Special Issue "Regulation of Mobile Genetic Elements at the Molecular Level"

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: 30 June 2021.

Special Issue Editor

Dr. Silke Jensen
E-Mail Website
Guest Editor
GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
Interests: transposable elements; small RNA; piRNA; PIWI pathway; RNA biology; epigenetics; piRNA cluster; germline; regulation of gene expression

Special Issue Information

Dear Colleagues,

When Barbara McClintock discovered mobile genetic elements in the 1950s, did she suspect the magnitude, extent, and consequences of the mobility of these elements in the living world? Indeed, mobile genetic elements, also called transposable elements, were subsequently discovered both in prokaryotes and in eukaryotes where they constitute a large part of genomes, as 45% in human, 80% in maize. Mobile elements are a source of mutations: in Drosophila, more than 80% of phenotypic mutations observed are due to transposition events; in humans, de novo insertions of transposable elements have been implicated in mutations leading to disease, as haemophilia, cancer, muscular dystrophy. Due to their repeated nature, mobile elements dispersed in the genome are also at the origin of important chromosomal rearrangements.

Today, we know that mobile genetic elements can have devastating or, on the contrary, beneficial effects on genomes. They can create disorders but they also play an essential role in the fluidity of genomes and in evolution. It is therefore extremely important to elucidate the regulatory mechanisms controlling mobile genetic elements in all their aspects at the molecular level, in the animal kingdom, in plants as in prokaryotes.

A number of different regulatory systems exist and operate in different organisms and in different tissues. In the metazoans germline, small RNAs interacting with PIWI family proteins (piRNAs) and small interfering RNAs (siRNAs) are key components of the pathways controlling transposable elements. Chromatin remodeling leads to transcriptional silencing of mobile elements. Truncated proteins derived from transposable elements themselves can control mobility as in the case of P elements in Drosophila. Somatic silencing mechanisms may be totally different from germline mechanisms in the same organism. Bringing together different areas of research in this Special Issue will help to expand our knowledge of the molecular mechanisms controlling mobile genetic elements in all their diversity.

Dr. Silke Jensen
Guest Editor

Manuscript Submission Information

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Keywords

  • mobile genetic elements
  • transposable elements
  • post-transcriptional silencing
  • transcriptional silencing
  • small RNA
  • chromatin structure
  • epigenetics
  • genome plasticity

Published Papers (1 paper)

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Research

Article
Quadruplex-Forming Motif Inserted into 3′UTR of Ty1his3-AI Retrotransposon Inhibits Retrotransposition in Yeast
Biology 2021, 10(4), 347; https://doi.org/10.3390/biology10040347 - 20 Apr 2021
Viewed by 459
Abstract
Guanine quadruplexes (G4s) serve as regulators of replication, recombination and gene expression. G4 motifs have been recently identified in LTR retrotransposons, but their role in the retrotransposon life-cycle is yet to be understood. Therefore, we inserted G4s into the 3′UTR of Ty1his3-AI retrotransposon [...] Read more.
Guanine quadruplexes (G4s) serve as regulators of replication, recombination and gene expression. G4 motifs have been recently identified in LTR retrotransposons, but their role in the retrotransposon life-cycle is yet to be understood. Therefore, we inserted G4s into the 3′UTR of Ty1his3-AI retrotransposon and measured the frequency of retrotransposition in yeast strains BY4741, Y00509 (without Pif1 helicase) and with G4-stabilization by N-methyl mesoporphyrin IX (NMM) treatment. We evaluated the impact of G4s on mRNA levels by RT-qPCR and products of reverse transcription by Southern blot analysis. We found that the presence of G4 inhibited Ty1his3-AI retrotransposition. The effect was stronger when G4s were on a transcription template strand which leads to reverse transcription interruption. Both NMM and Pif1p deficiency reduced the retrotransposition irrespective of the presence of a G4 motif in the Ty1his3-AI element. Quantity of mRNA and products of reverse transcription did not fully explain the impact of G4s on Ty1his3-AI retrotransposition indicating that G4s probably affect some other steps of the retrotransposon life-cycle (e.g., translation, VLP formation, integration). Our results suggest that G4 DNA conformation can tune the activity of mobile genetic elements that in turn contribute to shaping the eukaryotic genomes. Full article
(This article belongs to the Special Issue Regulation of Mobile Genetic Elements at the Molecular Level)
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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.

Title: Bioinformatics and Machine Learning Approaches to Understand Mobile Genetic Elements
Authors: Ilektra-Chara Giassa; Eva Klimentova; Panagiotis Alexiou
Affiliation: CEITEC – Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
Abstract: Transposable elements (TEs, or mobile genetic elements, MGEs) are ubiquitous genetic elements that make up a substantial proportion of the genome of many species. The recent growing interest in understanding the evolution and function of TEs has revealed that TEs play a dual role in genome evolution, development, disease and drug resistance. Cells regulate TE expression, against uncontrolled activity that can lead to developmental defects and disease, using multiple strategies, such as DNA chemical modification, small RNA silencing (sRNA), chromatin modification, as well as sequence-specific repressors. Advancements in bioinformatics and machine learning approaches are increasingly contributing to the analysis of the regulation mechanisms. A plethora of tools and machine learning approaches have been developed for prediction, annotation and expression profiling of sRNAs, for methylation analysis of TEs as well as for genome-wide methylation analysis through bisulfite sequencing data. In this review, we provided a guided overview of the bioinformatic and machine learning state of the art of fields closely associated with TE regulation and function.

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