An Evolutionary Classification of Genomic Function

graur, dan ; zheng, yichen ; azevedo, ricardo b.r.;

The pronouncements of the ENCODE Project Consortium regarding “junkDNA” exposed the need for a nevolutionary classification of genomic elements according to their selected-effect function. In the classifications cheme 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 sub divided into “literal DNA” and “indifferent DNA.” In literal DNA, the order of nucleotidesis 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 omnipotentnor instantaneous. Each of these four functional categories canbe 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 soon ;however, determining the functionality or nonfunctionality of agenomic 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 affiliationare divided into pseudogenes, Lazarus DNA, zombie DNA, and Jekyll-to-Hyde DNA