This press release (Sea anemone is genetically half animal, half plant) got us curious about two interesting papers recently published in Genome Research. The original genome paper of N. vectensis sequenced by JGI came out in Science in 2007 (“Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization”), but the following new paper found something that nobody noticed before. It seems sea anemone genome has HYL-1, a gene needed for miRNA biogenesis in plants !!
Yehu Moran, David Fredman and Daniela Praher from the Technau team were able to show that the microRNAs of the sea anemone depict all the hallmarks of plant microRNAs: They have an almost perfect complementarity to their target RNAs, which are subsequently cleaved and not inhibited like in other animals. Moran also discovered a gene in the sea anemone, HYL-1, which is essential for the microRNA biogenesis in plants and was never detected in any other animal model organism before. Moreover, when one compares the sequences of microRNAs, one microRNA with similarity to a plant microRNA as well as one microRNA with similarity to an animal microRNA can be found. Altogether, these findings suggest the first evolutionary link between microRNAs of plants and animals.
More detail below -
In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA seed) to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA- like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state.
Despite considerable differences in morphology and complexity of body plans among animals, a great part of the gene set is shared among Bilateria and their basally branching sister group, the Cnidaria. This suggests that the common ancestor of eumetazoans already had a highly complex gene repertoire. At present it is therefore unclear how morphological diversification is encoded in the genome. Here we address the possibility that differences in gene regulation could contribute to the large morphological divergence between cnidarians and bilaterians. To this end, we generated the first genome-wide map of gene regulatory elements in a nonbilaterian animal, the sea anemone Nematostella vectensis. Using chromatin immunoprecipitation followed by deep sequencing of five chromatin modifications and a transcriptional cofactor, we identified over 5000 enhancers in the Nematostella genome and could validate 75% of the tested enhancers in vivo. We found that in Nematostella, but not in yeast, enhancers are characterized by the same combination of histone modifications as in bilaterians, and these enhancers preferentially target developmental regulatory genes. Surprisingly, the distribution and abundance of gene regulatory elements relative to these genes are shared between Nematostella and bilaterian model organisms. Our results suggest that complex gene regulation originated at least 600 million yr ago, predating the common ancestor of eumetazoans.