The draft human genome: A repetitious genome 28/2/01. By Richard Gallagher and Carina Dennis The human genome is littered with repeat regions. What are they, and where did they come from?

The general arrangement of the human genome provides a startling jolt. In some ways it may resemble your garage/bedroom/refrigerator/life: highly individualistic, but unkempt; little evidence of organisation; much accumulated clutter (referred to by the uninitiated as 'junk'); virtually nothing ever discarded; and the few patently valuable items indiscriminately, apparently carelessly, scattered throughout.

Those valuable items are the genes themselves. Actual exons take up as little as 1 per cent of the genome, while introns account for 24 per cent.

More than half of the euchromatic genome consists of repeat sequences, with the vast majority (45 per cent) are accounted for by repeats derived from 'parasitic DNA', called transposable elements or transposons (see Figure). These elements propagate by replicating and then inserting a new copy of themselves into another site in the genome.

The sheer numbers of repeated elements is unprecedented in any other sequenced genome: repeats account for just 1.5 per cent of a typical bacterial genome and 3 per cent of fly euchromatin.

Curiously, much of our repeat content represents ancient remnants of long-'dead' transposons, unlike fly and mouse genomes, which harbour younger, more active, elements. Freed from many of the evolutionary constraints on functional sequences, repeat elements have accumulated mutations and diverged from each other over time. Analysis of these gradual changes thus provides a fascinating window on the evolution of our species.

Most transposable elements entered our genome before the appearance of placental mammals. Some types flourished, such as those known as LINE1 and Alu elements (which represent more than 60 per cent of all interspersed repeat sequences in our genome).

Others appear to have found the environment unsavoury: for example, only faint traces of LTR retrotransposons are detectable in the human genome - though they are alive and kicking in the mouse genome. DNA transposons, another type of repeat, have marked our genome with two bursts of activity - before and after the appearance of placental mammals. As DNA transposons can mediate chromosomal rearrangements, it is tempting to speculate that they had an important part in speciation.

Why does the genome carry such a heavy load of parasitic DNA? Are we unusually sloppy at cleaning out the ancient debris of past invaders? Could we be considered simply to be vehicles for proliferation of these selfish elements? Or do we retain them because they serve some useful purpose? It is likely that there is some truth in each of these propositions.

There is evidence that transposons shaped the evolution of the genome and mediated the creation of new genes. Analysis of the draft genome has identified 47 transposon-derived genes, including the genes encoding telomerase - an RNA-containing enzyme that synthesises telomeres, the DNA that caps the ends of chromosomes - and RAG1 and RAG2 - the enzymes that assemble the immunoglobulin and T-cell receptor genes from smaller gene segments, producing an extraordinary diversity of immune system molecules.

Fragments of transposons are found in the regulatory sequences that control the expression of several hundred other genes. So it is not inconceivable that, at least in part, transposons are retained because they confer an advantage.

Image credit: Kate Whitley