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ncRNA
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Non-Coding RNA and Intracellular Structures
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Non-Coding RNA and Intracellular Structures

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

Deadline for manuscript submissions: closed (31 March 2020) | Viewed by 74592

Special Issue Editors

Prof. Dr. Tetsuro Hirose

E-Mail Website
Guest Editor
Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
Interests: lncRNAs; RNP complex; Cell organization by liquid phase separation
Prof. Dr. Shinichi Nakagawa

grade E-Mail Website
Guest Editor
RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
Interests: lncRNAs; nuclear structures; paraspeckles; animal models

Special Issue Information

Dear Colleagues,

Multiple non-coding RNAs (ncRNAs) can be found in various intracellular structures, where they perform regulatory functions by recruiting specific proteins, RNAs, and chromatin loci. Some of these ncRNAs are present in heterochromatins and regulate their formation and/or maintenance by recruiting specific epigenetic regulatory proteins to the site of their accumulation. Other ncRNAs act as structural scaffolds of intracellular bodies without membranes by sequestering a specific set of RNA-binding proteins that contain an intrinsically-disordered domain, which triggers the liquid–liquid phase transition or hydrogel formation under certain conditions. Other ncRNAs have been reported to preferentially interact with a non-classical binding partner, such as membrane-lipids. The accumulating evidence regarding the distribution and interaction partners of ncRNAs suggest that ncRNAs localized in intracellular structures arrange the formation of a specific microenvironment consisting of the ncRNAs and their binding proteins around the respective ncRNA molecules. This Special Issue on non-coding RNAs and intracellular structures aims to unravel the diverse roles of ncRNAs in the formation and regulation of RNA-related intracellular structures, especially focusing on the molecular mechanisms and the physiological consequences.

Prof. Tetsuro Hirose
Prof. Shinichi Nakagawa
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. Non-Coding RNA 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 1800 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

  • non-coding RNA 
  • chromatin 
  • nuclear bodies 
  • RNP complex 
  • phase separation 
  • animal model

Published Papers (10 papers)

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Review

17 pages, 763 KiB  
Review
MALAT1 Long Non-Coding RNA: Functional Implications
by Gayatri Arun, Disha Aggarwal and David L. Spector
Non-Coding RNA 2020, 6(2), 22; https://0-doi-org.brum.beds.ac.uk/10.3390/ncrna6020022 - 03 Jun 2020
Cited by 115 | Viewed by 9515
Abstract
The mammalian genome is pervasively transcribed and the functional significance of many long non-coding RNA (lncRNA) transcripts are gradually being elucidated. Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) is one of the most well-studied lncRNAs. MALAT1 is a highly conserved nuclear [...] Read more.
The mammalian genome is pervasively transcribed and the functional significance of many long non-coding RNA (lncRNA) transcripts are gradually being elucidated. Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) is one of the most well-studied lncRNAs. MALAT1 is a highly conserved nuclear retained lncRNA that is abundantly expressed in cells and tissues and has been shown to play a role in regulating genes at both the transcriptional and post-transcriptional levels in a context-dependent manner. However, Malat1 has been shown to be dispensable for normal development and viability in mice. Interestingly, accumulating evidence suggests that MALAT1 plays an important role in numerous diseases including cancer. Here, we discuss the current state-of-knowledge in regard to MALAT1 with respect to its function, role in diseases, and the potential therapeutic opportunities for targeting MALAT1 using antisense oligonucleotides and small molecules. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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12 pages, 976 KiB  
Review
Genome-Wide Technologies to Study RNA–Chromatin Interactions
by Masaki Kato and Piero Carninci
Non-Coding RNA 2020, 6(2), 20; https://0-doi-org.brum.beds.ac.uk/10.3390/ncrna6020020 - 27 May 2020
Cited by 16 | Viewed by 6932
Abstract
An increasing number of studies have revealed that long non-coding RNAs (lncRNAs) play important roles in gene regulation and nuclear organization. Although the mechanisms are still largely unknown, many lncRNAs have been shown to interact with chromatin. Thus, one approach to understanding the [...] Read more.
An increasing number of studies have revealed that long non-coding RNAs (lncRNAs) play important roles in gene regulation and nuclear organization. Although the mechanisms are still largely unknown, many lncRNAs have been shown to interact with chromatin. Thus, one approach to understanding the function of these lncRNAs is to identify their sites of genomic interaction. Hybridization capture methods using oligonucleotide probes have been used for years to study chromatin-associated RNA. Recently, several groups have developed novel methods based on proximity ligation to investigate RNA–chromatin interactions at a genome-wide scale. This review discusses these technologies and highlights their advantages and disadvantages for the consideration of potential users. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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15 pages, 2757 KiB  
Review
The Emerging Role of ncRNAs and RNA-Binding Proteins in Mitotic Apparatus Formation
by Kei K. Ito, Koki Watanabe and Daiju Kitagawa
Non-Coding RNA 2020, 6(1), 13; https://0-doi-org.brum.beds.ac.uk/10.3390/ncrna6010013 - 20 Mar 2020
Cited by 12 | Viewed by 10119
Abstract
Mounting experimental evidence shows that non-coding RNAs (ncRNAs) serve a wide variety of biological functions. Recent studies suggest that a part of ncRNAs are critically important for supporting the structure of subcellular architectures. Here, we summarize the current literature demonstrating the role of [...] Read more.
Mounting experimental evidence shows that non-coding RNAs (ncRNAs) serve a wide variety of biological functions. Recent studies suggest that a part of ncRNAs are critically important for supporting the structure of subcellular architectures. Here, we summarize the current literature demonstrating the role of ncRNAs and RNA-binding proteins in regulating the assembly of mitotic apparatus, especially focusing on centrosomes, kinetochores, and mitotic spindles. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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9 pages, 964 KiB  
Review
Short Tandem Repeat-Enriched Architectural RNAs in Nuclear Bodies: Functions and Associated Diseases
by Kensuke Ninomiya and Tetsuro Hirose
Non-Coding RNA 2020, 6(1), 6; https://0-doi-org.brum.beds.ac.uk/10.3390/ncrna6010006 - 20 Feb 2020
Cited by 22 | Viewed by 5551
Abstract
Nuclear bodies are membraneless, phase-separated compartments that concentrate specific proteins and RNAs in the nucleus. They are believed to serve as sites for the modification, sequestration, and storage of specific factors, and to act as organizational hubs of chromatin structure to control gene [...] Read more.
Nuclear bodies are membraneless, phase-separated compartments that concentrate specific proteins and RNAs in the nucleus. They are believed to serve as sites for the modification, sequestration, and storage of specific factors, and to act as organizational hubs of chromatin structure to control gene expression and cellular function. Architectural (arc) RNA, a class of long noncoding RNA (lncRNA), plays essential roles in the formation of nuclear bodies. Herein, we focus on specific arcRNAs containing short tandem repeat-enriched sequences and introduce their biological functions and recently elucidated underlying molecular mechanism. In various neurodegenerative diseases, abnormal nuclear and cytoplasmic bodies are built on disease-causing RNAs or toxic RNAs with aberrantly expanded short tandem repeat-enriched sequences. We discuss the possible analogous functions of natural arcRNAs and toxic RNAs with short tandem repeat-enriched sequences. Finally, we describe the technical utility of short tandem repeat-enriched arcRNAs as a model for exploring the structures and functions of nuclear bodies, as well as the pathogenic mechanisms of neurodegenerative diseases. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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12 pages, 1927 KiB  
Review
Centromeric Non-Coding RNAs: Conservation and Diversity in Function
by Takashi Ideue and Tokio Tani
Non-Coding RNA 2020, 6(1), 4; https://0-doi-org.brum.beds.ac.uk/10.3390/ncrna6010004 - 17 Jan 2020
Cited by 9 | Viewed by 4766
Abstract
Chromosome segregation is strictly regulated for the proper distribution of genetic material to daughter cells. During this process, mitotic chromosomes are pulled to both poles by bundles of microtubules attached to kinetochores that are assembled on the chromosomes. Centromeres are specific regions where [...] Read more.
Chromosome segregation is strictly regulated for the proper distribution of genetic material to daughter cells. During this process, mitotic chromosomes are pulled to both poles by bundles of microtubules attached to kinetochores that are assembled on the chromosomes. Centromeres are specific regions where kinetochores assemble. Although these regions were previously considered to be silent, some experimental studies have demonstrated that transcription occurs in these regions to generate non-coding RNAs (ncRNAs). These centromeric ncRNAs (cenRNAs) are involved in centromere functions. Here, we describe the currently available information on the functions of cenRNAs in several species. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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8 pages, 1001 KiB  
Review
Identification of Genomic Loci Responsible for the Formation of Nuclear Domains Using Lampbrush Chromosomes
by Alla Krasikova and Tatiana Kulikova
Non-Coding RNA 2020, 6(1), 1; https://0-doi-org.brum.beds.ac.uk/10.3390/ncrna6010001 - 25 Dec 2019
Cited by 4 | Viewed by 4238
Abstract
In the cell nuclei, various types of nuclear domains assemble as a result of transcriptional activity at specific chromosomal loci. Giant transcriptionally active lampbrush chromosomes, which form in oocyte nuclei of amphibians and birds enable the mapping of genomic sequences with high resolution [...] Read more.
In the cell nuclei, various types of nuclear domains assemble as a result of transcriptional activity at specific chromosomal loci. Giant transcriptionally active lampbrush chromosomes, which form in oocyte nuclei of amphibians and birds enable the mapping of genomic sequences with high resolution and the visualization of individual transcription units. This makes avian and amphibian oocyte nuclei an advantageous model for studying locus-specific nuclear domains. We developed two strategies for identification and comprehensive analysis of the genomic loci involved in nuclear domain formation on lampbrush chromosomes. The first approach was based on the sequential FISH-mapping of BAC clones containing genomic DNA fragments with a known chromosomal position close to the locus of a nuclear domain. The second approach involved mechanical microdissection of the chromosomal region adjacent to the nuclear domain followed by the generation of FISH-probes and DNA sequencing. Furthermore, deciphering the DNA sequences from the dissected material by high throughput sequencing technologies and their mapping to the reference genome helps to identify the genomic region responsible for the formation of the nuclear domain. For those nuclear domains structured by nascent transcripts, identification of genomic loci of their formation is a crucial step in the identification of scaffold RNAs. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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28 pages, 2482 KiB  
Review
Understanding Long Noncoding RNA and Chromatin Interactions: What We Know So Far
by Kankadeb Mishra and Chandrasekhar Kanduri
Non-Coding RNA 2019, 5(4), 54; https://0-doi-org.brum.beds.ac.uk/10.3390/ncrna5040054 - 03 Dec 2019
Cited by 69 | Viewed by 8001
Abstract
With the evolution of technologies that deal with global detection of RNAs to probing of lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we have been updated with a comprehensive repertoire of chromatin interacting lncRNAs, their genome-wide chromatin binding regions and mode of action. Evidence [...] Read more.
With the evolution of technologies that deal with global detection of RNAs to probing of lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we have been updated with a comprehensive repertoire of chromatin interacting lncRNAs, their genome-wide chromatin binding regions and mode of action. Evidence from these new technologies emphasize that chromatin targeting of lncRNAs is a prominent mechanism and that these chromatin targeted lncRNAs exert their functionality by fine tuning chromatin architecture resulting in an altered transcriptional readout. Currently, there are no unifying principles that define chromatin association of lncRNAs, however, evidence from a few chromatin-associated lncRNAs show presence of a short common sequence for chromatin targeting. In this article, we review how technological advancements contributed in characterizing chromatin associated lncRNAs, and discuss the potential mechanisms by which chromatin associated lncRNAs execute their functions. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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Figure 1

15 pages, 1666 KiB  
Review
Assembly and Function of Gonad-Specific Non-Membranous Organelles in Drosophila piRNA Biogenesis
by Shigeki Hirakata and Mikiko C. Siomi
Non-Coding RNA 2019, 5(4), 52; https://0-doi-org.brum.beds.ac.uk/10.3390/ncrna5040052 - 06 Nov 2019
Cited by 6 | Viewed by 6539
Abstract
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that repress transposons in animal germlines. This protects the genome from the invasive DNA elements. piRNA pathway failures lead to DNA damage, gonadal development defects, and infertility. Thus, the piRNA pathway is indispensable for the continuation [...] Read more.
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that repress transposons in animal germlines. This protects the genome from the invasive DNA elements. piRNA pathway failures lead to DNA damage, gonadal development defects, and infertility. Thus, the piRNA pathway is indispensable for the continuation of animal life. piRNA-mediated transposon silencing occurs in both the nucleus and cytoplasm while piRNA biogenesis is a solely cytoplasmic event. piRNA production requires a number of proteins, the majority of which localize to non-membranous organelles that specifically appear in the gonads. Other piRNA factors are localized on outer mitochondrial membranes. In situ RNA hybridization experiments show that piRNA precursors are compartmentalized into other non-membranous organelles. In this review, we summarize recent findings about the function of these organelles in the Drosophila piRNA pathway by focusing on their assembly and function. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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Figure 1

14 pages, 1191 KiB  
Review
Evidence for and against Liquid-Liquid Phase Separation in the Nucleus
by Peng A and Stephanie C. Weber
Non-Coding RNA 2019, 5(4), 50; https://0-doi-org.brum.beds.ac.uk/10.3390/ncrna5040050 - 01 Nov 2019
Cited by 115 | Viewed by 13346
Abstract
Enclosed by two membranes, the nucleus itself is comprised of various membraneless compartments, including nuclear bodies and chromatin domains. These compartments play an important though still poorly understood role in gene regulation. Significant progress has been made in characterizing the dynamic behavior of [...] Read more.
Enclosed by two membranes, the nucleus itself is comprised of various membraneless compartments, including nuclear bodies and chromatin domains. These compartments play an important though still poorly understood role in gene regulation. Significant progress has been made in characterizing the dynamic behavior of nuclear compartments and liquid-liquid phase separation (LLPS) has emerged as a prominent mechanism governing their assembly. However, recent work reveals that certain nuclear structures violate key predictions of LLPS, suggesting that alternative mechanisms likely contribute to nuclear organization. Here, we review the evidence for and against LLPS for several nuclear compartments and discuss experimental strategies to identify the mechanism(s) underlying their assembly. We propose that LLPS, together with multiple modes of protein-nucleic acid binding, drive spatiotemporal organization of the nucleus and facilitate functional diversity among nuclear compartments. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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7 pages, 796 KiB  
Review
meiRNA, A Polyvalent Player in Fission Yeast Meiosis
by Akira Yamashita
Non-Coding RNA 2019, 5(3), 45; https://0-doi-org.brum.beds.ac.uk/10.3390/ncrna5030045 - 17 Sep 2019
Cited by 10 | Viewed by 4535
Abstract
A growing number of recent studies have revealed that non-coding RNAs play a wide variety of roles beyond expectation. A lot of non-coding RNAs have been shown to function by forming intracellular structures either in the nucleus or the cytoplasm. In the fission [...] Read more.
A growing number of recent studies have revealed that non-coding RNAs play a wide variety of roles beyond expectation. A lot of non-coding RNAs have been shown to function by forming intracellular structures either in the nucleus or the cytoplasm. In the fission yeast Schizosaccharomyces pombe, a non-coding RNA termed meiRNA has been shown to play multiple vital roles in the course of meiosis. meiRNA is tethered to its genetic locus after transcription and forms a peculiar intranuclear dot structure. It ensures stable expression of meiotic genes in cooperation with an RNA-binding protein Mei2. Chromosome-associated meiRNA also facilitates recognition of homologous chromosome loci and induces robust pairing. In this review, the quarter-century history of meiRNA, from its identification to functional characterization, will be outlined. Full article
(This article belongs to the Special Issue Non-Coding RNA and Intracellular Structures)
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