J Mol Evol (1992) 35:286-291 Journal of Molecular Evolution © Springer-Verlag New YorkInc. 1992 Prototypic Sequences for Human Repetitive DNA Jerzy Jurka, Jolanta Walichiewicz, and Aleksandar Milosavljevic Linus Pauling Institute of Science and Medicine, 440 Page Mill Road, Palo Alto, CA 94306, USA Summary. We report a collection of 53 prototypic sequences representing known families of repetitive elements from the human genome. The prototypic sequences are either consensus sequences or se- lected examples of repetitive sequences. The col- lection includes: prototypes for high and medium reiteration frequency interspersed repeats, long ter- minal repeats of endogenous retroviruses, alphoid repeats, telomere-associated repeats, and some miscellaneous repeats. The collection is annotated and available electronically. Key words: Repetitive DNA w Database -- Hu- man Genome w Primates Introduction Proliferation of repetitive elements has long been viewed as a powerful evolutionary force reshaping eukaryotic genomes. At the level of an individual organism this "reshaping" means that repetitive el- ements can lead to significant genetic instability and to genetic diseases more often than to positive ev- olutionary changes. Thus, in addition to the evolu- tionary significance, studies on repetitive elements in the human genome are increasingly important from the medical point of view. Furthermore, de- tailed knowledge of repetitive elements is essential for the ongoing genome-mapping and sequencing projects. As the sequencing continues with ever-increas- ing speed, so does the number of the known repet- Offprint requests to: J. Jurka itive sequences in the databanks. Some arguments have been proposed that this DNA should be viewed as "junk" or even "trash" DNA and that the sequencing of the repetitive portions of eukary- otic genomes should be abandoned. Fortunately, this is becoming a minority view as we are increas- ingly aware that for better or worse, repetitive ele- ments are integral components of genes, that they affect them in a variety of ways and, in addition, that they can provide us with important evolution- ary information. Repetitive elements can cause illegitimate re- combinations (Lerman et al. 1987; Groffen et al. 1989; Chen et al. 1989; Jurka 1990; Hu et al. 1991), introduce regulatory signals for transcription (Wu et al. 1990), or new splice sites (Mitchell et al. 1991). They can even be incorporated in open reading frames of functional genes (Caras et al. 1987; Brownell et al. 1989; Post et al. 1990). Repetitive elements can serve as powerful evolutionary mark- ers (Del Pozzo and Guardiola 1990; Raisonnier 1991; Okada 1991; Chuat et al. 1992). Finally, they are important for physical and genetic mapping (Nelson et al. 1989; Zucchi and Schlesinger 1992). Knowledge of repetitive elements is also indispens- able for accurate sequence assembly. Other chap- ters on repetitive DNA are yet to be written. We know that many repetitive elements are retroposed from a limited number of genes which are evolu- tionarily preserved for tens of millions of years (Britten et al. 1988; Jurka and Milosavljevic 1991). The biological function of these genes remains to be determined although we tend to believe that they interfere with viral infections at the intracellular level (Jurka 1989; Jurka and Milosavljevic 1991).