The following guest post was kindly provided by Dr. Kimberly Chen. I have edited only for formatting.
MicroRNAs (miRNAs) are a class of non-coding small RNAs that regulate numerous developmental processes in plants and animals and are generally associated with the evolution of multicellularity and cellular differentiation. They are processed from long hairpin precursors to mature forms and subsequently loaded into a multi-protein complex, of which the Argonaute (AGO) family protein is the core component. The small RNAs then guide the protein complex to recognize complementary mRNA transcripts and conduct post-transcriptional gene silencing.
In a new article at BMC Genomics, Anne Dueck and colleagues identified the miRNAs in the multicellular green alga Volvox carteri, a model system for the evolution of multicellularity and development. In particular, they used a functional approach by sequencing V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental stages and cell types.
In total, the authors identified 490 miRNAs that fall into 324 miRNA families in Volvox. They showed that at least some of these small RNAs are differentially expressed in somatic and reproductive cells and at different developmental stages. In addition, many of these miRNAs originate from transposons and other small RNAs like siRNAs and phased siRNAs were also found in transposons.
Previously, miRNAs have been identified in Chlamydomonas reinhardtii, the unicellular relative of V. carteri (Molnár et al 2007, Zhao et al 2007). As the authors point out:
Given the importance of different small RNAs in processes closely associated with multicellular development in land plants, we speculated that they might have played a role in the transition from uni- to multicellularity in green algae.
Intriguingly, the miRNAs identified in this study are not conserved in C. reinhardtii, suggesting rapid evolution of miRNAs in the volvocine algae, and probably more importantly, “evolution of different miRNAs presumably required for multicellularity and division of labor between somatic and reproductive cells.”
It has been postulated that evolution of gene expression and regulation plays a key role during multicellular innovation and allows different genes expressed in different cell types. Genomic comparison of C. reinhardtii and V. carteri has revealed similar contents of protein-coding genes and even the diversity and abundance of transcription factors between the two species. How the miRNAs repertoires detected in Volvox correlate with the evolution of multicellularity might help understand the genetic basis underlying the major evolutionary transitions.
An earlier article by Jingrui Li and colleagues also attempted to identify miRNAs in V. carteri with a different strain. Nevertheless, there is no overlap between miRNAs reported in the two studies, likely due to different RNA sequencing strategies. In Li’s study, only one miRNA identified in V. carteri is conserved in C. reinhardtii.
Last but not least, despite tremendous efforts in characterizing the roles of miRNAs in developmental gene regulation in multicellular lineages, little is known about their ancestral functions. The ones identified in the unicellular C. reinhardtii therefore lay the groundwork to study the ancestral roles of miRNAs.
Dueck, A., Evers, M., Henz, S.R., Unger, K., Eichner, N., Merkl, R., Berezikov, E., Engelmann, J.C., Weigel, D., Wenzl, S., Meister, G., 2016. Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants. BMC Genomics 17, 853.
Li, J., Wu, Y., Qi, Y., 2014. MicroRNAs in a multicellular green alga Volvox carteri. Sci China Life Sci 57, 36-45.
Molnár, A., Schwach, F., Studholme, D.J., Thuenemann, E.C., Baulcombe, D.C., 2007. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447, 1126-1129.
Zhao, T., Li, G., Mi, S., Li, S., Hannon, G.J., Wang, X.J., Qi, Y., 2007. A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev 21, 1190-1203.