Junk DNA

History

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.

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.

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.

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:

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

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:

A book published in 2020 states:

The common theme is that the original proponents of junk DNA thought that all non-coding DNA was junk. This claim has been attributed to a paper by David Comings in 1972

The idea that all non-coding DNA was thought to be junk has been criticized by numerous authors for distorting the history of junk DNA; for example: Some of the criticisms have been strong:

Functional vs non-functional

The main challenge of identifying junk DNA is to distinguish between "functional" and "non-functional" sequences. This is non-trivial, but there is some good evidence for both categories.

Functional

Protein-coding sequences are the most obvious functional sequences in genomes. However, they make up only 1-2% of most vertebrate genomes. However, there are also functional but non-coding DNA sequences such as regulatory sequences, origins of replication, and centromeres. These sequences are usually conserved in evolution and make up another 3-8% of the human genome.

The Encyclopedia of DNA Elements (ENCODE) project reported that detectable biochemical activity was observed in regions covering at least 80% of the human genome, with biochemical activity defined primarily as being transcribed. While these findings were announced as the demise of junk DNA it is important to point out that transcription does not mean a sequence is "functional", analogous to some meaningless text that can be transcribed or copied without having any meaning.

In a few cases it has been shown that repetitive DNA, such as microsatellites, can have a function. For instance, the HRAS1 minisatellite is a region located approximately 1000 bp downstream from the gene's coding sequences and is composed of 30 to 100 units of a 28-bp consensus sequence. Thirty alleles of 1000 to 3000 bp have been described. Some mutant alleles were found in cancer patients and it was concluded that the region likely binds transcription factors that activate HRAS1 and, as a consequence, causes cancer.

Non-functional

Non-functional DNA is rare in bacterial genomes which typically have an extremely high gene density, with only a few percent being not protein-coding.

However, in most animal or plant genomes, a large fraction of DNA is non-functional, given that there is no obvious selective pressure on these sequences. More importantly, there is strong evidence that these sequences are not functional in other ways (using the human genome as example):

(1) Repetitive elements, especially mobile elements make up a large fraction of the human genome, such as LTR retrotransposons (8.3% of total genome), SINEs (13.1% of total genome) including Alu elements, LINEs (20.4% of total genome), SVAs (SINE-VNTR-Alu) and Class II DNA transposons (2.9% of total genome). Many of these sequences are the descendents of ancient virus infections and are thus "non-functional" in terms of human genome function.

(2) Many sequences can be deleted as shown by comparing genomes. For instance, an analysis of 14,623 individuals identified 42,765 structural variants in the human genome of which 23.4% affected multiple genes (by deleting them or part of them). This study also found 47 deletions of 1 MB, showing that large chunks of the human genome can get deleted without obvious consequences.

(3) Only a small fraction of the human genome is conserved, indicating that there is no strong (functional) selection pressure on these sequences, so they can rather freely mutate. About 11% or less of the human genome is conserved and about 7% is under 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. According to some 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.

References

References

1. (November 2012). "The C-value paradox, junk DNA and ENCODE". Current Biology.
2. (May 2014). "The case for junk DNA". PLOS Genetics.
3. (October 2012). "Factors behind junk DNA in bacteria". Genes.
4. (1972). "An argument for the genetic simplicity of man and other mammals". Journal of Human Evolution.
5. (2014). "Genome as a multipurpose structure built by evolution". Perspectives in Biology and Medicine.
6. (2022). "Non-Darwinian Molecular Biology". Frontiers in Genetics.
7. (2014). "Junk or functional DNA? ENCODE and the function controversy". Biology & Philosophy.
8. Mattick, John S. (2023). "RNA out of the mist". Trends in Genetics.
9. (April 2014). "Defining functional DNA elements in the human genome". Proceedings of the National Academy of Sciences of the United States of America.
10. (June 1950). "Our load of mutations". American Journal of Human Genetics.
11. Haldane, JBS. (1949). "The rate of mutation of human genes". Hereditas.
12. (September 1966). "The gene material as the initiator and the organizing basis of life". The American Naturalist.
13. (February 1968). "Evolutionary rate at the molecular level". Nature.
14. (May 1969). "Non-Darwinian evolution". Science.
15. (September 1971). "Functional organization of genetic material as a product of molecular evolution". Nature.
16. (1971). "The genetic organization of chromosomes". Annual Review of Genetics.
17. (August 1968). "Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms". Science.
18. (July 1969). "Gene regulation for higher cells: a theory". Science.
19. Lewin, Benjamin. (1974). "Gene Expression-2: Eukaryotic Chromosomes". John Wiley & Sons.
20. Lewin, Benjamin. (1974). "Sequence Organization of Eukaryotic DNA: Defining the Unit of Gene Expression". Cell.
21. Lewin, Benjamin. (1974). "Gene Expression-2: Eukaryotic Chromosomes". John Wiley & Sons.
22. (March 1973). "On estimating functional gene number in eukaryotes". Nature.
23. (June 1974). "The gene numbers game". Cell.
24. (February 1971). "Protein polymorphism as a phase of molecular evolution". Nature.
25. Sweet, Amalia. (2022). "Requiem for a Gene: The Problem of Junk DNA for the Molecular Paradigm". University of Chicago.
26. (1972). "So much "junk" DNA in our genome". Brookhaven Symposia in Biology.
27. (1972). "Advances in human genetics". Springer.
28. Morange, Michel. (2020). "The Black Box of Biology: A History of the Molecular Revolution". Harvard University Press.
29. (February 1978). "Why genes in pieces?". Nature.
30. (May 1985). "Genes-in-pieces revisited". Science.
31. (April 1979). "Split genes and RNA splicing". Science.
32. Doolittle. W.F.. (1978). "Genes in pieces: were they ever together?". Nature
33. (April 1980). "Selfish genes, the phenotype paradigm and genome evolution". Nature.
34. (April 1980). "Selfish DNA: the ultimate parasite". Nature.
35. (June 1980). "Ignorant DNA?". Nature.
36. (December 1980). "Modes of genome evolution". Nature.
37. (December 1980). "Incidental DNA". Nature.
38. (June 1980). "How selfish is DNA?". Nature.
39. (December 1978). "Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox". Journal of Cell Science.
40. Thomas, Jukes. (December 29, 1979). "letter to Francis Crick".
41. (2021). "Turning Junk into Us: How Genes Are Born". American Scientist.
42. (2020). "DNA Demystified: Unraveling the Double Helix". Oxford University Press.
43. Comings, DE. (1972). "Review of ''Evolution of Genetics Systems''". American Journal of Human Genetics.
44. (2013). "Can ENCODE tell us how much junk DNA we carry in our genome?". Biochemical and Biophysical Research Communications.
45. (2015). "An evolutionary classification of genomic function". Genome Biology and Evolution.
46. (2014). "Conceptual and empirical challenges of ascribing functions to transposable elements". The American Naturalist.
47. Graur, Dan. (2017). "Evolution of the Human Genome I". Springer.
48. (1965). "Molecular Biology of the Gene". W. A. Benjamin, Inc..
49. (August 2005). "Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes". Genome Research.
50. (September 2012). "An integrated encyclopedia of DNA elements in the human genome". Nature.
51. (September 2012). "Genomics. ENCODE project writes eulogy for junk DNA". Science.
52. (2015). "[ENCODE apophenia or a panglossian analysis of the human genome]". Médecine/Sciences.
53. (February 24, 2013). "Scientists attacked over claim that 'junk DNA' is vital to life". The Observer.
54. (April 2013). "The ENCODE project: missteps overshadowing a success". Current Biology.
55. (April 2013). "Is junk DNA bunk? A critique of ENCODE". Proceedings of the National Academy of Sciences of the United States of America.
56. (August 2014). "Getting "function" right". Proceedings of the National Academy of Sciences of the United States of America.
57. (2013). "On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE". Genome Biology and Evolution.
58. (May 2014). "Distinguishing between "function" and "effect" in genome biology". Genome Biology and Evolution.
59. (September 2020). "Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life". BMC Bioinformatics.
60. (November 2011). "Repetitive DNA and next-generation sequencing: computational challenges and solutions". Nature Reviews. Genetics.
61. (July 2020). "Mapping and characterization of structural variation in 17,795 human genomes". Nature.
62. (2016). "Molecular and Genome Evolution". Sinauer Associates, Inc..
63. (July 2014). "8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage". PLOS Genetics.
64. (April 2023). "Evolutionary constraint and innovation across hundreds of placental mammals". Science.
65. (July 2022). "The sequences of 150,119 genomes in the UK Biobank". Nature.
66. (July 2013). "A meta-analysis of the genomic and transcriptomic composition of complex life". Cell Cycle.
67. (September 2023). "A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs". BioEssays.
68. (2015). "Non-coding RNA: what is functional and what is junk?". Frontiers in Genetics.