LF-SINE electronic supplement
Nature. 2006 May 4;441(7089):87-90. Epub 2006 Apr 16.
A distal enhancer and an ultraconserved exon are derived from a novel retroposon.
Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D.
of highly conserved distal cis-regulatory elements have been
characterized so far in vertebrate genomes. Many thousands more are
predicted on the basis of comparative genomics. However, in stark
contrast to the genes that they regulate, in invertebrates virtually
none of these regions can be traced by using sequence similarity,
leaving their evolutionary origins obscure. Here we show that a class
of conserved, primarily non-coding regions in tetrapods originated from
a previously unknown short interspersed repetitive element (SINE)
retroposon family that was active in the Sarcopterygii (lobe-finned
fishes and terrestrial vertebrates) in the Silurian period at least 410
million years ago, and seems to be recently active in the
'living fossil' Indonesian coelacanth, Latimeria menadoensis. Using a
mouse enhancer assay we show that one copy, 0.5 million bases from the
neuro-developmental gene ISL1, is an enhancer that recapitulates
multiple aspects of Isl1 expression patterns. Several other copies
represent new, possibly regulatory, alternatively spliced exons in the
middle of pre-existing Sarcopterygian genes. One of these, a more than
200-base-pair ultraconserved region, 100% identical in mammals, and 80%
identical to the coelacanth SINE, contains a 31-amino-acid-residue
alternatively spliced exon of the messenger RNA processing gene PCBP2.
These add to a growing list of examples in which relics of
transposable elements have acquired a function that serves their host,
a process termed 'exaptation', and provide an origin for at least some
of the many highly conserved vertebrate-specific genomic sequences.
LF-SINE instances in tetrapods
Table & Launcher for human LF-SINE instances in the UCSC Genome Browser.
Corresponding Author: Gill Bejerano