heterozygous for the mutation, so about 25% of the offspring of two heterozygotes will be homozygous for the knockout genes. These are called null mutants; they don't have a functioning int-2 gene. These mice can be screened for developmental, anatomical, biochemical, or behavioral differences. Sometimes a phenotype can be the result of partial gene function. By using homologous recombination, knockouts or other types of very specific mutations can be made. For example, later work with the homeotic (Hox) genes of mice produced an extremely striking illustration of how homeotic genes work together to determine the mammalian body plan. We studied the effect of essentially duplicate copies of a Hox gene found on different chromosomes – Hoxa-11 and Hoxd-11. Null mutants for either gene showed only subtle differences in the anatomy of the forelimb. However, in double mutants the radius and ulna were essentially missing! One limitation of my knockout system is that the gene is knocked out in all cells right from the beginning of development. Some null mutants simply don't survive. Hi, I'm Brian Sauer. I refined Mario's method to get around the problem of specifying the timing and location of gene knockouts. The refinement takes advantage of the Cre recombinase system in P1 bacteriophage. Cre is a protein that eliminates DNA between two sites called loxP. Each loxP contains a 13-base pair sequence at the 5' end, and an inverted version of this sequence at the 3' end. There are eight base pairs in the middle. One molecule of Cre binds to each of the 13-base pair sequences. The four Cre molecules then form a tetramer that removes the DNA between the loxP sites. One loxP site is left in the chromosome. I discovered that the Cre/lox recombination system also works in mammalian cells! When this system is combined with Capecchi's homologous recombination system, we can knock out genes after the mice grow into adults. Researchers interested in learning and memory did this when they knocked out the mouse NMDA receptor in one type of brain cell called CA1. We believe that the receptors in these cells are crucial for memory formation. First, using homologous recombination, they created a mouse strain with one of its NMDA receptors flanked by two loxP sites. When these sites surround a gene, we say the gene is "floxed." Another mouse was created that not only had a floxed NMDA gene, it also carried the cre gene on another chromosome. The cre gene was under control of a promoter that is only active in CA1 brain cells. When the two strains were crossed, some of the progeny received two floxed genes and one cre gene. Southern blotting detected the floxed genes, and PCR detected the cre gene. In these mice, the NMDA gene was not excised by Cre until the CA1 cells had formed and turned on the promoter – about three weeks after birth. Only these cells and no others were missing NMDR receptors. Without NMDA receptors in their CA1 cells, the knockout mice could not use landmarks to remember where they were in space. They couldn't remember the location of an underwater platform – that they had been placed on earlier – based on surrounding landmarks. The mutant's siblings, who had NMDA receptors, located the platform after lining up the surrounding landmarks. Together, gene targeting by homologous recombination and the Cre-lox recombination system allow us to make essentially any change in the mouse genome — from point mutations to large-scale chromosome deletions. These changes can be activated in essentially any tissue at any time during development.

Gallery


Mario Capecchi, Distinguished Professor, Eccles Institute of Human Genetics.
Mario Capecchi in his laboratory.
Mario Capecchi and members of his lab.
Mario Capecchi and his daughter Misha.
Mario Capecchi with his wife, Laurie Fraser, and daughter Misha.

Audio/Video


Audio Glossary

Southern blot, Knockout, Mouse model, Polymerase chain reaction (PCR), Primer

Video Interviews

Brian Sauer

Dr. Brian Sauer is the head of the developmental biology research program at Oklahoma Medical Research Foundation.

Clip 1 (1:03)
The simplicity of the cre/lox system.

Clip 2 (0:48)
How the cre/lox system works.

Clip 3 (1:04)
How to cut out a gene and why would anyone want to.

Clip 4 (1:25)
How the idea of the cre/lox system come about.

Biography


 

Mario Capecchi developed a technique to target and mutate genes in mice using homologous recombination. Brian Sauer adapted the cre/lox recombinase system from phage for mammalian gene knock outs.

MARIO RENATO CAPECCHI (1937-)

In 1980, Mario Capecchi faced an uncertain future. Reviewers deemed the research proposal he sent to NIH "not worthy of pursuit," so Capecchi gambled and diverted money from other projects into the new research. If the gamble didn't pay off, Capecchi risked losing all his research funding, a death sentence for researchers in today's publish-or-perish universities. But for a man who spent five years as a homeless orphan on the streets of war-torn Italy, the risk probably seemed insignificant.

During the first four years of his life, Capecchi lived with his mother, Lucy Dodd-Ramberg, a poet. Lucy joined a group of artists opposed to fascism in northern Italy, where she met Mario's father, an officer in the Italian air force. Capecchi says they had a passionate love affair, but she wisely refused to marry him.

When World War II started, Mario's mother, along with the other Bohemian artists, was arrested by the Gestapo and sent to Dachau. Lucy anticipated the arrest and arranged for Mario to live with friends with the money she received from selling all her possessions. After a year, however, the money ran out - or was stolen by Mario's father - and the five-year-old was left to fend for himself.

Mario headed south and joined gangs of other homeless orphans, stealing food from open-air markets and sleeping in bombed-out buildings. The police captured him again and again and sent him to orphanages and hospitals, but life there was worse. In the hospital, a cup of coffee and a piece of bread once a day were used to treat his malnutrition, and Mario spent the days lying naked on a stripped bed in a feverish delirium.

After the war, Capecchi's mother was released from prison and searched Italy for a year before finding Mario in a hospital in Reggio Emelia, a city near Bologna. The woman didn't look like the mother he remembered, but she promised to take him from the hospital, so he traveled with her to his uncle's Quaker commune outside Philadelphia in the United States. Edward Ramberg and his wife, Sarah, struggled to tame Mario, now 9, when it became clear that Lucy was too psychologically scarred from the war to care for him.

Mario entered third grade at the local public school without knowing English and spent most of his time beating up his classmates. By high school, he had been socialized, partly through his participation in sports. Capecchi thinks playing on the school's football, baseball, soccer, and wrestling teams taught him lessons in human psychology that he eventually transferred to later relationships.

In college at Antioch, Capecchi began studying for a political science degree to combine his esteem for science with his sense of social responsibility. But he found little science in politics and abandoned it for physics and chemistry. Before he graduated in 1961, though, he knew he would make another switch to molecular biology in graduate school. The field was so new that anything was possible and you could ask any question.

Capecchi's graduate advisor at Harvard, James Watson, steered Mario away from small questions that were only likely to produce small answers. By 1967, Capecchi had his doctorate and, in 1968, joined the biochemistry faculty at Harvard Medical School.

Even though there were thousands of researchers and potential collaborators in the Boston area, Capecchi felt he needed more isolation to freely pursue the big questions in his head. In 1973, he moved to the University of Utah in Salt Lake City where he had 20 colleagues in a department that covered everything from evolution to molecular biology.

The professional gamble Capecchi took with his research funding in 1980 paid off, and he was on his way to harnessing the machinery of mammalian cells to precisely mutate any gene he wished. The technique not only helps researchers generate mice with human diseases for study, but it may be used in future gene therapies to correct disease-causing genes. When he reapplied to NIH in 1984, the reviewers admitted their goof: "We are glad that you didn't follow our advice."

Mario Capecchi is currently a professor of Human Genetics at the University of Utah and lives with his wife and daughter in a remote house in the mountains near Salt Lake City. In 1996, he received the Kyoto Prize honoring his lifetime achievement in the betterment of humanity.

BRIAN SAUER (1949-)

Brian Sauer may be one of the few scientists whose interest in science nearly got him arrested. Sauer (pronounced 'sour') set up his telescope in a dark lot in a nearly deserted housing development to watch Halley's comet. The few houses scattered about looked empty, but one little old lady spotted him and called the state police. Sauer avoided a night in jail after offering the officer a close-up view of the comet.

Growing up on his family's dairy farm north of Madison, Wisconsin, Sauer's first scientific interest was astronomy. He constructed his first telescope from a cardboard tube and fitted it with four lenses. "I grew up in the country, and the sky was always dark," he said. "In school, I told people I was going to be an astrophysicist."

For his first five years of school, Sauer attended a one-room schoolhouse with children in grades one through eight. Around December, he remembers, "there was always a school play and there would be no more classes because the teacher was too busy teaching everyone their parts." To kill time between rehearsals, Sauer played poker with the older students.

Along with the telescope, Sauer also built a short-wave radio and listened to Canadian stations. "But when you're living in Wisconsin, that's not much of a challenge," he confessed. Upping his range, he also managed to pull in European stations and listened to the shows they beamed to the U.S. in English. The experience led him to write a school essay on the propaganda the Nazis broadcasted to the Allied troops during World War II.

During recess at school, Sauer would join the other boys for a game of baseball. (Before astrophysics, Sauer wanted to be a Major League pitcher and he still thinks ex-Milwaukee Brave Warren Spahn was one of the best ever). Their baseball field bordered a swift-running creek, so left-field foul balls would land in the water. Since they only had one ball to play with, Sauer and his teammates would yell "Creek ball!," and everyone had to run to the creek to fish the ball out. "We had to get it before it flowed under the overpass," Sauer says, "because if it flowed past that, it was gone forever."

After high school, Sauer began studying physics at the University of Wisconsin in 1967 but found it tedious and switched to mathematics. One day during his senior year while he was working on a math problem on the big blackboard in his living room, his roommate came in and started sketching the structure of DNA. Intrigued by the molecule, Sauer went to work in a lab in Madison after graduating with a mathematics degree.

"I was a mathematician who was interested in doing some biology, and the most interesting thing about biology, according to my view, was genetics," Sauer recalls. With that in mind, Sauer started graduate school at the University of California, Berkeley in 1973. He worked on the P2 phage, what he calls the "other" phage, since most virologists worked on lambda at the time. When Sauer traveled to conferences to give talks, only ten or so hungover scientists would hear his presentation, because the session on the "other" phage was always scheduled for Sunday morning.

Following a post-doc at Stanford University and a position at the National Cancer Institute, Sauer followed his NCI boss to DuPont in 1984. His colleagues had worked out the biochemistry of the cre/lox recombinase system in the P1 phage, and because the biochemistry was simple, he thought it would also work in eukaryotic cells. Sauer picked the brains of the yeast experts next door and inserted the system into the fungus, expecting sluggish recombination. Instead, "it turned out that the cre worked very efficiently," Sauer says. After the system also worked in mouse cells, he realized "now we could do things [in mammalian cells] that had been done in Drosophila 50 years before."

In 1998, Sauer moved to the Oklahoma Medical Research Foundation where he runs the Developmental Biology Research Program and the mouse knock-out facility. His research tries to untangle the mechanism of DNA recombination with the ultimate goal of applying this knowledge to more precise redesign of the mouse genome.

Factoid

Links


 

Links

Embryo Images

This site has scanning electron micrographs of developing mammalian embryos, mostly mice though there are human embryo pictures. Normal and abnormal development are featured in tutorials based on body parts.

Of Mice and Men

From the Howard Hughes Medical Institute, an article on the how gene targetting works in mice.

Holliday Structure

A brief description with an animated gif of how strand exchange works between two pieces of DNA.

Bibliography

  • Capecchi, M.R., 1997, Hox Genes and Mammalian Development, Cold Spring Harbor Symposia on Quantitative Biology, 62: 273-281.

  • Capecchi, M.R., 1989, Altering the Genome by Homologous Recombination, Science, 244: 1288-1292.

  • Capecchi, M.R., 1994, Targeted Gene Replacement, Scientific American, March, 52-59.

  • Davis, A.P., Witte, D.P., Hsieh-Li, H.M., Potter, S.S., and Capecchi, M.R., 1995, Absence of radius and ulna in mice lacking hoxa-11 and hoxd-11, Nature, 375: 791-795.

  • Fukushige, S., Sauer, B., 1992, Genomic targeting with a positive-selection lox integration vector allows highly reproducible gene expression in mammalian cells, Proc. Natl. Acad. Sci., 89: 7905-7909.

  • Mansour, S.L., Thomas, K.R., Capecchi, M.R., 1988, Disruption of the proto-oncogene int-2 in mouse embryo-derived stem cells: a general strategy for targeting mutations to non-selectable genes, Nature, 336: 348-352.

  • Sauer, B., Henderson, N., 1988, Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1, Proc. Natl. Acad. Sci., 85: 5166-5170.

Glossary


Southern blot -
Knockout - Inactivation of specific genes. Knockouts are often created in laboratory organisms such as yeast or mice so that scientists can study the knockout organism as a model for a particular disease.
Mouse model - A laboratory mouse useful for medical research because it has specific characteristics that resemble a human disease or disorder. Strains of mice having natural mutations similar to human ones may serve as models of such conditions. Scientists can also create mouse models by transferring new genes into mice or by inactivating certain existing genes in them.
Polymerase chain reaction (PCR) -
Primer - A short oligonucleotide sequence used in a polymerase chain reaction.

Children resemble their parents.
Genes come in pairs.
Genes don't blend.
Some genes are dominant.
Genetic inheritance follows rules.
Genes are real things.
All cells arise from pre-existing cells.
Sex cells have one set of chromosomes; body cells have two.
Specialized chromosomes determine gender.
Chromosomes carry genes.
Genes get shuffled when chromosomes exchange pieces.
Evolution begins with the inheritance of gene variation.
Mendelian laws apply to human beings.
Mendelian genetics cannot fully explain human health and behavior.
DNA and proteins are the molecules of the cell nucleus.
One gene makes one protein.
A gene is made of DNA.
Bacteria and viruses have DNA too.
The DNA molecule is shaped like a twisted ladder.
A half DNA ladder is a template for copying the whole.
RNA is an intermediary between DNA and protein.
DNA words are three letters long.
A gene is a discrete sequence of DNA nucleotides.
The RNA message is sometimes edited.
Some viruses store genetic information in RNA.
RNA was the first genetic molecule.
Mutations are changes in genetic information.
Some types of mutations are automatically repaired.
A chromosome is a package for DNA.
Higher cells incorporate an ancient chromosome.
Some DNA does not encode protein.
Some DNA can jump.
Genes can be turned on and off.
Genes can be moved between species.
DNA responds to signals from outside the cell.
Different genes are active in different kinds of cells.
Master genes control basic body plans.
Development balances cell growth and death.
A genome is an entire set of genes.
Living things share common genes.
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