18 SINEs and LINEs: Troublemakers, Saboteurs, Benefactors, Ancestors

Abstract

We will never know whether the world is better or worse for viruses, mosquitoes, protozoan pathogens, poison ivy, raptors, or retroposons. We must take the natural world or leave it; we cannot pick and choose. But if we could pick and choose, retroposons would be a tough call, because they have given much, and taken much away. Thanks to the human genome project, we now know that almost half of the human genome is squandered on retroposons (SINEs, LINEs, and retroviral-like elements), a fact we can regard as humbling, puzzling, or amazing, but certainly nothing to be proud of. On the other hand, a good case can be made that retroposons have contributed richly to genomic diversification in the DNA World, and are most likely not newborn saboteurs or benefactors but molecular fossils of transitional genomes that enabled the RNA World to turn into a DNA World.

THE REVERSE FLOW OF GENETIC INFORMATION FROM RNA INTO DNA
The earliest hints that RNA information might flow back into DNA were the discoveries that (1) the major family of interspersed repeated sequences in the human genome was about 300 bp long, exhibited about 14% average sequence divergence, and typically contained a nearly central Alu restriction site—hence the name Alu family elements (Houck et al. 1979); (2) the Alu family was homologous to an abundant, homogeneous, small cytoplasmic RNA of then unknown function called 7S RNA (Weiner 1980); and (3) many Alu family elements were strong RNA polymerase III transcription units, at...