Genomic scrap yard: how genomes utilize all that junk

Interspersed repetitive sequences are major components of eukaryotic genome s. Repetitive elements comprise over 50% of the mammalian genome. Because t he specific function of these elements remains to be defined and because of their unusual 'behavior' in the genome, they are often quoted as a selfish or junk DNA. Our view of the entire phenomenon of repetitive elements has to now be revised in light of data on their biology and evolution, especial ly in the light of what we know about the retroposons. I would like to argu e that even if we cannot define the specific functions of these elements, w e still can show that they are not useless pieces of the genomes. The repet itive elements interact with the whole genome and influence its evolution. Repetitive elements interact with the surrounding sequences and nearby gene s. They may serve as recombination hot spots or acquire specific cellular f unctions such as RNA transcription control or even become part of protein c oding regions. Finally, they provide very efficient mechanism for genomic s huffling. As such, repetitive elements should be called genomic scrap yard rather than junk DNA. Tables listings examples of recruited (exapted) trans posable elements are available at http://www.ncbi.nlm.nih.gov/Makalowski/Sc rapYard/. (C) 2000 Elsevier Science B.V. All rights reserved.