Editing Junk DNA (section)

=== Functional ===
[[Coding region|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<ref name="PalazzoGregory2014" /> such as [[regulatory sequence]]s, [[Origin of replication|origins of replication]], and [[centromere]]s.<ref name="Watson1965">{{cite book | vauthors = Watson J | title = Molecular Biology of the Gene | date = 1965 | publisher = W. A. Benjamin, Inc. | place = New York, New York, USA}}</ref> These sequences are usually conserved in evolution and make up another 3-8% of the human genome.<ref name=":0">{{cite journal | vauthors = Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D | title = Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes | journal = Genome Research | volume = 15 | issue = 8 | pages = 1034–1050 | date = August 2005 | pmid = 16024819 | pmc = 1182216 | doi = 10.1101/gr.3715005 }}</ref>

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.<ref name="Nature489p57">{{cite journal | title = An integrated encyclopedia of DNA elements in the human genome | journal = Nature | volume = 489 | issue = 7414 | pages = 57–74 | date = September 2012 | pmid = 22955616 | pmc = 3439153 | doi = 10.1038/nature11247 | bibcode = 2012Natur.489...57T | collaboration = The ENCODE Project Consortium | vauthors = Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, etal }}</ref> While these findings were announced as the demise of junk DNA<ref name="Pennisi 2012">{{cite journal | vauthors = Pennisi E | title = Genomics. ENCODE project writes eulogy for junk DNA | journal = Science | volume = 337 | issue = 6099 | pages = 1159, 1161 | date = September 2012 | pmid = 22955811 | doi = 10.1126/science.337.6099.1159 }}</ref><ref name="Casane et al 2015">{{cite journal | vauthors = Casane D, Fumey J, Laurenti P | title = [ENCODE apophenia or a panglossian analysis of the human genome] | journal = Médecine/Sciences | volume = 31 | issue = 6–7 | pages = 680–686 | date = 2015 | pmid = 26152174 | doi = 10.1051/medsci/20153106023 }}</ref> 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.<ref name="observer">{{cite news |date=February 24, 2013 |title=Scientists attacked over claim that 'junk DNA' is vital to life |work=The Observer |url=https://www.theguardian.com/science/2013/feb/24/scientists-attacked-over-junk-dna-claim |vauthors=McKie R}}</ref><ref name="Eddy2012" /><ref name="Eddy 2013">{{cite journal | vauthors = Eddy SR | title = The ENCODE project: missteps overshadowing a success | journal = Current Biology | volume = 23 | issue = 7 | pages = R259–R261 | date = April 2013 | pmid = 23578867 | doi = 10.1016/j.cub.2013.03.023 | doi-access = free | bibcode = 2013CBio...23.R259E }}</ref><ref name="doolittle2013">{{cite journal | vauthors = Doolittle WF | title = Is junk DNA bunk? A critique of ENCODE | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 110 | issue = 14 | pages = 5294–5300 | date = April 2013 | pmid = 23479647 | pmc = 3619371 | doi = 10.1073/pnas.1221376110 | bibcode = 2013PNAS..110.5294D | doi-access = free | author-link = W. Ford Doolittle }}</ref><ref name="Brunet and Doolittle 2014">{{cite journal | vauthors = Brunet TD, Doolittle WF | title = Getting "function" right | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 33 | pages = E3365 | date = August 2014 | pmid = 25107292 | pmc = 4143013 | doi = 10.1073/pnas.1409762111 | doi-access = free | bibcode = 2014PNAS..111E3365P }}</ref><ref name="PalazzoGregory2014" /><ref name="Grauretal2013">{{cite journal | vauthors = Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E | title = On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE | journal = Genome Biology and Evolution | volume = 5 | issue = 3 | pages = 578–590 | year = 2013 | pmid = 23431001 | pmc = 3622293 | doi = 10.1093/gbe/evt028 }}</ref><ref name="Doolittle et al 2014">{{cite journal | vauthors = Doolittle WF, Brunet TD, Linquist S, Gregory TR | title = Distinguishing between "function" and "effect" in genome biology | journal = Genome Biology and Evolution | volume = 6 | issue = 5 | pages = 1234–1237 | date = May 2014 | pmid = 24814287 | pmc = 4041003 | doi = 10.1093/gbe/evu098 }}</ref><ref name="Morange2014" /><ref name="Niu&Jiang2013" /><ref name="kellis" />