Evolution and Functional Diversification of <i>MIRNA</i> Genes

Cuperus, Josh T.; Fahlgren, Noah; Carrington, James C.

doi:10.1105/tpc.110.082784

Cited by 664 publications

(711 citation statements)

References 120 publications

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“…The origin of miRNA pathways have been discussed many times and the prevailing belief is that miRNAs evolved independently several times during the course of evolution although this idea of convergent evolution has recently been challenged [6,27,70,71]. The phylogenetic position of D. discoideum within the Amoebozoa supergroup, which branched off after plants (Archaeplastida) but before animals (Opisthokonta) [72], gives us glimpses into the evolution of the miRNA machinery.…”

Section: Resultsmentioning

confidence: 99%

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

et al. 2018

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Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3ʹ-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.

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Section: Resultsmentioning

confidence: 99%

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

et al. 2018

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“…These lower representations might occurred because the corresponding miRNAs might be 'youngmiRNAs' (Cuperus et al 2011). Unlike highly conserved, ancient miRNAs, young miRNAs are often weakly expressed, lack targets, and their gene loci tend to evolve neutrally (Cuperus et al 2011). Those young miRNAs may have some species-specific regulatory roles inside the organisms (Sun et al 2012;Fahlgren et al 2007).…”

Section: Representation Of Putative Mirna Families In C Avellana Genomementioning

confidence: 99%

Identification of microRNA elements from genomic data of European hazelnut (Corylus avellana L.) and its close relatives

Avşar¹,

Esmaeilialiabadi²

2017

Plant Omics

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Plant microRNAs (miRNAs) are small and non-coding endogenous RNAs which have numerous regulatory roles in cells. These critical players regulate pathways either by inducing translational repression or messenger RNA (mRNA) decay. Newly developed bioinformatics tools and computational methods have been increased to identify miRNAs with their targets inside the genome. In this study, we predicted and identified 57 putative miRNAs through Corylus avellana (C. avellana) genomic data in silico. We also predicted some other putative miRNAs from Arabidopsis thaliana (A. thaliana), Ricinus communis (R. communis), Populus trichocarpa (P. trichocarpa) and Vitis vinifera (V. vinifera) to compare with the C. avellana organism since previous studies have indicated high similarities between these genomes and proteome atlases. The miRBase 21 was used as a reference dataset and the putative miRNAs were identified for the genome of each organism. We used homology conserved method to identify putative miRNAs. Based on our findings, C. avellana miRNA content was found to be highly similar to V. vinifera, R. communis and P. trichocarpa. Also, we found the targets of these hazelnut putative miRNAs and their possible functions inside the cell. One of our major discoveries is that miR171 families are highly represented (the copy number of miRNA) in the hazelnut genome to provide clues for microRNA domestication. The miR396, miR482, and miR2118 families were found as in silico expressed putative miRNAs by using computational methods. All these findings may help us better understanding the miRNA repertoire of the hazelnut organism and provide valuable insight about the regulatory roles of predicted putative miRNAs which are shared with other organisms (A. thaliana, R. communis, P. trichocarpa, V. vinifera) for further studies.

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“…The majority are lineage specific or species specific. Even conserved miRNAs, however, have species-specific functions, as demonstrated by comparisons of Arabidopsis and poplar [62]. Only 80% of known miRNAs identified in the T. parvula genome share sequence similarity with A. thaliana miRNAs.…”

Section: Epigenetic Modifications and Non-coding Rnasmentioning

confidence: 99%