On GATAGATA and other “junk” in the barren stretch of genomic desert

Abstract

(GATA)_n and additional simple repeated DNA sequences have long been known but functional analyses along traditional research strategies have not yielded definitive results. Therefore these elements are commonly regarded as genomic “junk” although they represent assets for innovative methodological approaches and especially for speculations. While extensively using microsatellites for genome mapping and genetic relationship analyses, it was also realized that certain simple repeats can cause human trinucleotide block expansion diseases. Hence these simple repeat elements comprise an exceptional range of biological meaning, i.e. from genetically absolutely neutral markers for genome analysis, behavioral and population genetic studies to dominant and invariably disease causing mutations with complete penetrance. The quest into why there is so much repetitive junk in recent genomes can be answered only in part and sequentially, but sometimes – even after substantial efforts – not for the given element.

Microsatellites

“…. Perfect di-or tetranucleotide periodicity warrants evolutionary success for simple repeats ((GT) n , (GA) n , (AT) n , (GATA) n , (GGAA) n , (GAAA) n , (AAAT) n ) (Epplen et al, 1998).…”

DNA Fiber Mapping Techniques for the Assembly of High-resolution Physical Maps

“…Most mammalian genomes contain very large blocks of heterochromatin. Certain regions such as the (near)-centromeric heterochromatin seem to be involved in karyokinesis and chromosome association during meiosis (Dozortsev et al 2000), but the overall role of these clusters of "junk DNA" remains largely unknown (Epplen et al 1998). Physical map assembly in heterochromatic regions by more conventional methods, i.e., clone fingerprinting or STS content mapping, has proved less efficient, and initial releases of maps of the human, Drosophila , and other complex genomes might suffer from the presence of major gaps.…”

Isolation and characterization of polymorphic tetranucleotide microsatellite loci in the Fire salamander Salamandra salamandra (Amphibia: Caudata)

“…We assume that this leads to a relative dilution of microsatellites by about 10-fold with respect to normal frequencies. Thus, we employed an enrichment protocol with a special focus on (GATA) n tetranucleotide stretches, because these seem to occur frequently (Epplen et al . 1998) and because tetranucleotide repeats are generally easier to type.…”