Intergenic region: Difference between revisions
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{{short description|In genetics, a stretch of DNA sequences located between genes}} |
{{short description|In genetics, a stretch of DNA sequences located between genes}} |
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[[File:Intergenic DNA.gif|thumb|Illustration of intergenic DNA]] |
[[File:Intergenic DNA.gif|thumb|Illustration of intergenic DNA]] |
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An '''intergenic region (IGR)''' is a stretch of [[DNA]] sequences located between [[gene]]s.<ref name='tropp'>{{Cite book| publisher = Jones & Bartlett Learning| isbn = 9780763709167| vauthors = Tropp BE | title = Molecular Biology: Genes to Proteins| year = 2008}}</ref> Intergenic regions |
An '''intergenic region (IGR)''' is a stretch of [[DNA]] sequences located between [[gene]]s.<ref name='tropp'>{{Cite book| publisher = Jones & Bartlett Learning| isbn = 9780763709167| vauthors = Tropp BE | title = Molecular Biology: Genes to Proteins| year = 2008}}</ref> Intergenic regions may contain functional elements and [[Non-coding DNA#Junk DNA | junk DNA]]. |
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== Properties == |
== Properties == |
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== Functions == |
== Functions == |
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Intergenic regions contain a number of functional DNA sequences such as [[Non-coding DNA#Promoters and regulatory elements | promoters and regulatory elements]] and [[Non-coding DNA#Centromeres | centromeres]]. They may also contain [[Non-coding DNA#Origins of replication | origins of replication]], [[Non-coding DNA#Scaffold attachment regions | scaffold attachment regions]], [[Non-coding DNA#Repeat sequences, transposons and viral elements | transposons and viruses]]. Non-functional DNA elements such as [[Non-coding DNA#Pseudogenes | pseudogenes]], [[Non-coding DNA#Repeat sequences, transposons and viral elements | repetitive DNA]], and [[Non-coding DNA#Junk DNA | junk DNA]] can also be found in intergenic regions although they may also be located within genes in introns. |
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Historically intergenic regions have sometimes been called junk DNA suggesting that they have no function. However, it has been known for a long time that these regions do contain functionally important elements such as promoters and enhancers. In particular, intergenic regions often contain enhancer DNA sequences, which can activate expression of discrete sets of genes over distances of several thousand base pairs. Changes in the proteins bound on enhancers reprogram gene expression and affect the cell phenotype. <ref>{{cite journal | vauthors = Schmidt SF, Larsen BD, Loft A, Nielsen R, Madsen JG, Mandrup S | title = Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers | journal = Genome Research | volume = 25 | issue = 9 | pages = 1281–94 | date = September 2015 | pmid = 26113076 | pmc = 4561488 | doi = 10.1101/gr.188300.114 }}</ref> <ref>{{cite journal | vauthors = Vlahopoulos SA | title = Aberrant control of NF-κB in cancer permits transcriptional and phenotypic plasticity, to curtail dependence on host tissue: molecular mode | journal = Cancer Biology & Medicine | volume = 14 | issue = 3 | pages = 254–270 | date = August 2017 | pmid = 28884042 | pmc = 5570602 | doi = 10.20892/j.issn.2095-3941.2017.0029 }}</ref> Also intergenic regions may contain as yet unidentified genes such as [[noncoding RNA]]s. Though little is known about them, they are thought to have regulatory functions. In recent years the [[ENCODE]] project has been studying intergenic regions in humans in more detail.<ref name="pmid17571346">{{cite journal | vauthors = Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ | display-authors = 6 | title = Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project | journal = Nature | volume = 447 | issue = 7146 | pages = 799–816 | date = June 2007 | pmid = 17571346 | pmc = 2212820 | doi = 10.1038/nature05874 | bibcode = 2007Natur.447..799B | authorlink2 = John Stamatoyannopoulos }}</ref><ref name="pmid22955616">{{cite journal | vauthors = Dunham I | 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 }}</ref> Statistical methods have been specifically developed to detect trait- or disease-associated regions located in intergenic region using [[whole genome sequencing]] data, including the sliding window procedure<ref>{{cite journal | vauthors = Morrison AC, Huang Z, Yu B, Metcalf G, Liu X, Ballantyne C, Coresh J, Yu F, Muzny D, Feofanova E, Rustagi N, Gibbs R, Boerwinkle E | display-authors = 6 | title = Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits | journal = American Journal of Human Genetics | volume = 100 | issue = 2 | pages = 205–215 | date = February 2017 | pmid = 28089252 | doi = 10.1016/j.ajhg.2016.12.009 | pmc = 5294677 }}</ref> and dynamic window procedure.<ref>{{cite journal | vauthors = Li Z, Li X, Liu Y, Shen J, Chen H, Zhou H, Morrison AC, Boerwinkle E, Lin X | display-authors = 6 | title = Dynamic Scan Procedure for Detecting Rare-Variant Association Regions in Whole-Genome Sequencing Studies | journal = American Journal of Human Genetics | volume = 104 | issue = 5 | pages = 802–814 | date = May 2019 | pmid = 30982610 | pmc = 6507043 | doi = 10.1016/j.ajhg.2019.03.002 }}</ref><ref>{{Cite journal|last1=Li|first1=Zilin|last2=Liu|first2=Yaowu|last3=Lin|first3=Xihong|date=2020-09-14|title=Simultaneous Detection of Signal Regions Using Quadratic Scan Statistics With Applications to Whole Genome Association Studies|url=https://www.tandfonline.com/doi/full/10.1080/01621459.2020.1822849|journal=Journal of the American Statistical Association|volume=117 |issue=538 |language=en|pages=823–834|doi=10.1080/01621459.2020.1822849|issn=0162-1459|arxiv=1710.05021|s2cid=198893271}}</ref> |
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Intergenic regions may contain as yet unidentified functional elements such as non-coding RNA genes or regulatory sequences. |
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== Intergenic regions in organisms == |
== Intergenic regions in organisms == |
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Revision as of 15:49, 19 August 2022
An intergenic region (IGR) is a stretch of DNA sequences located between genes.[1] Intergenic regions may contain functional elements and junk DNA.
Properties
Intergenic regions are different from intragenic regions (or introns), which are short, non-coding regions that are found within genes, especially within the genes of eukaryotic organisms.
According to the ENCODE project's study of the human genome, due to "both the expansion of genic regions by the discovery of new isoforms and the identification of novel intergenic transcripts, there has been a marked increase in the number of intergenic regions (from 32,481 to 60,250) due to their fragmentation and a decrease in their lengths (from 14,170 bp to 3,949 bp median length)"[2]
Scientists have now artificially synthesized proteins from intergenic regions.[3]
Functions
Intergenic regions contain a number of functional DNA sequences such as promoters and regulatory elements and centromeres. They may also contain origins of replication, scaffold attachment regions, transposons and viruses. Non-functional DNA elements such as pseudogenes, repetitive DNA, and junk DNA can also be found in intergenic regions although they may also be located within genes in introns.
Intergenic regions may contain as yet unidentified functional elements such as non-coding RNA genes or regulatory sequences.
Intergenic regions in organisms
In humans, intergenic regions comprise about 50% of the genome, whereas this number is much less in bacteria (15%) and yeast (30%).[4]
In Plasmodium falciparum, many intergenic regions have an AT content of 90%.[5]
See also
- Exon
- Promoter (biology)
- ENCODE
- Heterochromatin
- Noncoding DNA
- Repetitive DNA
- Regulator gene
- Whole genome sequencing
References
- ^ Tropp BE (2008). Molecular Biology: Genes to Proteins. Jones & Bartlett Learning. ISBN 9780763709167.
- ^ Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, et al. (September 2012). "Landscape of transcription in human cells". Nature. 489 (7414): 101–8. Bibcode:2012Natur.489..101D. doi:10.1038/nature11233. PMC 3684276. PMID 22955620.
- ^ Dhar PK, Thwin CS, Tun K, Tsumoto Y, Maurer-Stroh S, Eisenhaber F, Surana U (February 2009). "Synthesizing non-natural parts from natural genomic template". Journal of Biological Engineering. 3: 2. doi:10.1186/1754-1611-3-2. PMC 2642765. PMID 19187561.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Francis WR, Wörheide G (June 2017). "Similar Ratios of Introns to Intergenic Sequence across Animal Genomes". Genome Biology and Evolution. 9 (6): 1582–1598. doi:10.1093/gbe/evx103. PMC 5534336. PMID 28633296.
- ^ Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, et al. (October 2002). "Genome sequence of the human malaria parasite Plasmodium falciparum". Nature. 419 (6906): 498–511. Bibcode:2002Natur.419..498G. doi:10.1038/nature01097. PMC 3836256. PMID 12368864.
External links
- ENCODE threads Explorer Characterization of intergenic regions and gene definition. Nature (journal)