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Cells
Special Issues
Technologies and Applications of RNA Imaging
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Technologies and Applications of RNA Imaging

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cellular Biophysics".

Deadline for manuscript submissions: closed (20 April 2023) | Viewed by 12963

Special Issue Editors

Dr. Christos K. Kontos

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
Interests: colorectal cancer; leukemia; tumor biomarkers; anticancer drugs; apoptosis; BCL2 family; alternative splicing; kallikrein-related peptidases (KLKs); nanopore sequencing; next-generation sequencing (NGS)
Special Issues, Collections and Topics in MDPI journals
Dr. Mona Batish

E-Mail Website
Guest Editor
Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
Interests: RNA biology; single molecule RNA imaging; regulation of transcription; post transcriptional modification; non-coding RNA; Ewing's sarcoma
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

RNA imaging is a transformative technology that has enabled us to answer questions about the dynamics of gene expression. With the advent of single molecule RNA imaging, multiplexing, co-labeling of RNAs with proteins, a number of basic biology phenomena have been understood. Such technologies have also enabled a number of translational applications. The most noteworthy breakthrough of the impact of RNA biology is the development of RNA vaccines for Coronavirus in a historic record time. Thus, this is a perfect time to launch a Special Issue on technologies and applications of RNA imaging.

Therefore, we would like to solicit research articles, reviews and commentaries pertaining to development, applications, challenges and future directions in the field of RNA imaging. It will be a great opportunity to showcase your novel work and share the innovative ideas with like-minded scientists across the world. Articles with insights from a perspective of Cell and Molecular Biology are especially welcome. Relevant topics include—but are not limited to—regulation of gene expression, method development for RNA imaging, imaging RNA–protein interactions, applications of RNA imaging in diverse systems, single molecule RNA imaging to address transcriptional heterogeneity, and any other topics related to the imaging of RNA in any biological context.

Dr. Christos K. Kontos
Dr. Mona Batish
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. Cells 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

  • RNA imaging
  • single molecule RNA imaging
  • gene expression
  • multiplexing
  • RNA biology
  • RNA–protein interactions

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Published Papers (3 papers)

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Research

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19 pages, 6269 KiB  
Article
The Association of MEG3 lncRNA with Nuclear Speckles in Living Cells
by Sarah E. Hasenson, Ella Alkalay, Mohammad K. Atrash, Alon Boocholez, Julianna Gershbaum, Hodaya Hochberg-Laufer and Yaron Shav-Tal
Cells 2022, 11(12), 1942; https://doi.org/10.3390/cells11121942 - 16 Jun 2022
Cited by 5 | Viewed by 3366
Abstract
Nuclear speckles are nuclear bodies containing RNA-binding proteins as well as RNAs including long non-coding RNAs (lncRNAs). Maternally expressed gene 3 (MEG3) is a nuclear retained lncRNA found to associate with nuclear speckles. To understand the association dynamics of MEG3 lncRNA with nuclear [...] Read more.
Nuclear speckles are nuclear bodies containing RNA-binding proteins as well as RNAs including long non-coding RNAs (lncRNAs). Maternally expressed gene 3 (MEG3) is a nuclear retained lncRNA found to associate with nuclear speckles. To understand the association dynamics of MEG3 lncRNA with nuclear speckles in living cells, we generated a fluorescently tagged MEG3 transcript that could be detected in real time. Under regular conditions, transient association of MEG3 with nuclear speckles was observed, including a nucleoplasmic fraction. Transcription or splicing inactivation conditions, known to affect nuclear speckle structure, showed prominent and increased association of MEG3 lncRNA with the nuclear speckles, specifically forming a ring-like structure around the nuclear speckles. This contrasted with metastasis-associated lung adenocarcinoma (MALAT1) lncRNA that is normally highly associated with nuclear speckles, which was released and dispersed in the nucleoplasm. Under normal conditions, MEG3 dynamically associated with the periphery of the nuclear speckles, but under transcription or splicing inhibition, MEG3 could also enter the center of the nuclear speckle. Altogether, using live-cell imaging approaches, we find that MEG3 lncRNA is a transient resident of nuclear speckles and that its association with this nuclear body is modulated by the levels of transcription and splicing activities in the cell. Full article
(This article belongs to the Special Issue Technologies and Applications of RNA Imaging)
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20 pages, 4075 KiB  
Article
Analysis of the Expression and Subcellular Distribution of eEF1A1 and eEF1A2 mRNAs during Neurodevelopment
by Zoe Wefers, Celia Alecki, Ryan Huang, Suleima Jacob-Tomas and Maria Vera
Cells 2022, 11(12), 1877; https://doi.org/10.3390/cells11121877 - 9 Jun 2022
Cited by 7 | Viewed by 3530
Abstract
Neurodevelopment is accompanied by a precise change in the expression of the translation elongation factor 1A variants from eEF1A1 to eEF1A2. These are paralogue genes that encode 92% identical proteins in mammals. The switch in the expression of eEF1A variants has been well [...] Read more.
Neurodevelopment is accompanied by a precise change in the expression of the translation elongation factor 1A variants from eEF1A1 to eEF1A2. These are paralogue genes that encode 92% identical proteins in mammals. The switch in the expression of eEF1A variants has been well studied in mouse motor neurons, which solely express eEF1A2 by four weeks of postnatal development. However, changes in the subcellular localization of eEF1A variants during neurodevelopment have not been studied in detail in other neuronal types because antibodies lack perfect specificity, and immunofluorescence has a low sensitivity. In hippocampal neurons, eEF1A is related to synaptic plasticity and memory consolidation, and decreased eEF1A expression is observed in the hippocampus of Alzheimer’s patients. However, the specific variant involved in these functions is unknown. To distinguish eEF1A1 from eEF1A2 expression, we have designed single-molecule fluorescence in-situ hybridization probes to detect either eEF1A1 or eEF1A2 mRNAs in cultured primary hippocampal neurons and brain tissues. We have developed a computational framework, ARLIN (analysis of RNA localization in neurons), to analyze and compare the subcellular distribution of eEF1A1 and eEF1A2 mRNAs at specific developmental stages and in mature neurons. We found that eEF1A1 and eEF1A2 mRNAs differ in expression and subcellular localization over neurodevelopment, and eEF1A1 mRNAs localize in dendrites and synapses during dendritogenesis and synaptogenesis. Interestingly, mature hippocampal neurons coexpress both variant mRNAs, and eEF1A1 remains the predominant variant in dendrites. Full article
(This article belongs to the Special Issue Technologies and Applications of RNA Imaging)
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Review

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26 pages, 2691 KiB  
Review
Technologies Enabling Single-Molecule Super-Resolution Imaging of mRNA
by Mark Tingey, Steven J. Schnell, Wenlan Yu, Jason Saredy, Samuel Junod, Dhrumil Patel, Abdullah A. Alkurdi and Weidong Yang
Cells 2022, 11(19), 3079; https://doi.org/10.3390/cells11193079 - 30 Sep 2022
Cited by 10 | Viewed by 5000
Abstract
The transient nature of RNA has rendered it one of the more difficult biological targets for imaging. This difficulty stems both from the physical properties of RNA as well as the temporal constraints associated therewith. These concerns are further complicated by the difficulty [...] Read more.
The transient nature of RNA has rendered it one of the more difficult biological targets for imaging. This difficulty stems both from the physical properties of RNA as well as the temporal constraints associated therewith. These concerns are further complicated by the difficulty in imaging endogenous RNA within a cell that has been transfected with a target sequence. These concerns, combined with traditional concerns associated with super-resolution light microscopy has made the imaging of this critical target difficult. Recent advances have provided researchers the tools to image endogenous RNA in live cells at both the cellular and single-molecule level. Here, we review techniques used for labeling and imaging RNA with special emphases on various labeling methods and a virtual 3D super-resolution imaging technique. Full article
(This article belongs to the Special Issue Technologies and Applications of RNA Imaging)
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