Gene silencing through RNA interference (RNAi) pathway is a well known phenomenon ,where in long double stranded is processed into small interfering RNAs and which in turn silence the genes in sequence specific manner. These micro RNAs are pretty much conserved throughout the Bilaterians, such as Humans,flies and worms,which play pivotal role in substantial fraction of transcription.MicroRNAs (miRNAs) are ~21-24 nucleotide RNAs ,derived from distinctive hairpin precursors ,bind with mRNA and brings post transcriptional repression.In performing this function micro RNAs use the basal pathway of Dicer endonucleases and Argonaute effector protein.
Micro RNAs present in plants and algae have a different gene structure,biogenesis and targeting properties from those of animals, and these miRNAs are not found in fungi. Based on the above facts its generally considered that miRNAs in plants and animals had independent origin.

One of the popular hypothesis believed that miRNAs are not present in earliest branching animal lineages like sponges and thats the reason for the complexity among bilaterians.If one take a look at the miRNAs present in Bilaterians ,around 30 were believed to be present among ancestral bilaterians.Similarly to miRNAs ,other class of RNAs called Piwi RNAs were also not reported in lower metazoans. So in order to test whether a rich-small RNA biology is the reason for complexity of bilaterians animals or these small RNAs have emerged earlier in metazoan evolution, David Bartel’s group took the task of identification of the Small RNAs in lower metazoans.

As Eumetazoans include Cnidarians also along with Bilaterians , authors took the advantage of complete genome sequence of starlet Nematostella vectensis.High through put sequencing of complementary DNA libraries generated by 18-20 nucleotide RNAs isolated from Nematostella were checked for the presence of miRNAs and they could identify 40 miRNAs which passed the three criterion like
1) Presence of reads mapping to an inferred RNA hairpin with pairing characteristics of known miRNA.
2) Presence of reads from both arms of the hairpin so that they could form duplex with each other through 2 nucleotide 3′ overhangs.
3) To look of homogeneity of miRNA 5′ terminus.

Micro RNAs in Sponges and Trichoplax :

In order to look for miRNAs in deeply branching lineages like Sponges ,which comprises of animals that diverged early in metazoan evolution.Authors generated 2.5 million reads from small RNAs of desmosponge Amphimedon queenslandica and could trace 8 miRNAs in Amphimedon adult and embryo samples.Like the miRNAs of Bilaterians and Nematostella ,reads from one arm of hairpin is generally exceed from those of other arm.The important thing to note is that pre-miRNA hairpins were larger than most of those of other animals and also the miRNAs of sponges dont share any significant similarity with any known miRNA raising the possibility of independent origin of miRNAs in sponges and Eumetazoans.But this can not the case as Amphimedon also possess a copy of Drosha and Pasha genes which recognizes the miRNA primary transcript and cut it to release pre miRNA hairpin.As the homologue’s of Drosha and Pasha are found in only metazoans (animals) indicates a single origin for processing factors early during metazoan evolution and also a single origin for their miRNA substrates.

Authors then moved ahead in search of miRNAs in Trichoplax ,which represents Placozoa.Recent genome data of Trichoplax shares a common ancestor with Cnidarians ,meaning they branched out after sponges in the evolution og metazoans. Despite acquiring many more reads than required to identify mi RNAs in other animals ,authors failed to detect any miRNA from the genome of Trichoplax and they predict that miRNAs have been lost in this lineage during the course of evolution.Trichoplax is considered to be very derived from a complex ancestor ,as it has lost hedgehog and Notch signalling pathways .There is also no evidence of Pasha homologue but Dicer,Drosha and argonaute genes are present, proving miRNAs were once produced and used.Normally in miRNA biogenesis pathway Pasha is the only one gene which doesnot have any other function apart from in miRNA pathway and this could be the reason why all miRNAs have been lost along with pasha gene. Results produced from this work supports that increase in complexity in metazoans depend on number of miRNAs as evident by 8 in Amphimedon, 40 in Nematostella ,0 in Trichoplax and above 600 in humans.

Reference:

Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP.
Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals.
Nature. 2008 Oct 1.

Image credits:
Nematostella : pelagosphera’s photostream / Flickr
Trichoplax : Ana Signorovitch, Yale University

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