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Plants
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mRNA Metabolism in Plants
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mRNA Metabolism in Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (31 May 2020) | Viewed by 19018

Special Issue Editors

Prof. Dr. Jean-Marc Deragon

E-Mail Website
Guest Editor
Laboratoire Génome et Développement des Plantes, LGDP, UMR5096, CNRS/Université de Perpignan, 66860 Perpignan, France
Interests: plant genome; mRNA metabolism; epitranscriptomic; heat stress response
Dr. Rémy Merret

E-Mail Website
Guest Editor
Laboratoire Génome et Développement des Plantes, LGDP, UMR5096, CNRS/Université de Perpignan, 66860 Perpignan, France
Interests: mRNA metabolism; mRNA decay; translation regulation; mRNA storage; post-transcriptional regulation; heat stress response
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent extraordinary advances in our understanding of eukaryote messenger RNA (mRNA) metabolism, in part linked to the huge development of high-throughput approaches such as RNA sequencing, ribosome profiling, degradome or RIP sequencing revealed how important fine-tuning the mRNA life cycle is to proper gene expression and, more generally, organism development and stress responses.

The primary purpose is this Special Issue of Plants is to highlight these latest advances in the fast-developing area of mRNA metabolism in plants. All aspects of mRNA metabolism will be considered, including but not limited to translation regulation, mRNA modifications, mRNA splicing, and RNA-binding proteins regulation.

This Special Issue invites submissions that describe new aspects related to mRNA metabolism in different plant organisms in response to stress (biotic or abiotic) or across development. Original research papers, methods, reviews, and perspectives are welcome.

Prof. Jean-Marc Deragon
Dr. Rémy Merret
Guest Editors

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. Plants 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 2700 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

  • mRNA metabolism
  • mRNA decay
  • mRNA storage
  • mRNA modifications
  • mRNA transport
  • mRNA splicing
  • mRNA editing
  • mRNA translation
  • mRNA-binding proteins
  • epitranscriptomic
  • transcriptomic
  • genome-wide analysis

Published Papers (5 papers)

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Review

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11 pages, 846 KiB  
Review
Dynamics and Functions of Stress Granules and Processing Bodies in Plants
by Geng-Jen Jang, Jyan-Chyun Jang and Shu-Hsing Wu
Plants 2020, 9(9), 1122; https://doi.org/10.3390/plants9091122 - 30 Aug 2020
Cited by 21 | Viewed by 6205
Abstract
RNA granules, such as stress granules and processing bodies, can balance the storage, degradation, and translation of mRNAs in diverse eukaryotic organisms. The sessile nature of plants demands highly versatile strategies to respond to environmental fluctuations. In this review, we discuss recent findings [...] Read more.
RNA granules, such as stress granules and processing bodies, can balance the storage, degradation, and translation of mRNAs in diverse eukaryotic organisms. The sessile nature of plants demands highly versatile strategies to respond to environmental fluctuations. In this review, we discuss recent findings of the dynamics and functions of these RNA granules in plants undergoing developmental reprogramming or responding to environmental stresses. Special foci include the dynamic assembly, disassembly, and regulatory roles of these RNA granules in determining the fate of mRNAs. Full article
(This article belongs to the Special Issue mRNA Metabolism in Plants)
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15 pages, 1176 KiB  
Review
First Come, First Served: Sui Generis Features of the First Intron
by David Zalabák and Yoshihisa Ikeda
Plants 2020, 9(7), 911; https://doi.org/10.3390/plants9070911 - 19 Jul 2020
Cited by 6 | Viewed by 4372
Abstract
Most of the transcribed genes in eukaryotic cells are interrupted by intervening sequences called introns that are co-transcriptionally removed from nascent messenger RNA through the process of splicing. In Arabidopsis, 79% of genes contain introns and more than 60% of intron-containing genes [...] Read more.
Most of the transcribed genes in eukaryotic cells are interrupted by intervening sequences called introns that are co-transcriptionally removed from nascent messenger RNA through the process of splicing. In Arabidopsis, 79% of genes contain introns and more than 60% of intron-containing genes undergo alternative splicing (AS), which ostensibly is considered to increase protein diversity as one of the intrinsic mechanisms for fitness to the varying environment or the internal developmental program. In addition, recent findings have prevailed in terms of overlooked intron functions. Here, we review recent progress in the underlying mechanisms of intron function, in particular by focusing on unique features of the first intron that is located in close proximity to the transcription start site. The distinct deposition of epigenetic marks and nucleosome density on the first intronic DNA sequence, the impact of the first intron on determining the transcription start site and elongation of its own expression (called intron-mediated enhancement, IME), translation control in 5′-UTR, and the new mechanism of the trans-acting function of the first intron in regulating gene expression at the post-transcriptional level are summarized. Full article
(This article belongs to the Special Issue mRNA Metabolism in Plants)
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11 pages, 506 KiB  
Review
Long-Distance Movement of mRNAs in Plants
by Chao Xia and Cankui Zhang
Plants 2020, 9(6), 731; https://doi.org/10.3390/plants9060731 - 10 Jun 2020
Cited by 9 | Viewed by 3121
Abstract
Long-distance transport of information molecules in the vascular tissues could play an important role in regulating plant growth and enabling plants to cope with adverse environments. Various molecules, including hormones, proteins, small peptides and small RNAs have been detected in the vascular system [...] Read more.
Long-distance transport of information molecules in the vascular tissues could play an important role in regulating plant growth and enabling plants to cope with adverse environments. Various molecules, including hormones, proteins, small peptides and small RNAs have been detected in the vascular system and proved to have systemic signaling functions. Sporadic studies have shown that a number of mRNAs produced in the mature leaves leave their origin cells and move to distal tissues to exert important physiological functions. In the last 3–5 years, multiple heterograft systems have been developed to demonstrate that a large quantity of mRNAs are mobile in plants. Further comparison of the mobile mRNAs identified from these systems showed that the identities of these mRNAs are very diverse. Although species-specific mRNAs may regulate the unique physiological characteristic of the plant, mRNAs with conserved functions across multiple species are worth more effort in identifying universal physiological mechanisms existing in the plant kingdom. Full article
(This article belongs to the Special Issue mRNA Metabolism in Plants)
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Other

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10 pages, 2245 KiB  
Technical Note
Fast and Efficient 5′P Degradome Library Preparation for Analysis of Co-Translational Decay in Arabidopsis
by Marie-Christine Carpentier, Cécile Bousquet-Antonelli and Rémy Merret
Plants 2021, 10(3), 466; https://doi.org/10.3390/plants10030466 - 01 Mar 2021
Cited by 5 | Viewed by 2272
Abstract
The recent development of high-throughput technologies based on RNA sequencing has allowed a better description of the role of post-transcriptional regulation in gene expression. In particular, the development of degradome approaches based on the capture of 5′monophosphate decay intermediates allows the discovery of [...] Read more.
The recent development of high-throughput technologies based on RNA sequencing has allowed a better description of the role of post-transcriptional regulation in gene expression. In particular, the development of degradome approaches based on the capture of 5′monophosphate decay intermediates allows the discovery of a new decay pathway called co-translational mRNA decay. Thanks to these approaches, ribosome dynamics could now be revealed by analysis of 5′P reads accumulation. However, library preparation could be difficult to set-up for non-specialists. Here, we present a fast and efficient 5′P degradome library preparation for Arabidopsis samples. Our protocol was designed without commercial kit and gel purification and can be easily done in one working day. We demonstrated the robustness and the reproducibility of our protocol. Finally, we present the bioinformatic reads-outs necessary to assess library quality control. Full article
(This article belongs to the Special Issue mRNA Metabolism in Plants)
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11 pages, 1667 KiB  
Brief Report
Long-Distance Movement of Mineral Deficiency-Responsive mRNAs in Nicotiana Benthamiana/Tomato Heterografts
by Chao Xia, Jing Huang, Hai Lan and Cankui Zhang
Plants 2020, 9(7), 876; https://doi.org/10.3390/plants9070876 - 10 Jul 2020
Cited by 6 | Viewed by 2343
Abstract
Deficiencies in essential mineral nutrients such as nitrogen (N), phosphorus (P), and iron (Fe) severely limit plant growth and crop yield. It has been discovered that both the local sensing system in roots and shoot-to-root systemic signaling via the phloem are involved in [...] Read more.
Deficiencies in essential mineral nutrients such as nitrogen (N), phosphorus (P), and iron (Fe) severely limit plant growth and crop yield. It has been discovered that both the local sensing system in roots and shoot-to-root systemic signaling via the phloem are involved in the regulation of the adaptive alterations in roots, in response to mineral deficiency. mRNAs are one group of molecules with systemic signaling functions in response to intrinsic and environmental cues; however, the importance of shoot-to-root mobile mRNAs stimulated by low mineral levels is not fully understood. In this study, we established a Nicotiana benthamiana/tomato heterograft system to identify shoot-to-root mobile mRNAs that are produced in response to low N, P or Fe. Multiple long-distance mobile mRNAs were identified to be associated with low mineral levels and a few of them may play important roles in hormonal metabolism and root architecture alteration. A comparison of the mobile mRNAs from our study with those identified from previous studies showed that very few transcripts are conserved among different species. Full article
(This article belongs to the Special Issue mRNA Metabolism in Plants)
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