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Researchers Trace Small RNAs Back to Early Animal Evolution

NEW YORK (GenomeWeb News) – MicroRNAs and Piwi-interacting RNAs were present in the earliest animal lineages, new research suggests.
In a paper appearing in the advanced online publication of Nature today, an international team of researchers looked for miRNAs and piRNAs in three groups of animals that diverged from the animal family tree before the development of bilateral symmetry. They detected both types of small RNAs in a sponge — which belongs to the earliest diverging group of animals — and in a starlet sea anemone — which belongs to a group diverging slightly later. Together, the results suggest that small RNAs were around early in animal evolution.
“It appears that both microRNAs and piRNAs have been available to shape gene expression throughout the evolution of animals and perhaps even helped to usher in the era of multicellular life,” senior author David Bartel, a biologist at the Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute investigator, said in a statement.
MicroRNAs are 21- to 24-nucleotide RNAs that typically prevent gene translation by binding to specific messenger RNA and targeting it for destruction. Piwi-interacting RNAs, meanwhile, are usually slightly longer, ranging from around 25 to 30 nucleotides. These piRNAs are not well understood in any species, lead author Andrew Grimson, a post-doctoral fellow in Bartel’s lab, told GenomeWeb Daily News, though they seem to regulate transposons, bits of DNA that move around in the genome.
While a lot is known about the presence or absence of miRNAs and piRNAs in animals with bilateral symmetry, Grimson explained, it was unclear whether these small RNAs are found in more basal animal lineages.
In an effort to explore this, the researchers isolated 18- to 30-nucleotide RNAs from the starlet sea anemone Nematostella vectensis, a cnidarian, and sequenced complementary DNA libraries using high-throughput sequencing. They then flushed out miRNAs by looking for sequences that matched predictions based on bilateral miRNA pairing characteristics. “MicroRNAs make a very characteristic pattern,” Grimson said. “They really stand out.”
The researchers found 40 loci that matched all of the criteria for miRNA detection. Consistent with the notion that these represented miRNA, 31 of the loci mapped between known protein-coding genes and eight mapped within introns.
Even so, just one miRNA — miR-100 — seemed to be homologous to a bilaterian miRNA. And that miRNA contained a sequence shift that likely targets it differently in the starlet sea anemone than in other animals.
While previous research suggested that the sea anemone genome contained at least one miRNA, it was completely unknown whether the sponge — a “very, very early diverging organism” — contained any miRNAs, Grimson said.
So to look back even further back in evolutionary history, the researchers used the same approach to look for small RNAs in the demosponge, Amphimedon queenslandica. The researchers found eight miRNA in A. queenslandica — six mapping between protein-coding regions and two mapping within introns.
But there were differences between the miRNAs found in Nematostella and Amphimedon. For instance, the pre-miRNA hairpins found in the sponge were larger than those found in other animals, while those in the sea anemone were significantly smaller than bilaterian pre-miRNAs.
“In a relatively narrow spectrum of evolution microRNAs are often conserved,” Grimson said in a statement. “But in a broader spectrum they have completely changed. This suggests that microRNA evolution is more flexible and may be evolving more rapidly than suspected.”
Both Nematostella and Amphimedon also contained two classes of piRNAs. And although the researchers didn’t directly gauge miRNA or piRNA function in these animals, Grimson said, their genomes contain hallmarks suggesting that their piRNAs do target transposons.
Even so, miRNAs and piRNAs aren’t found in all animals. The researchers failed to detect either type of small RNA in Trichoplax adhaerans, a member of the placozoan group, which diverged after sponges. They did find proteins involved in the RNAi pathway, though, suggesting that miRNA genes may have been lost from the Trichoplax genome.
Whether or not miRNA contributes to bilateral complexity is still an open question, Grimson said. But, he added, the work illustrates that miRNAs and piRNAs are not a defining feature of bilaterians. Instead, the findings suggest that these small RNAs were available much earlier in animal evolution.
By continuing to explore the function and diversity of small RNAs, researchers may eventually tease apart their role in animal life over time and across lineages. “[O]ur results indicate that miRNAs and piRNAs, as classes of small riboregulators, have been present since the dawn of animal life, and indeed might have helped to usher in the era of multicellular animal life,” the authors wrote.

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