Editing Junk DNA (section)

== 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 Joseph Muller|Hermann Muller]], that only a small percentage of the human genome contains functional DNA elements (genes) that can be destroyed by mutation.<ref name = Muller1950 >{{cite journal | vauthors = Muller HJ | title = Our load of mutations | journal = American Journal of Human Genetics | volume = 2 | issue = 2 | pages = 111–176 | date = June 1950 | pmid = 14771033 | pmc = 1716299 }}</ref><ref name= Haldane1949>{{ cite journal | last = Haldane | first = JBS | date = 1949 | title = The rate of mutation of human genes | journal = Hereditas | volume = 35 | pages = 267–273 |  doi = 10.1111/j.1601-5223.1949.tb03339.x | doi-access = free }}</ref>  (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.<ref name = Muller1966>{{cite journal | vauthors = Muller HJ | title = The gene material as the initiator and the organizing basis of life | journal = The American Naturalist | volume = 100 | issue = 915 | pages = 493-517 | date = September 1966 | doi = 10.1086/282445 | jstor = 2459205 }}</ref> 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.<ref name = Kimura1968>{{cite journal | vauthors = Kimura M | title = Evolutionary rate at the molecular level | journal = Nature | volume = 217 | issue = 5129 | pages = 624–626 | date = February 1968 | pmid = 5637732 | doi = 10.1038/217624a0 | s2cid = 4161261 | bibcode = 1968Natur.217..624K }}</ref><ref name = KingJukes1969>{{cite journal | vauthors = King JL, Jukes TH | title = Non-Darwinian evolution | journal = Science | volume = 164 | issue = 3881 | pages = 788–798 | date = May 1969 | pmid = 5767777 | doi = 10.1126/science.164.3881.788 | bibcode = 1969Sci...164..788L }}</ref><ref name = Ohno1972b/><ref name = Ohta&Kimura1971>{{cite journal | vauthors = Ohta T, Kimura M | title = Functional organization of genetic material as a product of molecular evolution | journal = Nature | volume = 233 | issue = 5315 | pages = 118–119 | date = September 1971 | pmid = 16063236 | doi = 10.1038/233118a0 | s2cid = 13344748 | bibcode = 1971Natur.233..118O }}</ref>

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]].<ref name = Thomas1971 >{{cite journal | vauthors = Thomas CA | title = The genetic organization of chromosomes | journal = Annual Review of Genetics | volume = 5 | pages = 237–256 | date = 1971 | pmid = 16097657 | doi = 10.1146/annurev.ge.05.120171.001321 }}</ref> 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.<ref name = Thomas1971/><ref name = Britten&Kohne1968 >{{cite journal | vauthors = Britten RJ, Kohne DE | title = Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms | journal = Science | volume = 161 | issue = 3841 | pages = 529–540 | date = August 1968 | pmid = 4874239 | doi = 10.1126/science.161.3841.529 | bibcode = 1968Sci...161..529B }}</ref> 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.<ref name = Britten&Davidson1969 >{{cite journal | vauthors = Britten RJ, Davidson EH | title = Gene regulation for higher cells: a theory | journal = Science | volume = 165 | issue = 3891 | pages = 349–357 | date = July 1969 | pmid = 5789433 | doi = 10.1126/science.165.3891.349 | bibcode = 1969Sci...165..349B }}</ref><ref name = Thomas1971/><ref name = Gregory2005>{{cite book | last = Gregory | first = TR | date = 2005 | chapter = Genome Size Evolution in Animals | title = The Evolution of the Genome | pages = 3–87 | publisher = Elsevier }}</ref><ref name = Lewin1972>{{ cite book | last = Lewin | first = Benjamin | date = 1974 | chapter = Chapter 4: Sequences of Eukaryotic DNA | title = Gene Expression-2: Eukaryotic Chromosomes | publisher = John Wiley & Sons }}</ref><ref name=Lewin1974c>{{cite journal|last = Lewin | first = Benjamin | date = 1974 | title = Sequence Organization of Eukaryotic DNA: Defining the Unit of Gene Expression | journal = Cell | volume =  1 | issue = 3 | pages = 107–111 | doi = 10.1016/0092-8674(74)90125-1 }}</ref>

[[File:Tomoko Harada cropped 1 Tomoko Harada 201611.png|thumb|[[Tomoko Ohta]] (Tomoko Harada) developed the nearly neutral theory that led to an understanding of how slightly deleterious junk DNA could be maintained in the genomes of species with small effective population sizes. In 2015 she was awarded the [[Crafoord Prize]] by the Royal Swedish Academy (with Richard Lewontin).]]At about the same time (late 1960s) the newly developed technique of [[Cot analysis|C<sub>0</sub>t 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.<ref name = Lewin1972b>{{ cite book | last = Lewin | first = Benjamin | date = 1974 | chapter = Chapter 5: Transcription and Processing of RNA | title = Gene Expression-2: Eukaryotic Chromosomes | publisher = John Wiley & Sons }}</ref><ref name = OBrian1973>{{cite journal | vauthors = O'Brien SJ | title = On estimating functional gene number in eukaryotes | journal = Nature | volume = 242 | issue = 115 | pages = 52–54 | date = March 1973 | pmid = 4512011 | doi = 10.1038/newbio242052a0 }}</ref><ref name = Bishop1974>{{cite journal | vauthors = Bishop JO | title = The gene numbers game | journal = Cell | volume = 2 | issue = 2 | pages = 81–86 | date = June 1974 | pmid = 4616752 | doi = 10.1016/0092-8674(74)90095-6 }}</ref>

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 of molecular evolution|neutral theory]] and the [[Nearly neutral theory of molecular evolution|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.<ref name=KingJukes1969/><ref name=Kimura1968/><ref name = Kimura&Ohta1971>{{cite journal | vauthors = Kimura M, Ohta T | title = Protein polymorphism as a phase of molecular evolution | journal = Nature | volume = 229 | issue = 5285 | pages = 467–469 | date = February 1971 | pmid = 4925204 | doi = 10.1038/229467a0 | s2cid = 4290427 | bibcode = 1971Natur.229..467K }}</ref>

The term "junk DNA" began to be used in the late 1950s<ref>{{cite thesis |type=MA |last=Sweet |first=Amalia |date=2022 |title=Requiem for a Gene: The Problem of Junk DNA for the Molecular Paradigm |publisher=University of Chicago| url = https://knowledge.uchicago.edu/record/5164}}</ref> but [[Susumu Ohno]] popularized the term in a 1972 paper titled "So much 'junk' DNA in our genome"<ref name=Ohno1972a>{{cite journal | vauthors = Ohno S | title = So much "junk" DNA in our genome | journal = Brookhaven Symposia in Biology | volume = 23 | pages = 366–370 | date = 1972 | pmid = 5065367 }}</ref> where he summarized the current evidence that had accumulated by then.<ref name = Ohno1972a/> In a second paper that same year, he concluded that 90% of mammalian genomes consisted of nonfunctional DNA.<ref name = Ohno1972b/> 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:<ref name="Comings1972a">{{cite book |title=Advances in human genetics |vauthors=Comings DE |date=1972 |publisher=Springer |pages=237–431 |chapter=The structure and function of chromatin}}</ref>

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

The discovery of [[intron]]s 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.<ref name="Morange2020a">{{cite book | last = Morange | first = Michel | date = 2020 | chapter = Chapter 17: Split Genes and Splicing | title = The Black Box of Biology: A History of the Molecular Revolution | publisher = Harvard University Press }}</ref><ref name="Gilbert1978">{{cite journal | vauthors = Gilbert W | title = Why genes in pieces? | journal = Nature | volume = 271 | issue = 5645 | pages = 501 | date = February 1978 | pmid = 622185 | doi = 10.1038/271501a0 | s2cid = 4216649 | doi-access = free | bibcode = 1978Natur.271..501G }}</ref><ref name="Gilbert1985">{{cite journal | vauthors = Gilbert W | title = Genes-in-pieces revisited | journal = Science | volume = 228 | issue = 4701 | pages = 823–824 | date = May 1985 | pmid = 4001923 | doi = 10.1126/science.4001923 | bibcode = 1985Sci...228..823G }}</ref><ref name="Crick1978">{{cite journal | vauthors = Crick F | title = Split genes and RNA splicing | journal = Science | volume = 204 | issue = 4390 | pages = 264–271 | date = April 1979 | pmid = 373120 | doi = 10.1126/science.373120 | bibcode = 1979Sci...204..264C }}</ref><ref name="Doolittle1978">{{cite journal | last = Doolittle | first = W.F. | date = 1978 |  title = Genes in pieces: were they ever together? | journal = Nature | volume =  272 | issue = 5654 | pages = 581–582 | doi = 10.1038/272581a0 | bibcode = 1978Natur.272..581D | s2cid = 4162765 | doi-access = free }}</ref>

[[File:Francis Crick crop.jpg|thumb|[[Francis Crick]] and others promoted the idea that transposons were examples of selfish DNA and were responsible for the proliferation of junk DNA.]]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.<ref name=Doolittle&Sapienza1980>{{cite journal | vauthors = Doolittle WF, Sapienza C | title = Selfish genes, the phenotype paradigm and genome evolution | journal = Nature | volume = 284 | issue = 5757 | pages = 601–603 | date = April 1980 | pmid = 6245369 | doi = 10.1038/284601a0 | s2cid = 4311366 | bibcode = 1980Natur.284..601D }}</ref><ref name = Orgel&Crick1980>{{cite journal | vauthors = Orgel LE, Crick FH | title = Selfish DNA: the ultimate parasite | journal = Nature | volume = 284 | issue = 5757 | pages = 604–607 | date = April 1980 | pmid = 7366731 | doi = 10.1038/284604a0 | s2cid = 4233826 | bibcode = 1980Natur.284..604O }}</ref><ref name=Dover1980>{{cite journal | vauthors = Dover G | title = Ignorant DNA? | journal = Nature | volume = 285 | issue = 5767 | pages = 618–620 | date = June 1980 | pmid = 7393318 | doi = 10.1038/285618a0 | s2cid = 4261755 | doi-access = free | bibcode = 1980Natur.285..618D }}</ref><ref name = Dover&Doolittle1980>{{cite journal | vauthors = Dover G, Doolittle WF | title = Modes of genome evolution | journal = Nature | volume = 288 | issue = 5792 | pages = 646–647 | date = December 1980 | pmid = 6256636 | doi = 10.1038/288646a0 | s2cid = 8938434 | doi-access = free | bibcode = 1980Natur.288..646D }}</ref><ref name = Jain1980>{{cite journal | vauthors = Jain HK | title = Incidental DNA | journal = Nature | volume = 288 | issue = 5792 | pages = 647–648 | date = December 1980 | pmid = 7453799 | doi = 10.1038/288647a0 | s2cid = 31899622 | doi-access = free | bibcode = 1980Natur.288..647J }}</ref>

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.<ref name = Cavalier-Smith1980>{{cite journal | vauthors = Cavalier-Smith T | title = How selfish is DNA? | journal = Nature | volume = 285 | issue = 5767 | pages = 617–618 | date = June 1980 | pmid = 7393317 | doi = 10.1038/285617a0 | s2cid = 27111068 | doi-access = free | bibcode = 1980Natur.285..617C }}</ref> 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.<ref name = Cavalier-Smith1978>{{cite journal | vauthors = Cavalier-Smith T | title = Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox | journal = Journal of Cell Science | volume = 34 | pages = 247–278 | date = December 1978 | pmid = 372199 | doi = 10.1242/jcs.34.1.247 }}</ref>

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 H. Jukes|Thomas Jukes]], a proponent of junk DNA, to Francis Crick on December 20, 1979:<ref>{{ cite web | url = https://profiles.nlm.nih.gov/spotlight/sc/catalog/nlm:nlmuid-101584582X199-doc | title = letter to Francis Crick | first = Jukes | last = Thomas | date = December 29, 1979 | website = National Institutes of Health (USA) }}</ref>

<blockquote>"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."</blockquote>

The other point of view was expressed by [[Roy John Britten]] and Kohne in their seminal paper on repetitive DNA.<ref name = Britten&Kohne1968/>

<blockquote>"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)."</blockquote>