Compositional domain

File:CompositionalDomainsInGenome.jpg

A compositional domain in genetics is a region of DNA with a distinct guanine (G) and cytosine (C) G-C and C-G content (collectively GC content).{{cite journal |doi=10.1093/nar/gkq532 |title=Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm |year=2010 |last1=Elhaik |first1=Eran |last2=Graur |first2=Dan |last3=Josić |first3=Krešimir |last4=Landan |first4=Giddy |journal=Nucleic Acids Research |volume=38 |issue=15 |pages=e158 |pmid=20571085 |pmc=2926622}} The homogeneity of compositional domains is compared to that of the chromosome on which they reside. As such, compositional domains can be homogeneous or nonhomogeneous domains. Compositionally homogeneous domains that are sufficiently long (= 300 kb) are termed isochores or isochoric domains.

The compositional domain model was proposed as an alternative to the isochoric model. The isochore model was proposed by Bernardi and colleagues to explain the observed non-uniformity of genomic fragments in the genome.{{cite journal |doi=10.1126/science.4001930 |title=The mosaic genome of warm-blooded vertebrates |year=1985 |last1=Bernardi |first1=G |last2=Olofsson |first2=B |last3=Filipski |first3=J |last4=Zerial |first4=M |last5=Salinas |first5=J |last6=Cuny |first6=G |last7=Meunier-Rotival |first7=M |last8=Rodier |first8=F |journal=Science |volume=228 |issue=4702 |pages=953–8 |pmid=4001930|bibcode = 1985Sci...228..953B }} However, recent sequencing of complete genomic data refuted the isochoric model. Its main predictions were:

• GC content of the third codon position (GC3) of protein coding genes is correlated with the GC content of the isochores embedding the corresponding genes.{{cite journal |doi=10.1016/S0378-1119(01)00644-8 |title=Misunderstandings about isochores. Part 1 |year=2001 |last1=Bernardi |first1=Giorgio |journal=Gene |volume=276 |pages=3–13 |pmid=11591466 |issue=1–2}} This prediction was found to be incorrect. GC3 could not predict the GC content of nearby sequences.{{cite journal |doi=10.1093/molbev/msp100 |title=Can GC Content at Third-Codon Positions Be Used as a Proxy for Isochore Composition? |year=2009 |last1=Elhaik |first1=E. |last2=Landan |first2=G. |last3=Graur |first3=D. |journal=Molecular Biology and Evolution |volume=26 |issue=8 |pages=1829–33 |pmid=19443854|doi-access=free }}{{cite journal |doi=10.1186/1471-2164-11-308 |title=GC3 biology in corn, rice, sorghum and other grasses |year=2010 |last1=Tatarinova |first1=Tatiana V |last2=Alexandrov |first2=Nickolai N |last3=Bouck |first3=John B |last4=Feldmann |first4=Kenneth A |journal=BMC Genomics |volume=11 |pages=308 |pmid=20470436 |pmc=2895627 |doi-access=free }}
• The genome organization of warm-blooded vertebrates is a mosaic of isochores.{{cite journal |doi=10.1016/S0378-1119(00)00441-8 |title=The compositional evolution of vertebrate genomes |year=2000 |last1=Bernardi |first1=Giorgio |journal=Gene |volume=259 |pages=31–43 |pmid=11163959 |issue=1–2}} This prediction was rejected by many studies that used the complete human genome data.{{cite journal |doi=10.1038/35057062 |title=Initial sequencing and analysis of the human genome |year=2001 |last1=Lander |first1=Eric S. |last2=Linton |first2=Lauren M. |last3=Birren |first3=Bruce |last4=Nusbaum |first4=Chad |last5=Zody |first5=Michael C. |last6=Baldwin |first6=Jennifer |last7=Devon |first7=Keri |last8=Dewar |first8=Ken |last9=Doyle |first9=Michael |last10=Fitzhugh |first10=William |last11=Funke |first11=Roel |last12=Gage |first12=Diane |last13=Harris |first13=Katrina |last14=Heaford |first14=Andrew |last15=Howland |first15=John |last16=Kann |first16=Lisa |last17=Lehoczky |first17=Jessica |last18=Levine |first18=Rosie |last19=McEwan |first19=Paul |last20=McKernan |first20=Kevin |last21=Meldrim |first21=James |last22=Mesirov |first22=Jill P. |last23=Miranda |first23=Cher |last24=Morris |first24=William |last25=Naylor |first25=Jerome |last26=Raymond |first26=Christina |last27=Rosetti |first27=Mark |last28=Santos |first28=Ralph |last29=Sheridan |first29=Andrew |last30=Sougnez |first30=Carrie |journal=Nature |volume=409 |issue=6822 |pages=860–921 |pmid=11237011|display-authors=8 |bibcode = 2001Natur.409..860L |url=https://deepblue.lib.umich.edu/bitstream/2027.42/62798/1/409860a0.pdf |doi-access=free }}{{cite journal |doi=10.1007/s00239-004-2587-x |title=The Decline of Isochores in Mammals: An Assessment of the GC ContentVariation Along the Mammalian Phylogeny |year=2004 |last1=Belle |first1=Elise M. S. |last2=Duret |first2=Laurent |last3=Galtier |first3=Nicolas |last4=Eyre-Walker |first4=Adam |journal=Journal of Molecular Evolution |volume=58 |issue=6 |pages=653–60 |pmid=15461422|citeseerx=10.1.1.333.2159 |bibcode=2004JMolE..58..653B |s2cid=18281444 }}{{cite journal |doi=10.1093/molbev/msi115 |title=GC Composition of the Human Genome: In Search of Isochores |year=2005 |last1=Cohen |first1=N. |journal=Molecular Biology and Evolution |volume=22 |issue=5 |pages=1260–72 |pmid=15728737 |last2=Dagan |first2=T |last3=Stone |first3=L |last4=Graur |first4=D|doi-access=free }}
• The genome organization of cold-blooded vertebrates is characterized by low GC content levels and lower compositional heterogeneity.{{cite journal |doi=10.1016/S0378-1119(99)00485-0 |title=Isochores and the evolutionary genomics of vertebrates |year=2000 |last1=Bernardi |first1=Giorgio |journal=Gene |volume=241 |pages=3–17 |pmid=10607893 |issue=1}}{{cite journal |doi=10.1266/ggs.78.195 |title=Presence of isochore structures in reptile genomes suggested by the relationship between GC contents of intron regions and those of coding regions |year=2003 |last1=Hamada |first1=Kazuo |last2=Horiike |first2=Tokumasa |last3=Ota |first3=Hidetoshi |last4=Mizuno |first4=Keiko |last5=Shinozawa |first5=Takao |journal=Genes & Genetic Systems |volume=78 |issue=2 |pmid=12773820 |pages=195–8|doi-access=free }}{{cite journal |doi=10.1093/icb/icn062 |title=Turtle isochore structure is intermediate between amphibians and other amniotes |year=2008 |last1=Chojnowski |first1=J. L. |last2=Braun |first2=E. L. |journal=Integrative and Comparative Biology |volume=48 |issue=4 |pages=454–62 |pmid=21669806|doi-access=free }} This prediction was disproved by finding high and low GC content domains in fish genomes.{{cite journal |doi=10.1007/s00412-006-0078-0 |title=Human chromosomal bands: Nested structure, high-definition map and molecular basis |year=2006 |last1=Costantini |first1=Maria |last2=Clay |first2=Oliver |last3=Federico |first3=Concetta |last4=Saccone |first4=Salvatore |last5=Auletta |first5=Fabio |last6=Bernardi |first6=Giorgio |journal=Chromosoma |volume=116 |pages=29–40 |pmid=17072634 |issue=1|s2cid=22571376 }}

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T. |last20=Helmkampf |first20=M |last21=Hu |first21=H |last22=Johnson |first22=B. R. |last23=Kim |first23=J |last24=Marsh |first24=S. E. |last25=Moeller |first25=J. A. |last26=Muñoz-Torres |first26=M. C. |last27=Murphy |first27=M. C. |last28=Naughton |first28=M. C. |last29=Nigam |first29=S |last30=Overson |first30=R |journal=PLOS Genetics |volume=7 |issue=2 |pages=e1002007 |pmid=21347285 |pmc=3037820|display-authors=8 |doi-access=free }} The human genome was described as consisting of a mixture of compositionally nonhomogeneous domains with numerous short compositionally homogeneous domains and relatively few long ones.