Intergenic DNA is often called "junk DNA," but current research indicates it is anything but that. As the name implies, intergenic DNA refers to the DNA sequences located between the gene clusters on DNA. It comprises as much as 97% of the human genome (and a similarly high percentage of other species genomes) but contains few genes or no genes at all.
Most recognized genes code for proteins; intergenic DNA does not. Itís function is largely unknown. It is copied into RNA and spliced out during processing; yet though it appears that it's just thrown away, it can't be spliced out of DNA and result in a viable strand.
Much of intergenic DNA may be an evolutionary artifact, coding for things like ancient proteins that are no longer expressed. But it's also possible, even probable, that this artifact serves an essential function we do not yet understand. This is why most researchers prefer to call it intergenic or noncoding DNA instead of junk.
Recent studies indicate that intergenic DNA exerts a subtle influence on nearby and even distant genes. It may represent the accumulated DNA of retroviruses and thus serve an important immune system function. It may also act as a buffer against genetic damage and negative mutations; when chromosomes crossover, they're more likely to switch in an intergenic region rather than a gene-bearing region, making the DNA more tolerant to genetic recombination. It may be a bank for advantageous new genes yet evolving. Or it could serve the function of spacers, allowing enzymes to form around protein-forming genes more easily.
Much intergenic DNA may help regulate the development of embryos into mature stages. Non-coding RNAs are sometimes found in intergenic DNA sections. And it may genuinely have no function. With 97% of human DNA made up of intergenic DNA, it is unlikely that all of it actually does have activity; and it's also likely that many of the above possible uses for intergenic DNA are valid.
Web Resources On Intergenic DNA
The regulatory content of intergenic DNA
Patterns of Evolutionary Constraints in Intronic and Intergenic DNA
Book Resources On Intergenic DNA
DNA Microarrays and Gene Expression : From Experiments to Data Analysis and Modeling by Pierre Baldi et al
DNA Science: A First Course by David A. Miklos et al