Special Issue "Non-Coding RNAs, from an Evolutionary Perspective"

A special issue of Non-Coding RNA (ISSN 2311-553X).

Deadline for manuscript submissions: 13 December 2018

Special Issue Editors

Guest Editor
Dr. Claire Rougeulle

Paris Diderot University, Department of Epigenetics and Cell Fate, Paris, France
Website | E-Mail
Interests: long non-coding RNAs; X-chromosome inactivation; stem cells; development; non-coding RNA evolution; epigenetics
Guest Editor
Dr. Yehu Moran

Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
Website | E-Mail
Phone: (+972)-2-6585714
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 papers will be 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 quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) is waived for well-prepared manuscripts submitted to this issue. 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

Published Papers (2 papers)

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Research

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Open AccessArticle Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks
Non-Coding RNA 2018, 4(1), 6; https://doi.org/10.3390/ncrna4010006
Received: 1 December 2017 / Revised: 5 February 2018 / Accepted: 27 February 2018 / Published: 7 March 2018
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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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Open AccessReview Local Tandem Repeat Expansion in Xist RNA as a Model for the Functionalisation of ncRNA
Non-Coding RNA 2018, 4(4), 28; https://doi.org/10.3390/ncrna4040028
Received: 19 September 2018 / Revised: 15 October 2018 / Accepted: 16 October 2018 / Published: 19 October 2018
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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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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

1) Miguel Almeida, Miguel Andrade, René Ketting. Function and evolution of nematode RNAi pathways.

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, have evolved to counteract these elements. Amongst these, endogenous small interfering RNA (endo-siRNA) 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.

2) Yirong Wang, Shengqian Dou, and Jian Lu. tRNA derived small RNAs (tsRNAs): sequence conservation, target recognition, and repression modes in metazoans.

Abstract: Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of regulatory small non-coding RNAs. tsRNAs play an important role in post-transcriptional regulation in many biological processes. Emerging evidences have shown that tsRNAs are involved in ribosome biogenesis, mRNA stability, translation regulation and many other physiological or pathological processes in metazoan. In this review, we overviewed comparative genomic analyses of tsRNAs in previous studies, and depicted the evolutionary trajectories of tsRNAs in different species. Then, we elaborated comprehensive repression modes in various biological processes, especially in translational inhibition and mRNA stability. Furthermore, we focused on the coevolution of tsRNAs and targets, as well as targetome shifting during evolution. In addition to that, we put forward some conundrum that need further investigations. By uncovering the evolutionary dynamics and generalizing functional mechanisms of tsRNA, this review will greatly deepen our understanding of the tsRNA-mediated biological processes, and may shed light on potential application of tsRNAs in human diseases.

1. Brief introduction of tsRNAs

1.1. Biogenesis of tsRNAs: classification; condition-induced/specific tsRNAs; modifications

1.2. Species-specific features of tsRNAs biogenesis, e.g., type, enzyme, fragment

1.3. tsRNA-involved biological processes and diseases

2. Evolutionary trajectories of tsRNAs

2.1. Sequence conservation

2.2. Evolutionary dynamics of tsRNAs in different species

3. Repression modes and function models

3.1. tsRNAs inhibit translation:

a. initiation/elongation

b. specific targeting/global

3.2. tsRNAs cleavage mRNA

3.3. tsRNAs influence ribosome biogenesis

4. Coevolution of tsRNAs and targets

4.1. Target recognition of tsRNA in various manners

4.2. Target recognition in different species

4.3. Targetome shifting during evolution

3) Olga Rosspopoff, Claire Rougeulle and Jean-François Ouimette. Evolution of the non-coding RNA network controlling X chromosome inactivation in mammals.

4) Andrea Hatlen and Antonio Marco. The impact of population variation in the analysis of microRNA target sites.

5) Bastian Fromm et al. Occurrence and evolutionary implications of the piRNA- and miRNA complement of Lepidodermella squamata (Gastrotricha).

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