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Unit Chapters
Genomics
The Human Genome Project
Sequencing a Genome
Finding Genes
Is the Eukaryotic Genome a Vast Junkyard?
The Difference May Lie Not in the Sequence but in the Expression
Determining Gene Function from Sequence Information
The Virtues of Knockouts
Genetic Variation Within Species and SNPs
Identifying and Using SNPs
Practical Applications of Genomics
Examining Gene Expression
Ethics
Epilogue
Proteins & Proteomics
Evolution & Phylogenetics
Microbial Diversity
Emerging Infectious Diseases
HIV & AIDS
Genetics of Development
Cell Biology & Cancer
Human Evolution
Neurobiology
Biology of Sex & Gender
Biodiversity
Genetically Modified Organisms
Is the Eukaryotic Genome a Vast Junkyard?

Bacteria have small, compact genomes, rich in genes. These genes have fewer noncoding regions and no introns. Eukaryotic genomes, however, often have much more DNA content than prokaryotic genomes. While eukaryotes generally have more genes than bacteria, the difference in gene content is not as great as the difference in DNA content: there is much more noncoding DNA in eukaryotes. In fact, gene-coding regions comprise only about two percent of the human genome.

Most eukaryotic genes are interrupted by large introns. Even with these introns included, however, genes comprise only about twenty-five percent of the human genome. In eukaryotes, repeated sequences characterize great amounts of noncoding DNA. Some of this repetitive DNA is dispersed more or less randomly throughout the genome. There are also millions of copies of other, shorter repeats, but they are typically found in larger blocks. Some trinucleotide (3 bp) repeats are associated with diseases such as fragile X and Huntington's disease, which result from extra copies of the repeat sequence.

Most of these repeat sequences are transposable elements, that can replicate and insert a copy in a new location in the genome. The result is the amplification of these repetitive elements over time. Transposable elements can be harmful because they can cause mutation when they move into a gene. They also use cellular resources for replication and expression. Are these elements unwelcome guests gone wild or may they actually be useful components of the genome? We don't really know, but there are some tantalizing suggestions of functions for some of these elements. About one million copies of the repetitive DNA element called Alu repeats lurk in the genomes of each one of us. What are they doing? One study found that these bind to proteins used to reshape chromatin during cell division. Perhaps this apparent junk DNA is actually helping provide structure to the chromosome and regulate the production of proteins in different cell types.

Genomes differ in size, in part because they have different proportions of repetitive DNA. For example, the total genome size of the puffer fish is about one-tenth the size of the human genome. However, the puffer fish genome has about the same number of genes as the human genome, and the genes appear to have the same functions. The puffer fish genome is also smaller than the human genome. This is partially because it contains only about fifteen percent repetitive DNA, while more than half the human genome is repetitive DNA. Because most human genes are present in the puffer fish and the puffer fish genome is less cluttered by repetitive DNA, this model organism may help scientists identify the genes responsible for human diseases.

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