Editing Non-coding DNA (section)

== Fraction of non-coding genomic DNA ==
In [[bacteria]], the [[Coding region|coding regions]] typically take up 88% of the genome.<ref name=":0" /> The remaining 12% does not encode proteins, but much of it still has biological function through [[Gene|genes]] where the RNA transcript is functional (non-coding genes) and regulatory sequences, which means that almost all of the bacterial genome has a function.<ref name=":0">{{cite journal | vauthors = Kirchberger PC, Schmidt ML, and Ochman H | date = 2020 | title = The ingenuity of bacterial genomes | journal = Annual Review of Microbiology | volume = 74 | pages = 815–834 |  doi = 10.1146/annurev-micro-020518-115822| pmid = 32692614 | s2cid = 220699395 }}</ref> The amount of coding DNA in [[Eukaryote|eukaryotes]] is usually a much smaller fraction of the genome because eukaryotic genomes contain large amounts of repetitive DNA not found in prokaryotes. The [[human genome]] contains somewhere between 1–2% coding DNA.<ref name = Piovesan/><ref>{{ cite journal | vauthors = Omenn GS | date = 2021 | title = Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years | journal = Molecular & Cellular Proteomics | volume = 20 | pages = 100062 | doi = 10.1016/j.mcpro.2021.100062| pmid = 33640492 | pmc = 8058560 }}</ref> The exact number is not known because there are disputes over the number of functional coding [[Exon|exons]] and over the total size of the human genome. This means that 98–99% of the human genome consists of non-coding DNA and this includes many functional elements such as non-coding genes and regulatory sequences.

[[Genome size]] in eukaryotes can vary over a wide range, even between closely related species. This puzzling observation was originally known as the [[C-value |C-value Paradox]] where "C" refers to the haploid genome size.<ref>{{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 that most of the differences were due to the expansion and contraction of repetitive DNA and not the number of genes. Some researchers speculated that this repetitive DNA was mostly [[junk DNA]]. The reasons for the changes in genome size are still being worked out and this problem is called the C-value Enigma.<ref>{{ cite journal | vauthors = Elliott TA, Gregory TR | date = 2015 | title = What's in a genome? The C-value enigma and the evolution of eukaryotic genome content | journal =  Phil. Trans. R. Soc. B | volume = 370 | issue = 1678 | pages = 20140331 | doi = 10.1098/rstb.2014.0331| pmid = 26323762 | pmc = 4571570 | s2cid = 12095046 }}</ref>

This led to the observation that the number of genes does not seem to  correlate with perceived notions of complexity because the number of genes seems to be relatively constant, an issue termed the [[G-value paradox|G-value Paradox]].<ref>{{ cite journal | vauthors = Hahn MW, Wray GA | date = 2002 | title = The g-value paradox | journal = Evolution and Development | volume = 4 | issue = 2 | pages = 73–75 | doi  = 10.1046/j.1525-142X.2002.01069.x| pmid = 12004964 | s2cid = 2810069 }}</ref> For example, the genome of the unicellular ''[[Polychaos dubium]]'' (formerly known as ''Amoeba dubia'') has been reported to contain more than 200 times the amount of DNA in humans (i.e. more than 600 billion [[genome size|pairs of bases]] vs a bit more than 3 billion in humans).<ref name=Gregory>{{cite journal | vauthors = Gregory TR, Hebert PD | title = The modulation of DNA content: proximate causes and ultimate consequences | journal = Genome Research | volume = 9 | issue = 4 | pages = 317–324 | date = April 1999 | pmid = 10207154 | doi = 10.1101/gr.9.4.317 | s2cid = 16791399 | doi-access = free }}</ref> The [[pufferfish]] ''[[Takifugu]] rubripes'' genome is only about one eighth the size of the human genome, yet seems to have a comparable number of genes. Genes take up about 30% of the pufferfish genome and the coding DNA is about 10%. (Non-coding DNA = 90%.) The reduced size of the pufferfish genome is due to a reduction in the length of introns and less repetitive DNA.<ref>{{ cite journal | vauthors = Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A | date = 2002 |  title = Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes | journal = Science | volume = 297 | issue = 5585 | pages = 1301–1310 | doi = 10.1126/science.1072104| pmid = 12142439 | bibcode = 2002Sci...297.1301A | s2cid = 10310355 }}</ref><ref name="Ohno">{{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 | oclc = 101819442 }}</ref>

''[[Utricularia gibba]]'', a [[bladderwort]] plant, has a very small [[nuclear genome]] (100.7 Mb) compared to most plants.<ref name = Ibarra-Laclette>{{ cite journal | vauthors = Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Juárez MJ, Simpson J, etal | date = 2013 | title = Architecture and evolution of a minute plant genome | journal = Nature | volume = 498 | issue = 7452 | pages = 94–98 |  doi = 10.1038/nature12132| pmid = 23665961 | pmc = 4972453 | bibcode = 2013Natur.498...94I | s2cid = 18219754 }}</ref><ref name = Lan>{{ cite journal | vauthors = Lan T, Renner T, Ibarra-Laclette E, Farr KM, Chang TH, Cervantes-Pérez SA, Zheng C, Sankoff D, Tang H, and Purbojati RW | date = 2017 | title = Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome | journal = Proceedings of the National Academy of Sciences | volume = 114 | issue = 22 | pages = E4435–E4441 | doi = 10.1073/pnas.1702072114| pmid = 28507139 | pmc = 5465930 | bibcode = 2017PNAS..114E4435L | doi-access = free }}</ref> It likely evolved from an ancestral genome that was 1,500 Mb in size.<ref name = Lan/> The bladderwort genome has roughly the same number of genes as other plants but the total amount of coding DNA comes to about 30% of the genome.<ref name = Ibarra-Laclette/><ref name="Lan"/> 

The remainder of the genome (70% non-coding DNA) consists of [[Promoter (genetics)|promoters]] and regulatory sequences that are shorter than those in other plant species.<ref name = Ibarra-Laclette/> The genes contain introns but there are fewer of them and they are smaller than the introns in other plant genomes.<ref name = Ibarra-Laclette/> There are noncoding genes, including many copies of ribosomal RNA genes.<ref name = Lan/> The genome also contains telomere sequences and centromeres as expected.<ref name = Lan/> Much of the repetitive DNA seen in other eukaryotes has been deleted from the bladderwort genome since that lineage split from those of other plants. About 59% of the bladderwort genome consists of transposon-related sequences but since the genome is so much smaller than other genomes, this represents a considerable reduction in the amount of this DNA.<ref name = Lan/> The authors of the original 2013 article note that claims of additional functional elements in the non-coding DNA of animals do not seem to apply to plant genomes.<ref name = Ibarra-Laclette/>

According to a New York Times article, during the evolution of this species, "... genetic junk that didn't serve a purpose was expunged, and the necessary stuff was kept."<ref>{{cite news | vauthors = Klein J | title = Genetic Tidying Up Made Humped Bladderworts Into Carnivorous Plants | url = https://www.nytimes.com/2017/05/19/science/humped-bladderwort-carnivorous-plant-genome.html | work = New York Times | date = 19 May 2017 | access-date = May 30, 2022}}</ref>  According to Victor Albert of the University of Buffalo, the plant is able to expunge its so-called junk DNA and "have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the junk. Junk is not needed."<ref>{{ cite press release | vauthors = Hsu C, and Stolte D | date = May 13, 2013 | title = Carnivorous Plant Throws Out 'Junk' DNA | url = https://news.arizona.edu/story/carnivorous-plant-throws-out-junk-dna | location = Tucson, AZ, USA | publisher = University of Arizona | access-date = May 29, 2022}}</ref>