Junk DNA

Junk DNA (non-functional DNA) is a DNA sequence that has no relevant biological function. Most organisms have some junk DNA in their genomes—mostly pseudogenes and fragments of transposons and viruses—but it is possible that some organisms have substantial amounts of junk DNA.

All protein-coding regions of genes are generally considered as functional elements in genomes. Additionally, non-protein coding regions such as genes for ribosomal RNA and transfer RNA, regulatory sequences controlling expression of those genes, elements of the genome involving origins of replication (in all species), centromeres, telomeres, and scaffold attachment regions (in eukaryotes) are generally considered as functional elements of genomes as well. (See Non-coding DNA for more information.)

It is difficult to determine whether other regions of the genome are functional or nonfunctional. There is considerable controversy over which criteria should be used to identify function. Many scientists have an evolutionary view of the genome and they prefer criteria based on whether DNA sequences are preserved by natural selection. Other scientists dispute this view or have different interpretations of the data.

The history of junk DNA
The idea that only a fraction of the human genome could be functional dates back to the late 1940s. The estimated mutation rate in humans suggested that if a large fraction of those mutations were deleterious then the human species could not survive such a mutation load (genetic load). This led to predictions in the late 1940s by one of the founders of population genetics, J.B.S. Haldane, and by Nobel laureate Hermann Muller, that only a small percentage of the human genome contains functional DNA elements (genes) that can be destroyed by mutation. (see Genetic load for more information)

In 1966 Muller reviewed these predictions and concluded that the human genome could only contain about 30,000 genes based on the number of deleterious mutations that the species could tolerate. Similar predictions were made by other leading experts in molecular evolution who concluded that the human genome could not contain more than 40,000 genes and that less than 10% of the genome was functional.

The size of genomes in various species was known to vary considerably and there did not seem to be a correlation between genome size and the complexity of the species. Even closely related species could have very different genome sizes. This observation led to what came to be known as the C-value paradox. The paradox was resolved with the discovery of repetitive DNA and the observation that most of the differences in genome size could be attributed to repetitive DNA. Some scientists thought that most of the repetitive DNA was involved in regulating gene expression but many scientists thought that the excess repetitive DNA was nonfunctional.

At about the same time (late 1960s) the newly developed technique of C0t analysis was refined to include RNA:DNA hybridization leading to the discovery that considerably less than 10% of the human genome was complementary to mRNA and this DNA was in the unique (non-repetitive) fraction. This confirmed the predictions made from genetic load arguments and was consistent with the idea that much of the repetitive DNA is nonfunctional.

The idea that large amounts of eukaryotic genomes could be nonfunctional conflicted with the prevailing view of evolution in 1968 since it seemed likely that nonfunctional DNA would be eliminated by natural selection. The development of the neutral theory and the nearly neutral theory provided a way out of this problem since it allowed for the preservation of slightly deleterious nonfunctional DNA in accordance with fundamental principles of population genetics.

The term "junk DNA" began to be used in the late 1950s but Susumu Ohno popularized the term in a 1972 paper titled "So much 'junk' DNA in our genome" where he summarized the current evidence that had accumulated by then. In a second paper that same year, he concluded that 90% of mammalian genomes consisted of nonfunctional DNA. The case for junk DNA was summarized in a lengthy paper by David Comings in 1972 where he listed four reasons for proposing junk DNA:


 * 1) some organisms have a lot more DNA than they seem to require (C-value paradox),
 * 2) current estimates of the number of genes (in 1972) are much less than the number that can be accommodated,
 * 3) the mutation load would be too large if all the DNA were functional, and
 * 4) some junk DNA clearly exists.

The discovery of introns in the 1970s seemed to confirm the views of junk DNA proponents because it meant that genes were very large and even huge genomes could not accommodate large numbers of genes. The proponents of junk DNA tended to dismiss intron sequences as mostly nonfunctional DNA (junk) but junk DNA opponents advanced a number of hypotheses attributing functions of various sort to intron sequences.

By 1980 it was apparent that most of the repetitive DNA in the human genome was related to transposons. This prompted a series of papers and letters describing transposons as selfish DNA that acted as a parasite in genomes and produced no fitness advantage for the organism.

Opponents of junk DNA interpreted these results as evidence that most of the genome is functional and they developed several hypotheses advocating that transposon sequences could benefit the organism or the species. The most important opponent of junk DNA at this time was Thomas Cavalier-Smith who argued that the extra DNA was required to increase the volume of the nucleus in order to promote more efficient transport across the nuclear membrane.

The positions of the two sides of the controversy hardened with one side believing that evolution was consistent with large amounts of junk DNA and the other side believing that natural selection should eliminate junk DNA. These differing views of evolution were highlighted in a letter from Thomas Jukes, a proponent of junk DNA, to Francis Crick on December 20, 1979:

"Dear Francis, I am sure that you realize how frightfully angry a lot of people will be if you say that much of the DNA is junk. The geneticists will be angry because they think that DNA is sacred. The Darwinian evolutionists will be outraged because they believe every change in DNA that is accepted in evolution is necessarily an adaptive change. To suggest anything else is an insult to the sacred memory of Darwin."

The other point of view was expressed by Roy John Britten and Kohne in their seminal paper on repetitive DNA.

"A concept that is repugnant to us is that about half of the DNA of higher organisms is trivial or permanently inert (on an evolutionary timescale)."

Junk DNA and non-coding DNA
There is considerable confusion in the popular press and in the scientific literature about the distinction between non-coding DNA and junk DNA.

According to an article published in 2021 in American Scientist:

"Close to 99 percent of our genome has been historically classified as noncoding, useless 'junk' DNA. Consequently, these sequences were rarely studied."

A book published in 2020 states:

"When it was first discovered, the nongenic DNA was sometimes called—somewhat derisively by people who did not know better—'junk DNA' because it had no obvious utility, and they foolishly assumed that if it was not carrying coding information it must be useless trash."

The common theme is that the original proponents of junk DNA thought that all non-coding DNA was junk and generally ignored. This claim has been attributed to a paper by David Comings in 1972 where he is reported to have said that junk DNA refers to all non-coding DNA. But Comings never said that. In that paper he discusses non-coding genes for ribosomal RNA and tRNAs and non-coding regulatory DNA and he proposes several possible functions for the bulk of non-coding DNA. In another publication from the same year Comings again discusses the term junk DNA with the clear understanding that it does not include non-coding regulatory sequences.

These statements have been criticized by numerous authors for distorting the history of junk DNA; for example: "It is simply not true that noncoding DNA has long been dismissed as worthless junk and that functional hypotheses have only recently been proposed - despite the frequency with which this cliché is repeated in media reports and in the introduction of far too many scientific studies." Some of the criticisms have been strong: "Revisionist claims that equate noncoding DNA with junk merely reveal that people who are allowed to exhibit their logorrhea in Nature and other glam journals are as ignorant as the worst young-earth creationists."

Since the 1960s, proponents of junk DNA were well aware of functional non-coding DNA and even discussed possible functions when new types of non-coding sequences were identified. For instance, the existence of functional non-coding DNA elements such as noncoding genes, regulatory sequences, origins of replication, and centromeres were well known in the late 1960s when the idea of junk DNA was being proposed. Many of the main supporters of junk DNA explicitly mentioned the importance of (non-coding) regulatory sequences and addressed the issue of whether regulatory sequences were a minor part of the functional genome or whether regulatory sequences took up most of the human genome. Early proponents of junk DNA did not base their arguments on ignorance; they based their arguments on what was known about genome sizes, gene duplication, mutational load, and population genetics. (See The history of junk DNA.)

Some have argued that the term "non-coding DNA" is unfortunate because it sounds like "nonsense sequence which does nothing at all." They suggest that this misleading phrase be replaced with "untranslated DNA."

Identifying function
The phrase "junk DNA" is debatable, and differing precise definitions (and associated approaches) provide wildly disparate estimates of its prevalence. Strong objections to the term "junk DNA" have prompted some to advocate for more neutral nomenclature, such as "nonfunctional DNA."

Proponents of junk DNA define "functional" DNA as DNA that is currently under purifying selection. For instance, Dan Gaur in his textbook "Molecular and Genome Evolution."


 * "Functional DNA refers to any segment in the genome whose selected-effect function is that for which it was selected and/or by which it is maintained. Most functional sequences are maintained by purifying selection."

This definition of "function" is called the maintenance function. Other similar definitions have been published but they all have in common the idea that junk DNA is DNA that does not have a function and this means that it is not under negative selective pressure. About 11% or less of the human genome is conserved and about 7% is under purifying selection.

Biochemical activity is another criterion that has been used to estimate functional elements. Biochemical activity includes whether a given locus is transcribed or whether it binds a transcription factor. In a series of papers published in 2012, the Encyclopedia of DNA Elements (ENCODE) project reported that detectable biochemical activity was observed in regions covering at least 80% of the human genome. These conclusions were promoted by a publicity campaign announcing the demise of junk DNA. The ENCODE conclusions were challenged in a series of publications over the next few years with some suggesting that many transcripts are spurious transcripts that do not necessarily come from functional regions of the genome. They also suggested that many transcription factor binding sites are nonfunctional sites that occur by chance in large genomes.

In 2014, ENCODE researchers responded that there are both limitations and advantages to the different approaches (genetic, evolutionary, biochemical) used to get estimates of functional elements. They agreed that biochemical activity by itself is not a reliable indicator of function and they did not repeat their earlier claim that 80% of the genome is functional. Their revised position is that the ENCODE data can be used to identify candidate elements that can be further examined to see if they are functional and that this contribution is "far more important than any interim estimate of the fraction of the human genome that is functional." The most recent attempt to define function using biochemical activity focuses on identifying which transcripts have a function and which transcription factor binding sites are true regulatory sequences. One way of distinguishing between true functional biochemical activity and spurious nonfunctional biochemical activity is to look for evidence of sequence conservation or purifying selection. Opponents of junk DNA argue that biochemical activity detects functional regions of the genome that are not identified by sequence conservation or purifying selection.

Some scientists have argued that functionality can only be assessed in reference to an appropriate null hypothesis. In this case, the null hypothesis would be that these parts of the genome are non-functional and have properties, be it on the basis of conservation or biochemical activity, that would be expected of such regions based on our general understanding of molecular evolution and biochemistry. According to these scientists, until a region in question has been shown to have additional features, beyond what is expected of the null hypothesis, it should provisionally be labelled as non-functional.