RODENTS and people may not appear to be closely related, but consider this the next time you look in a mirror: the genes of human beings and mice are 85 percent identical. This similarity is one of the reasons Lawrence Livermore scientists are studying mice. At Livermore's Human Genome Center, biomedical scientist Lisa Stubbs is leading a team that is studying the mouse genome to better understand the functions of human genes. Comparative genomics-analyzing and comparing the genetic material of different species-is viewed by bioscientists as an important method for studying evolution, the functions of genes (what they do and why), and inherited diseases.
Hunting Down Damaged Chromosomes
To find out which gene is responsible, a researcher takes a small snip of skin from a mouse tail and grows the skin cells in a petri dish. Chromosomes from those cells are then spread on a microscope slide. In the laboratory, the researchers look for one particular kind of mutation called a translocation, which involves obvious changes in chromosome structure. Because the chromosomes are visibly disrupted, researchers can easily map the position of the mutated gene using only a simple light microscope. For example, the figure at right shows two mouse chromosomes-2 and 14-where such a translocation has occurred. "We knew immediately that the gene responsible for the trait would be found on one of those two chromosomes," Stubbs explains.|
The researchers then use a procedure called fluorescent in situ hybridization (FISH), a technique for painting chromosomes with a fluorescent dye, to pinpoint the gene's location. They label a gene from a normal chromosome 2 with the fluorescent dye and add it to a slide containing the mutant mouse chromosomes. The labeled gene probe recognizes DNA sequences spread over the slide that are identical to its own and binds to the chromosome at that site. "In this way," Stubbs says, "we can map any gene relative to the translocation and `trap' the mutated gene in a small, well-defined region."
The researchers repeat the process for other genes on chromosome 2 until they have narrowed down the "breakpoints," that is, the end pieces of the two broken and rejoined chromosome segments. Once they zero in on the chromosome section involved, they search the DNA sequence of that region to identify the genes that have been disrupted by the chromosome break.
"By the time we go to the DNA sequence and begin searching out individual genes," Stubbs says, "we know exactly which spot on the chromosome we must deal with." She continues, "When an organism is exposed to radiation or chemicals, we don't know ahead of time which genes will be affected. It's random, like potluck. All genes `do something,' but some genes are less important than others-their activities affect our development or our health in very subtle ways. If such genes are mutated, we see no visible effects. Others genes, such as those that predispose someone to cancer or obesity, are essential, and their mutations have very obvious impact. All of our mice have mutations. But by focusing specifically on those with visible abnormalities, we are aiming at those genes that play the most important roles in maintaining health."
Of Human Genes and the Department of Energy
Humans have 23 pairs of chromosomes that are made up of DNA (deoxyribonucleic acid), chemical characters arrayed in a particular order in a chain. The chromosomes contain the three billion characters that make up the human genome.
Sequencing is the work of determining the exact order of four individual chemical building blocks that form DNA. These four chemical bases-commonly abbreviated as A, G, C, and T-bind together to create base pairs of DNA molecules. After researchers sequence a piece of DNA, they search for the special strings of sequences that form genes.
The Department of Energy's Joint Genome Institute (JGI) combines the work of Lawrence Livermore, Lawrence Berkeley, and Los Alamos national laboratories. JGI operates around the clock as researchers work to determine the sequence of the information-carrying units that comprise the DNA of three human chromosomes-5, 16, and 19-as part of the international effort to decipher the human genetic code. The purpose is to understand the genetic basis of life. This understanding, in turn, will enable us to understand and attack the root causes of hereditary disorders and susceptibility to diseases such as cancer, heart disease, stroke, diabetes, schizophrenia, Alzheimer's disease, and many others. Because comparison to genomes of other, distant species such as the mouse aids in the discovery and analysis of genes embedded in the human sequence, the JGI will also contribute significantly to sequencing of the mouse genome. That sequencing is part of an international effort slated to proceed in earnest as the human sequence nears completion.
Tracking a Cancer Gene
Similar but Different
Imagine taking human chromosomes, shattering them into pieces of varying lengths, and putting them back together in a different order. "That's what mouse chromosomes look like," says Lisa Stubbs, a Lawrence Livermore bioresearcher. For instance, as the figure shows, almost all of the long arm of human chromosome 19 is related to mouse chromosome 7. That is, the two chromosomal regions contain human and mouse versions of the same genes, organized roughly in the same order. In contrast, the short arm of human chromosome 19 comprises nine segments, each containing 20 to 100 genes and corresponding to different mouse chromosomes. Despite this scrambling of the genetic material, gene content and order within each mouse and human segment mirrors the other quite closely. Humans have this genetic material contained in 23 pairs of chromosomes, whereas mice have 20 pairs. But this difference reflects organization of genes and not their relative numbers
Humans and mice also have about the same number of genes-now estimated to be approximately 140,000-and with some exceptions, each human gene has a clear and quite similar counterpart in the mouse. Those rare exceptions may prove to be quite important to the differences between humans and mice and must be understood more fully. For example, mice have some members of the cytochrome gene family that encode proteins needed to metabolize toxins, which humans do not possess. This genetic difference is reflected in the fact that mice and humans deal with certain toxins differently. Likewise, humans carry a gene encoding a protein called Apo(a) that plays an important role in developing atherosclerosis. Normal mice do not have the gene and never exhibit the symptoms of this deadly cardiovascular disease.
However, these species-specific genes altogether account for roughly 1 percent or less of the two gene sets and do not determine all the differences between humans and mice. The major differences between the species arise from the wide variation in the coding sequences of the counterpart genes. When the average 15 percent difference in mouse and human protein coding sequences is multiplied by 140,000 genes, the overall genetic difference is quite significant.
Not all genes are indispensable, and many of the differences found when mouse and human genes are compared have little effect on our biology. Many living organisms, including humans, carry single-gene changes and chromosomal defects such as translocations (swapped bits) and deletions (missing bits). These changes can mean nothing, or everything. "Consider," says Stubbs, "that because of the large coding capacity and complexity of the genome, a mere 15 percent difference in genes gives you a completely different organism-a human instead of a mouse. But turning the tables around, it is also quite remarkable that humans and mice are as genetically similar as we actually are."
For the Future: Playing Off the Strengths
Key Words: adenocarcinoma, chromosome, comparative genetics, DNA, fluorescent in situ hybridization (FISH), gene, Human Genome Center, Joint Genome Institute, translocation.
For further information contact Lisa Stubbs (925) 422-8473 (firstname.lastname@example.org).