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Special Issue Editors

Dr. Epaminondas Doxakis

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Guest Editor

Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
Interests: RNA-binding proteins and neurodegeneration; microRNAs and circRNAs as peripheral biomarkers; impact of microRNAs and circRNAs on neuronal function; therapeutic interventions in neurodegeneration
Special Issues, Collections and Topics in MDPI journals

Dr. Stylianos Ravanidis

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Guest Editor

Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
Interests: RNA-binding proteins and neurodegeneration; non-coding RNAs as peripheral biomarkers; neuronal function; neuroimmune interactions; immunomodulatory treatments
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The recognition of the critical role of alternative RNA processing, regulatory RNAs, and RNA-mediated enzymatic mechanisms in the regulation of gene expression, as well as the role of RNAs in normal development and disease pathogenesis, have made an understanding of the field of RNA biology central for all life science disciplines.

The purpose of this Special Issue is to further our knowledge with novel insights into RNA functions. We welcome both original research and review papers on any of the following specific topics:

RNA motifs, splicing and alternative polyadenylation mechanisms, subcellular localization, translation, and decay.
RNA interactions with DNA or RNA-binding proteins.
Regulatory functions of circRNAs, tiRNAs, tRFs, and lncRNAs.
Non-coding RNAs in disease pathogenesis.

Dr. Epaminondas Doxakis
Dr. Stylianos Ravanidis
Guest Editors

Manuscript Submission Information

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Keywords

RNA
motif
circRNA
tRNA fragments
lncRNA
RNA-binding proteins
alternative polyadenylation
subcellular localization
translation
decay

Published Papers (2 papers)

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Research

Jump to: Review

21 pages, 3855 KiB

Open AccessArticle

Identification of Pri-miRNA Stem-Loop Interacting Proteins in Plants Using a Modified Version of the Csy4 CRISPR Endonuclease

by Janina Lüders, Andreas R. Winkel, Marlene Reichel, Valentin W. Bitterer, Marion Scheibe, Christiane Widmann, Falk Butter and Tino Köster

Int. J. Mol. Sci. 2022, 23(16), 8961; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23168961 - 11 Aug 2022

Cited by 1 | Viewed by 1792

Abstract

Regulation at the RNA level by RNA-binding proteins (RBPs) and microRNAs (miRNAs) is key to coordinating eukaryotic gene expression. In plants, the importance of miRNAs is highlighted by severe developmental defects in mutants impaired in miRNA biogenesis. MiRNAs are processed from long primary-microRNAs (pri-miRNAs) with internal stem-loop structures by endonucleolytic cleavage. The highly structured stem-loops constitute the basis for the extensive regulation of miRNA biogenesis through interaction with RBPs. However, trans-acting regulators of the biogenesis of specific miRNAs are largely unknown in plants. Therefore, we exploit an RNA-centric approach based on modified versions of the conditional CRISPR nuclease Csy4* to pull down interactors of the Arabidopsis pri-miR398b stem-loop (pri-miR398b-SL) in vitro. We designed three epitope-tagged versions of the inactive Csy4* for the immobilization of the protein together with the pri-miR398b-SL bait on high affinity matrices. After incubation with nucleoplasmic extracts from Arabidopsis and extensive washing, pri-miR398b-SL, along with its specifically bound proteins, were released by re-activating the cleavage activity of the Csy4* upon the addition of imidazole. Co-purified proteins were identified via quantitative mass spectrometry and data sets were compared. In total, we identified more than 400 different proteins, of which 180 are co-purified in at least two out of three independent Csy4*-based RNA pulldowns. Among those, the glycine-rich RNA-binding protein AtRZ-1a was identified in all pulldowns. To analyze the role of AtRZ-1a in miRNA biogenesis, we determined the miR398 expression level in the atrz-1a mutant. Indeed, the absence of AtRZ-1a caused a decrease in the steady-state level of mature miR398 with a concomitant reduction in pri-miR398b levels. Overall, we show that our modified Csy4*-based RNA pulldown strategy is suitable to identify new trans-acting regulators of miRNA biogenesis and provides new insights into the post-transcriptional regulation of miRNA processing by plant RBPs. Full article

(This article belongs to the Special Issue Novel Insights into the Life Cycle of RNA Molecules)

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Review

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26 pages, 1726 KiB

Open AccessReview

Tweaking the Small Non-Coding RNAs to Improve Desirable Traits in Plant

by Koushik Halder, Abira Chaudhuri, Malik Z. Abdin and Asis Datta

Int. J. Mol. Sci. 2023, 24(4), 3143; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24043143 - 05 Feb 2023

Cited by 4 | Viewed by 1838

Abstract

Plant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants’ response to biotic/abiotic stresses. Typically, 20–30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here. Full article

(This article belongs to the Special Issue Novel Insights into the Life Cycle of RNA Molecules)

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