In molecular biology, junk DNA is a provisional label for the portions of the DNA sequence of a chromosome or a genome for which no function has been identified. Scientists expect to find functions for some, but not all, of this provisionally classified collection. About 95% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA. While much of this sequence may be an evolutionary artifact that serves no present-day purpose, some junk DNA may function in ways that are not currently understood. Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function. Some consider the "junk" label as something of a misnomer, but others consider it appropriate as junk is stored away for possible new uses, rather than thrown out; others prefer the term "noncoding DNA" (although junk DNA often includes transposons that encode proteins with no clear value to their host genome). About 80% of the bases in the human genome may be transcribed, but transcription does not necessarily imply function.
Broadly, the science of functional genomics has developed widely accepted techniques to characterize protein-coding genes, RNA genes, and regulatory regions. In the genomes of most plants and animals, however, these together constitute only a small percentage of genomic DNA (less than 2% in the case of humans). The function, if any, of the remainder remains under investigation. Most of it can be identified as repetitive elements that have no known biological function for their host (although they are useful to geneticists for analyzing lineage and phylogeny). Still, a large amount of sequence in these genomes falls under no existing classification other than "junk". For example, recent experiments removed 1% of the mouse genome and were unable to detect any effect on the phenotype. This result suggests that the DNA is nonfunctional. However, it remains a possibility that there is some function that the experiments performed on the mice were merely insufficient to detect.
While overall genome size, and by extension the amount of junk DNA, are correlated to organism complexity, it is not a solid rule of thumb. For example, the genome of the unicellular Amoeba dubia has been reported to contain more than 200 times the amount of DNA in humans" .
The pufferfish Takifugu rubripes genome is only about one tenth the size of the human genome, yet seems to have a comparable number of genes. Most of the difference appears to lie in what is now known only as junk DNA. This puzzle is known as the C-value enigma or, more conventionally, the C-value paradox.
There are some hypotheses, none conclusively established for how junk DNA arose and why it persists in the genome:
Comparative genomics is a promising direction in studying the function of junk DNA. Biologically functional sequences tend to undergo mutation at a slower rate than nonfunctional sequence, since mutations in these sequences are likely to be selected against. For example, the coding sequence of a human protein-coding gene is typically about 80% identical to its mouse ortholog, while their genomes as a whole are much more widely diverged. Analyzing the patterns of conservation between the genomes of different species can suggest which sequences are functional, or at least which functional sequences are shared by those species. Functional elements stand out in such analyses as having diverged less than the surrounding sequence.
Comparative studies of several mammalian genomes suggest that approximately 5% of the human genome has evolved under purifying selection since their divergence. Since known functional sequence comprises less than 2% of the human genome, there may be more junk DNA in the human genome than there is functional sequence.
A surprising recent finding was the discovery of nearly 500 ultraconserved elements, which are shared at extraordinarily high fidelity among the available vertebrate genomes, in what had previously been designated as junk DNA. The function of these sequences is currently under intense scrutiny, and there are preliminary indications that some may play a regulatory role in vertebrate development from embryo to adult.
Present results concerning evolutionarily conserved human junk DNA are expressed in preliminary, probabilistic terms, since only a handful of related genomes are available. As more vertebrate, and especially mammalian, genomes are sequenced, scientists will develop a clearer picture of this important class of sequence. However, it is always possible, though highly unlikely, that there are significant quantities of functional human DNA that are not shared among these species, and which would thus not be revealed by these studies. Conversely, there are some questions about the hypothesis that conserved sequences all must function .
Replication of junk DNA each time a cell divides may waste energy. Organisms with less junk DNA may therefore have a selective advantage, and natural selection would tend to eliminate it. There are several possible explanations for why it has not been eliminated: (1) The energy required to replicate even large amounts of junk DNA may be relatively insignificant on the cellular or organismal scale, so no selective pressure results (selection coefficients less than one over the population size are effectively neutral); (2) Junk DNA may provide a reservoir of potentially useful sequences or a protective buffer against harmful genetic damage or mutations; and (3) Junk DNA may accumulate faster than natural selection can eliminate it. In animals, the energy required for DNA synthesis is trivial compared to the metabolic energy invested in the movement of muscles.
Different studies remark the importance of junk DNA for social behavior in rodents (and, possibly humans) , regulation of gene expression and promotion of genetic diversity , evolution of sequences (for example, an antifreeze-protein gene in a species of fish ), as a source of microRNAs , and hosting DNA segments called LINE-1 capable of repairing broken strands of DNA.