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Study Suggests MicroRNA, Tissue Evolution Closely Linked in Bilaterian Animals

NEW YORK (GenomeWeb News) – Ancient microRNAs were largely tissue specific and their evolution seems to have occurred hand-in-hand with the evolution of animals with bilaterally symmetrical body plans, according to a paper appearing online yesterday in Nature.

A team of researchers from Germany and the US used small RNA sequencing, miRNA expression profiling, and comparative genomics to track down the active sites of conserved bilaterian miRNAs during bilaterian animal evolution. By comparing miRNA expression patterns in two marine worms — Platynereis dumerilii and Capitella — as well as the sea urchin, a sea anemone outgroup, and other animals, they found evidence that conserved miRNAs evolved in a tissue specific way in bilaterian animals.

"These findings reveal that microRNA evolution and the establishment of tissue identities were closely coupled in bilaterian evolution," senior author Detlev Arendt, a developmental biology researcher at the European Molecular Biology Laboratory, and his co-workers wrote.

Past studies suggest the evolution of complex animals with so-called bilateral symmetry was accompanied by a rise in the number of miRNAs in the animals' genome, the team explained. But the role of these miRNAs in tissue and body plan evolution was not well understood.

For the current study, the team did deep sequencing of P. dumerilii small RNA libraries with the Illumina platform to find 34 miRNA families shared by protostomes and deuterostomes — bilaterian groups that differ in their embryonic development.

They also relied on an approach called whole mount in situ hybridization, or WMISH, using labeled, locked nucleic acid probes to look at the localization of conserved bilaterian miRNAs.

Together, these methods allowed them to tease apart tissue-specific patterns for conserved bilaterian miRNAs. For instance, they found that miR-100, the oldest known conserved animal miRNA is specifically found in cells in the larval foregut, as are two related miRNAs involved in development (miR-125 and let-7) and miR-375, a miRNA previously found in foregut, neurosensory, and endocrine cells in vertebrate pancreas and pituitary tissue.

MiR-100, miR-125, and let-7 are also expressed in the foregut tissue of the Capitella worm and the sea urchin, the team found.

In contrast, though, miR-100 is expressed in cells near an early mouth-like opening during embryonic development in the outgroup animal, the sea anemone, suggesting the three miRNAs were originally found in neurosecretory cells around the mouth.

"These findings indicate that early in animal evolution miR-100 was active in a small population of cells located around a digestive opening," they wrote. "This expression was inherited by let-7 and by miR-125 once they evolved in the bilaterian stem line, to expand into other tissues only later in evolution."

Using similar methods, the researchers tracked down a set of miRNAs that seem to have been active in cells involved in movement- and brain-related tissues, respectively. More generally, they also found groups of conserved bilaterian miRNAs expressed in sensory, central nervous, muscle, and gut tissue.

These findings indicate that the evolution of conserved miRNA in animals with bilateral symmetry was tissue specific, they explained, and may have contributed to the way these tissues developed.

And because miRNAs provide information about cell types found in shared common ancestors, such research is expected to inform future evolutionary studies by providing clues about when various animal lineages diverged.

"We have thus established microRNAs as an important new tool for reconstructing ancient animal body plans at important evolutionary nodes, focusing here on the protostome-deuterostome divergence," the researchers wrote. "More complete inventories of microRNAs — yielding a refined picture of gains (and losses) of microRNAs in the diverging lineages — and concomitant expression analysis will allow expanding this approach to other key events in animal evolution."