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Non-Coding RNAs, from an Evolutionary Perspective
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Non-Coding RNAs, from an Evolutionary Perspective

A special issue of Non-Coding RNA (ISSN 2311-553X). This special issue belongs to the section "Evolution of Non-Coding RNA".

Deadline for manuscript submissions: closed (13 December 2018) | Viewed by 36937

Special Issue Editors

Dr. Claire Rougeulle

E-Mail Website
Guest Editor
Department of Epigenetics and Cell Fate, Paris Diderot University, Paris, France
Interests: long non-coding RNAs; X-inactivation; stem cells; differentiation; development; non-coding RNA evolution; epigenetics
Special Issues, Collections and Topics in MDPI journals
Dr. Yehu Moran

E-Mail Website
Guest Editor
Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
Interests: venom evolution; Cnidaria; sea anemones; post-transcriptional regulation; microRNA

Special Issue Information

Dear Colleagues,

Non-coding RNAs (ncRNAs), such as microRNAs and long ncRNAs (lncRNAs), pose a formidable challenge to biologists: they constitute a large fraction of eukaryotic transcriptomes and emerge as an important component of gene regulatory networks, yet, unlike protein-coding genes, their conservation in evolution is rather limited, at least at the sequence level. The evolutionary conservation of ncRNAs serves as an important indication for their functionality; however species differences in microRNAs and lncRNAs may be invaluable predictors of phylogenetic relationships and may contribute to promote plasticity and diversity in evolution.

This Special Issue will focus on evolutionary aspects of ncRNAs, from in silico to functional and mechanistic investigations. Manuscripts reporting original research, short communications and reviews will be considered.

Dr. Claire Rougeulle
Dr. Yehu Moran
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Non-Coding RNA is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Evolution of ncRNA (lncRNA, microRNA, piRNA, siRNA, etc.)
  • Transposable element-derived ncRNA
  • Brain and nervous system ncRNA
  • X-chromosome inactivation
  • Imprinting
  • ncRNA interactions
  • Post-transcriptional regulation by ncRNA

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Published Papers (6 papers)

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Research

Jump to: Review

8 pages, 1411 KiB  
Article
The Impact of Population Variation in the Analysis of microRNA Target Sites
by Mohab Helmy, Andrea Hatlen and Antonio Marco
Non-Coding RNA 2019, 5(2), 42; https://doi.org/10.3390/ncrna5020042 - 22 Jun 2019
Cited by 2 | Viewed by 4309
Abstract
The impact of population variation in the analysis of regulatory interactions is an underdeveloped area. MicroRNA target recognition occurs via pairwise complementarity. Consequently, a number of computational prediction tools have been developed to identify potential target sites that can be further validated experimentally. [...] Read more.
The impact of population variation in the analysis of regulatory interactions is an underdeveloped area. MicroRNA target recognition occurs via pairwise complementarity. Consequently, a number of computational prediction tools have been developed to identify potential target sites that can be further validated experimentally. However, as microRNA target predictions are done mostly considering a reference genome sequence, target sites showing variation among populations are neglected. Here, we studied the variation at microRNA target sites in human populations and quantified their impact in microRNA target prediction. We found that African populations carry a significant number of potential microRNA target sites that are not detectable in the current human reference genome sequence. Some of these targets are conserved in primates and only lost in Out-of-Africa populations. Indeed, we identified experimentally validated microRNA/transcript interactions that are not detected in standard microRNA target prediction programs, yet they have segregating target alleles abundant in non-European populations. In conclusion, we show that ignoring population diversity may leave out regulatory elements essential to understand disease and gene expression, particularly neglecting populations of African origin. Full article
(This article belongs to the Special Issue Non-Coding RNAs, from an Evolutionary Perspective)
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17 pages, 3093 KiB  
Article
Evolutionary Implications of the microRNA- and piRNA Complement of Lepidodermella squamata (Gastrotricha)
by Bastian Fromm, Juan Pablo Tosar, Felipe Aguilera, Marc R. Friedländer, Lutz Bachmann and Andreas Hejnol
Non-Coding RNA 2019, 5(1), 19; https://doi.org/10.3390/ncrna5010019 - 22 Feb 2019
Cited by 8 | Viewed by 5259
Abstract
Gastrotrichs—’hairy bellies’—are microscopic free-living animals inhabiting marine and freshwater habitats. Based on morphological and early molecular analyses, gastrotrichs were placed close to nematodes, but recent phylogenomic analyses have suggested their close relationship to flatworms (Platyhelminthes) within Spiralia. Small non-coding RNA data on e.g., [...] Read more.
Gastrotrichs—’hairy bellies’—are microscopic free-living animals inhabiting marine and freshwater habitats. Based on morphological and early molecular analyses, gastrotrichs were placed close to nematodes, but recent phylogenomic analyses have suggested their close relationship to flatworms (Platyhelminthes) within Spiralia. Small non-coding RNA data on e.g., microRNAs (miRNAs) and PIWI-interacting RNAs (piRNA) may help to resolve this long-standing question. MiRNAs are short post-transcriptional gene regulators that together with piRNAs play key roles in development. In a ‘multi-omics’ approach we here used small-RNA sequencing, available transcriptome and genomic data to unravel the miRNA- and piRNA complements along with the RNAi (RNA interference) protein machinery of Lepidodermella squamata (Gastrotricha, Chaetonotida). We identified 52 miRNA genes representing 35 highly conserved miRNA families specific to Eumetazoa, Bilateria, Protostomia, and Spiralia, respectively, with overall high similarities to platyhelminth miRNA complements. In addition, we found four large piRNA clusters that also resemble flatworm piRNAs but not those earlier described for nematodes. Congruently, transcriptomic annotation revealed that the Lepidodermella protein machinery is highly similar to flatworms, too. Taken together, miRNA, piRNA, and protein data support a close relationship of gastrotrichs and flatworms. Full article
(This article belongs to the Special Issue Non-Coding RNAs, from an Evolutionary Perspective)
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15 pages, 4690 KiB  
Article
Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks
by Federico Gaiti, William L. Hatleberg, Miloš Tanurdžić and Bernard M. Degnan
Non-Coding RNA 2018, 4(1), 6; https://doi.org/10.3390/ncrna4010006 - 7 Mar 2018
Cited by 8 | Viewed by 5617
Abstract
Although developmental regulation by long non-coding RNAs (lncRNAs) appears to be a widespread feature amongst animals, the origin and level of evolutionary conservation of this mode of regulation remain unclear. We have previously demonstrated that the sponge Amphimedon queenslandica—a morphologically-simple animal—developmentally expresses [...] Read more.
Although developmental regulation by long non-coding RNAs (lncRNAs) appears to be a widespread feature amongst animals, the origin and level of evolutionary conservation of this mode of regulation remain unclear. We have previously demonstrated that the sponge Amphimedon queenslandica—a morphologically-simple animal—developmentally expresses an array of lncRNAs in manner akin to more complex bilaterians (insects + vertebrates). Here, we first show that Amphimedon lncRNAs are expressed in specific cell types in larvae, juveniles and adults. Thus, as in bilaterians, sponge developmental regulation involves the dynamic, cell type- and context-specific regulation of specific lncRNAs. Second, by comparing gene co-expression networks between Amphimedon queenslandica and Sycon ciliatum—a distantly-related calcisponge—we identify several putative co-expression modules that appear to be shared in sponges; these network-embedded sponge lncRNAs have no discernable sequence similarity. Together, these results suggest sponge lncRNAs are developmentally regulated and operate in conserved gene regulatory networks, as appears to be the case in more complex bilaterians. Full article
(This article belongs to the Special Issue Non-Coding RNAs, from an Evolutionary Perspective)
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Review

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12 pages, 1381 KiB  
Review
Metazoan tsRNAs: Biogenesis, Evolution and Regulatory Functions
by Shengqian Dou, Yirong Wang and Jian Lu
Non-Coding RNA 2019, 5(1), 18; https://doi.org/10.3390/ncrna5010018 - 18 Feb 2019
Cited by 27 | Viewed by 5794
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of regulatory non-coding RNAs that play important roles in post-transcriptional regulation across a variety of biological processes. Here, we review the recent advances in tsRNA biogenesis and regulatory functions from the perspectives of functional [...] Read more.
Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of regulatory non-coding RNAs that play important roles in post-transcriptional regulation across a variety of biological processes. Here, we review the recent advances in tsRNA biogenesis and regulatory functions from the perspectives of functional and evolutionary genomics, with a focus on the tsRNA biology of Drosophila. We first summarize our current understanding of the biogenesis mechanisms of different categories of tsRNAs that are generated under physiological or stressed conditions. Next, we review the conservation patterns of tsRNAs in all domains of life, with an emphasis on the conservation of tsRNAs between two Drosophila species. Then, we elaborate the currently known regulatory functions of tsRNAs in mRNA translation that are independent of, or dependent on, Argonaute (AGO) proteins. We also highlight some issues related to the fundamental biology of tsRNAs that deserve further study. Full article
(This article belongs to the Special Issue Non-Coding RNAs, from an Evolutionary Perspective)
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24 pages, 2550 KiB  
Review
Function and Evolution of Nematode RNAi Pathways
by Miguel Vasconcelos Almeida, Miguel A. Andrade-Navarro and René F. Ketting
Non-Coding RNA 2019, 5(1), 8; https://doi.org/10.3390/ncrna5010008 - 15 Jan 2019
Cited by 50 | Viewed by 8537
Abstract
Selfish genetic elements, like transposable elements or viruses, are a threat to genomic stability. A variety of processes, including small RNA-based RNA interference (RNAi)-like pathways, has evolved to counteract these elements. Amongst these, endogenous small interfering RNA and Piwi-interacting RNA (piRNA) pathways were [...] Read more.
Selfish genetic elements, like transposable elements or viruses, are a threat to genomic stability. A variety of processes, including small RNA-based RNA interference (RNAi)-like pathways, has evolved to counteract these elements. Amongst these, endogenous small interfering RNA and Piwi-interacting RNA (piRNA) pathways were implicated in silencing selfish genetic elements in a variety of organisms. Nematodes have several incredibly specialized, rapidly evolving endogenous RNAi-like pathways serving such purposes. Here, we review recent research regarding the RNAi-like pathways of Caenorhabditis elegans as well as those of other nematodes, to provide an evolutionary perspective. We argue that multiple nematode RNAi-like pathways share piRNA-like properties and together form a broad nematode toolkit that allows for silencing of foreign genetic elements. Full article
(This article belongs to the Special Issue Non-Coding RNAs, from an Evolutionary Perspective)
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11 pages, 966 KiB  
Review
Local Tandem Repeat Expansion in Xist RNA as a Model for the Functionalisation of ncRNA
by Neil Brockdorff
Non-Coding RNA 2018, 4(4), 28; https://doi.org/10.3390/ncrna4040028 - 19 Oct 2018
Cited by 24 | Viewed by 6202
Abstract
Xist, the master regulator of the X chromosome inactivation in mammals, is a 17 kb lncRNA that acts in cis to silence the majority of genes along the chromosome from which it is transcribed. The two key processes required for Xist RNA [...] Read more.
Xist, the master regulator of the X chromosome inactivation in mammals, is a 17 kb lncRNA that acts in cis to silence the majority of genes along the chromosome from which it is transcribed. The two key processes required for Xist RNA function, localisation in cis and recruitment of silencing factors, are genetically separable, at least in part. Recent studies have identified Xist RNA sequences and associated RNA-binding proteins (RBPs) that are important for these processes. Notably, several of the key Xist RNA elements correspond to local tandem repeats. In this review, I use examples to illustrate different modes whereby tandem repeat amplification has been exploited to allow orthodox RBPs to confer new functions for Xist-mediated chromosome inactivation. I further discuss the potential generality of tandem repeat expansion in the evolution of functional long non-coding RNAs (lncRNAs). Full article
(This article belongs to the Special Issue Non-Coding RNAs, from an Evolutionary Perspective)
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