Intergenic regions
Related Terms
Chromosome, comparative biology, deoxyribonucleic acid (DNA), evolution, gene, gene expression, genetics, Human Genome Project, inheritance, intergenic region, microsatellite, mutation, molecular, noncoding DNA, regulatory elements, single nucleotide repeats (SNPs), tandem repeats, transcription, translation.
Background
Junk DNA (deoxyribonucleic acid), also called noncoding DNA or intergenic regions, are sections of DNA that do not form genes and thus do not create proteins. More than 90% of human DNA is junk DNA. Researchers originally called these sections of DNA "junk DNA" because they thought they served no functional purpose. However, additional research has demonstrated that this so-called "junk DNA" may play a role in the control of gene expression by increasing or decreasing gene activity and may also act in the repair of damaged chromosomes.
Chromosomes are found inside the cells of all organisms. Chromosomes are made of DNA molecules, which look like a twisted ladder. This unique shape is called a "double helix." The sides of the double helix are made of alternating sugar and phosphate molecules. The "rungs" of the "ladder" are made of smaller molecules called bases that contain nitrogen. These molecules include adenine, thymine, cytosine, and guanine.
All genes are made up of different combinations of these four molecules, which are arranged in different patterns. The sequence of these molecules provides the "code," or instructions, for each of the genes involved in the development, growth, and function of all the cells in the body. This code is used to create proteins, which may provide structure to the cells and tissues of the body, such as creating the membranes that surround cells, function in metabolism and repair of damaged tissue, for example, by breaking down food in the digestive tract, or function as signaling molecules within the body, such as hormones.
Regulation of gene activity affects how much protein is produced by causing genes to be more active (producing more protein) or less active (producing less protein). If a segment of junk DNA controls the activity of a nearby gene, the result could be more or less of a specific protein in the body. This activity can have a wide variety of effects depending upon the protein that is affected. For example, a gene involved in the production of antibodies, which fight infections, is known to be affected by segments of junk DNA that cause it to be more active. This causes the individual to produce more antibodies, but the effect of this increased production is not yet understood.
Junk DNA regulation is thought to be important during early prenatal development (embryogenesis). Segments of junk DNA have been found to regulate genes that are important in the development of the eyes and the nervous system.
Methods
DNA sequencing: DNA sequencing is a method of determining the exact pattern of adenine, guanine, cytosine, and thymine in a DNA fragment. First, DNA is extracted from the blood or tissue of an individual. Then, the DNA is mixed with an enzyme, which is a type of protein that creates copies of the genetic material; a primer, which is a segment of DNA that tells the enzyme where to begin copying; and the four nitrogen bases required to synthesize the DNA molecule. The primer attaches to the molecule of interest, and the enzyme creates copies with the nucleotide bases. The nucleotide bases have specific signals, for example, a fluorescent light, on them so that they can be detected and the sequence can be determined.
Knockout mice: Knockout mice are genetically altered mice that are missing a segment of their DNA. Using knockout mice, scientists can learn what specific segments of DNA do. When a section of junk DNA or a gene is deactivated, the function of that DNA segment may be revealed by the physical characteristics, or phenotype, of the knockout mouse.
To create a knockout mouse, scientists either replace or deactivate an existing segment of junk DNA or gene with a gene-targeting construct. Targeting constructs may contain "foreign" DNA from other organisms and are designed to contain sequences that are similar, or homologous, to the mouse DNA. There are several types of targeting constructs. Some insert a piece of foreign DNA into the gene, which interrupts the gene sequence. If designed properly, this interruption may inactivate the gene. Other targeting constructs are designed to replace a gene or critical gene sequence with foreign DNA. Some targeting constructs are designed so that an entire gene or a critical part of the gene is removed completely. Depending on the type of procedure used, the constructs may target either specific genes or random DNA sequences.
Research
Junk DNA is a very active area of research with many scientists working to determine the function of junk DNA in gene expression. Current research is focusing on determining the effects of junk DNA on gene activity in general and on its effects on embryological (prenatal) development specifically.
Implications
Once junk DNA is understood more clearly, it may help scientists to explain why some individuals are more susceptible to certain diseases than others. For instance, variations in junk DNA may cause genes that prevent cancer to be less active, therefore placing an individual at higher risk for the development of cancer.
The discovery that junk DNA plays a role in prenatal development may help doctors understand why some children develop congenital defects.
Gene therapy is an experimental procedure that may help treat or prevent inherited disorders and some types of cancer. In the future, it may be possible to use gene therapy to correct defects in junk DNA that cause disease. Although early research is promising, additional research is needed to determine whether gene therapy is a safe and effective treatment.
Limitations
Junk DNA is just beginning to be understood. Much more research will be required before knowledge of junk DNA is applicable to most individuals. Performing this research is expensive and time consuming. Scientists are still a long way from applying the study of junk DNA to medical practice.
In addition to determining the sequence of junk DNA and determining its actions, researchers will have to find a way to make this information useful. This means designing medications that can target junk DNA or laboratory tests that can detect junk DNA in individuals. Creating these will be costly and time consuming.
Future research
Research will continue to focus on finding new junk DNA elements and determining how they affect gene function. Identifying junk DNA segments that are involved in common diseases, such as cancer and diabetes, may one day lead to a better understanding of these diseases and how to treat them.
Once junk DNA segments that are associated with human disease are identified, drugs may be developed to directly affect this DNA segment in order to treat and prevent disease.
Author information
This information has been edited and peer-reviewed by contributors to the Natural Standard Research Collaboration (www.naturalstandard.com).
Bibliography
Genetics Online. .
Hasler J, Samuelsson T, Strub K. Useful 'junk': Alu RNAs in the human transcriptome. Cell Mol Life Sci. 2007;64(14):1793-800.
Jenuwein T, Forrester WC, Fernandez-Herrero LA, et al. Extension of chromatin accessibility by nuclear matrix attachment regions. Nature 1997;385:269-72.
Kohler J, Schafer-Preuss S, Buttgereit D. Related enhancers in the intron of the beta1 tubulin gene of Drosophila melanogaster are essential for maternal and CNS-specific expression during embryogenesis. Nucleic Acids Res 1996;24:2543-50.
National Center for Biotechnology Information. Genomes. .
National Human Genome Research Institute (NHGRI). .
Natural Standard: The Authority on Integrative Medicine. .
Nikolajczyk BS, Nelsen B, Sen R. Precise alignment of sites required for mu enhancer activation in B cells. Mol Cell Biol 1996;16:4544-54.
Tomilin NV. Regulation of mammalian gene expression by retroelements and non-coding tandem repeats. Bioessays. 2008;30(4):338-48.
Vandendries ER, Johnson D, Reinke R. Orthodenticle is required for photoreceptor cell development in the Drosophila eye. Dev Biol 1996;173:243-55.