title: An evolutionary classification of genomic function.
abstract: The pronouncements of the ENCODE Project Consortium regarding "junk DNA" exposed the need for an evolutionary classification of genomic elements according to their selected-effect function. In the classification scheme presented here, we divide the genome into "functional DNA," that is, DNA sequences that have a selected-effect function, and "rubbish DNA," that is, sequences that do not. Functional DNA is further subdivided into "literal DNA" and "indifferent DNA." In literal DNA, the order of nucleotides is under selection; in indifferent DNA, only the presence or absence of the sequence is under selection. Rubbish DNA is further subdivided into "junk DNA" and "garbage DNA." Junk DNA neither contributes to nor detracts from the fitness of the organism and, hence, evolves under selective neutrality. Garbage DNA, on the other hand, decreases the fitness of its carriers. Garbage DNA exists in the genome only because natural selection is neither omnipotent nor instantaneous. Each of these four functional categories can be 1) transcribed and translated, 2) transcribed but not translated, or 3) not transcribed. The affiliation of a DNA segment to a particular functional category may change during evolution: Functional DNA may become junk DNA, junk DNA may become garbage DNA, rubbish DNA may become functional DNA, and so on; however, determining the functionality or nonfunctionality of a genomic sequence must be based on its present status rather than on its potential to change (or not to change) in the future. Changes in functional affiliation are divided into pseudogenes, Lazarus DNA, zombie DNA, and Jekyll-to-Hyde DNA.
authors: Department of Biology and Biochemistry, University of Houston dgraur@uh.edu.
authors: Dan
authors: D
authors: Graur
authors: Department of Biology and Biochemistry, University of Houston.
authors: Yichen
authors: Y
authors: Zheng
authors: Department of Biology and Biochemistry, University of Houston.
authors: Ricardo B R
authors: RB
authors: Azevedo
mesh_terms: D004247:DNA / Q000145:classification*; D021901:DNA, Intergenic / Q000145:classification; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics; D009626:Terminology as Topic
chemical_list: D021901:DNA, Intergenic; D004247:DNA
keywords: Functional DNA; Jekyll-to-Hyde DNA; Lazarus DNA; garbage DNA; indifferent DNA; junk DNA; literal DNA; pseudogene; rubbish DNA; zombie DNA
references: Ann Neurol. 2013 May;73(5):A8-9
references: 23749745
references: Science. 2003 Jan 10;299(5604):251-4
references: 12522251
references: Curr Biol. 2012 Nov 6;22(21):R898-9
references: 23137679
references: PLoS Genet. 2014 May 08;10(5):e1004351
references: 24809441
references: Nature. 1973 Nov 9;246(5428):96-8
references: 4585855
references: Nature. 2012 Sep 6;489(7414):57-74
references: 22955616
references: RNA Biol. 2012 Jan;9(1):27-32
references: 22258143
references: Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3365
references: 25107292
references: Science. 2003 May 23;300(5623):1246-7
references: 12764185
references: BMC Biol. 2013 May 28;11:58
references: 23714162
references: J Cell Sci. 1978 Dec;34:247-78
references: 372199
references: Genome Biol Evol. 2013;5(3):578-90
references: 23431001
references: Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10706-10
references: 1279691
references: Brookhaven Symp Biol. 1972;23:366-70
references: 5065367
references: Hepatology. 2013 Jun;57(6):2532-5
references: 23609523
references: J Ultrastruct Res. 1963 Oct;23:SUPPL6:1-42
references: 14073743
references: Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5294-300
references: 23479647
references: Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8
references: 24753594
references: Curr Biol. 1998 Sep 24;8(19):R669
references: 9776723
references: Nature. 2004 Oct 21;431(7011):988-93
references: 15496924
references: Gastroenterology. 2011 May;140(6):1704-12
references: 21530736
references: Annu Rev Genet. 2013;47:97-120
references: 24274750
references: Annu Rev Genet. 2005;39:197-218
references: 16285858
references: Biochem Biophys Res Commun. 2013 Jan 25;430(4):1340-3
references: 23268340
references: Genome Res. 2014 Dec;24(12):1963-76
references: 25319995