In the coelacanth, the ultraconserved segments were produced by a retroposon known as a short interspersed repetitive element, or SINE, which is a piece of DNA that can make copies of itself and insert those copies elsewhere in an organism's genome. Haussler and his colleagues called this SINE the LF-SINE, where LF stands for lobe-finned fishes--the group of fishes that gave rise to both the coelacanth and terrestrial vertebrates.
The LF-SINE was very active in the evolutionary lineage leading to the terrestrial vertebrates, but much less active after animals moved onto land. Humans have 245 recognizable copies of the LF-SINE, most or all of which probably were in place before the origins of the mammals. But in the lineage leading to the coelacanth, the LF-SINE remained active, so that the coelacanth genome is now estimated to contain hundreds of thousands of copies of the sequence.
The close copies of the ultraconserved element scattered around vertebrate genomes have changed less than would be expected over evolutionary time, indicating that they are functionally important. But relatively few of the copies contain parts that code for proteins, which suggests they instead are helping to regulate when genes are turned on and off. Furthermore, when Bejerano analyzed the locations of the copies, he found that they tended to be near genes that control the development of the brain.
Haussler and his colleagues then looked at a particular example -- a copy of the ultraconserved element that is near a gene called Islet 1 (ISL1). ISL1 produces a protein that helps control the growth and differentiation of motor neurons. In the laboratory
Source:Howard Hughes Medical Institute