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Volume 6, June

Non-Coding RNA, Volume 6, Issue 3 (September 2020) – 16 articles

Cover Story (view full-size image): Non-coding RNAs are grouped by size, where those smaller than 200 nucleotides are defined as small non-coding RNAs and those longer than 200 nt are defined as long non-coding RNAs. The ncRNAs are key regulators in a wide range of cellular processes such as transcription, translation, RNA processing, and signalling. The lncRNAs can function via three general mechanisms: interaction with DNA, RNA modulation, and protein modulation. They are commonly dysregulated in disease and have recently been implicated in cancer. Many lncRNAs are differentially expressed in NSCLC, where, generally, upregulated lncRNAs function as tumour promoters and downregulated lncRNAs function as tumour suppressors. However, their precise mechanisms that lead to alterations in cancer cell proliferation, survival, migration, invasion, epithelial-to-mesenchymal transition (EMT), and metastasis are not fully understood. View this [...] Read more.
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Review
Long Non-Coding RNA-Ribonucleoprotein Networks in the Post-Transcriptional Control of Gene Expression
Non-Coding RNA 2020, 6(3), 40; https://doi.org/10.3390/ncrna6030040 - 17 Sep 2020
Cited by 6 | Viewed by 2799
Abstract
Although mammals possess roughly the same number of protein-coding genes as worms, it is evident that the non-coding transcriptome content has become far broader and more sophisticated during evolution. Indeed, the vital regulatory importance of both short and long non-coding RNAs (lncRNAs) has [...] Read more.
Although mammals possess roughly the same number of protein-coding genes as worms, it is evident that the non-coding transcriptome content has become far broader and more sophisticated during evolution. Indeed, the vital regulatory importance of both short and long non-coding RNAs (lncRNAs) has been demonstrated during the last two decades. RNA binding proteins (RBPs) represent approximately 7.5% of all proteins and regulate the fate and function of a huge number of transcripts thus contributing to ensure cellular homeostasis. Transcriptomic and proteomic studies revealed that RBP-based complexes often include lncRNAs. This review will describe examples of how lncRNA-RBP networks can virtually control all the post-transcriptional events in the cell. Full article
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Article
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora
Non-Coding RNA 2020, 6(3), 39; https://doi.org/10.3390/ncrna6030039 - 11 Sep 2020
Cited by 2 | Viewed by 3135
Abstract
Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed [...] Read more.
Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed to provide a curated characterization of six ncRNA classes in the Coffea canephora genome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in the C. canephora genome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity. Full article
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Review
Non-Coding RNAs: Strategy for Viruses’ Offensive
Non-Coding RNA 2020, 6(3), 38; https://doi.org/10.3390/ncrna6030038 - 10 Sep 2020
Cited by 1 | Viewed by 2772
Abstract
The awareness of viruses as a constant threat for human public health is a matter of fact and in this resides the need of understanding the mechanisms they use to trick the host. Viral non-coding RNAs are gaining much value and interest for [...] Read more.
The awareness of viruses as a constant threat for human public health is a matter of fact and in this resides the need of understanding the mechanisms they use to trick the host. Viral non-coding RNAs are gaining much value and interest for the potential impact played in host gene regulation, acting as fine tuners of host cellular defense mechanisms. The implicit importance of v-ncRNAs resides first in the limited genomes size of viruses carrying only strictly necessary genomic sequences. The other crucial and appealing characteristic of v-ncRNAs is the non-immunogenicity, making them the perfect expedient to be used in the never-ending virus-host war. In this review, we wish to examine how DNA and RNA viruses have evolved a common strategy and which the crucial host pathways are targeted through v-ncRNAs in order to grant and facilitate their life cycle. Full article
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Review
Non-Coding RNAs in Multiple Myeloma Bone Disease Pathophysiology
Non-Coding RNA 2020, 6(3), 37; https://doi.org/10.3390/ncrna6030037 - 09 Sep 2020
Cited by 3 | Viewed by 3074
Abstract
Bone remodeling is uncoupled in the multiple myeloma (MM) bone marrow niche, resulting in enhanced osteoclastogenesis responsible of MM-related bone disease (MMBD). Several studies have disclosed the mechanisms underlying increased osteoclast formation and activity triggered by the various cellular components of the MM [...] Read more.
Bone remodeling is uncoupled in the multiple myeloma (MM) bone marrow niche, resulting in enhanced osteoclastogenesis responsible of MM-related bone disease (MMBD). Several studies have disclosed the mechanisms underlying increased osteoclast formation and activity triggered by the various cellular components of the MM bone marrow microenvironment, leading to the identification of novel targets for therapeutic intervention. In this regard, recent attention has been given to non-coding RNA (ncRNA) molecules, that finely tune gene expression programs involved in bone homeostasis both in physiological and pathological settings. In this review, we will analyze major signaling pathways involved in MMBD pathophysiology, and report emerging evidence of their regulation by different classes of ncRNAs. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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Perspective
Genesis of Non-Coding RNA Genes in Human Chromosome 22—A Sequence Connection with Protein Genes Separated by Evolutionary Time
Non-Coding RNA 2020, 6(3), 36; https://doi.org/10.3390/ncrna6030036 - 03 Sep 2020
Cited by 2 | Viewed by 2711
Abstract
A small phylogenetically conserved sequence of 11,231 bp, termed FAM247, is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or [...] Read more.
A small phylogenetically conserved sequence of 11,231 bp, termed FAM247, is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or mice genomes, and the long noncoding RNA genes and pseudogenes the most recent as they appear to be present only in the human genome. We propose that the conserved sequence provides a nucleation site for new gene development at evolutionarily conserved chromosomal loci where the FAM247 sequences reside. The FAM247 sequence also carries information in its open reading frames that provides protein exon amino acid sequences; one exon plays an integral role in immune system regulation, specifically, the function of ubiquitin-specific protease (USP18) in the regulation of interferon. An analysis of this multifaceted sequence and the genesis of genes that contain it is presented. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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Review
Non-Coding RNA Databases in Cardiovascular Research
Non-Coding RNA 2020, 6(3), 35; https://doi.org/10.3390/ncrna6030035 - 02 Sep 2020
Cited by 4 | Viewed by 3656
Abstract
Cardiovascular diseases (CVDs) are of multifactorial origin and can be attributed to several genetic and environmental components. CVDs are the leading cause of mortality worldwide and they primarily damage the heart and the vascular system. Non-coding RNA (ncRNA) refers to functional RNA molecules, [...] Read more.
Cardiovascular diseases (CVDs) are of multifactorial origin and can be attributed to several genetic and environmental components. CVDs are the leading cause of mortality worldwide and they primarily damage the heart and the vascular system. Non-coding RNA (ncRNA) refers to functional RNA molecules, which have been transcribed into DNA but do not further get translated into proteins. Recent transcriptomic studies have identified the presence of thousands of ncRNA molecules across species. In humans, less than 2% of the total genome represents the protein-coding genes. While the role of many ncRNAs is yet to be ascertained, some long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been associated with disease progression, serving as useful diagnostic and prognostic biomarkers. A plethora of data repositories specialized in ncRNAs have been developed over the years using publicly available high-throughput data from next-generation sequencing and other approaches, that cover various facets of ncRNA research like basic and functional annotation, expressional profile, structural and molecular changes, and interaction with other biomolecules. Here, we provide a compendium of the current ncRNA databases relevant to cardiovascular research. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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Review
Long Non-Coding RNAs in Liver Cancer and Nonalcoholic Steatohepatitis
Non-Coding RNA 2020, 6(3), 34; https://doi.org/10.3390/ncrna6030034 - 29 Aug 2020
Cited by 6 | Viewed by 2838
Abstract
This review aims to highlight the recent findings of long non-coding RNAs (lncRNAs) in liver disease. In particular, we focus on the functions of lncRNAs in hepatocellular carcinoma (HCC) and non-alcoholic steatohepatitis (NASH). We summarize the current research trend in lncRNAs and their [...] Read more.
This review aims to highlight the recent findings of long non-coding RNAs (lncRNAs) in liver disease. In particular, we focus on the functions of lncRNAs in hepatocellular carcinoma (HCC) and non-alcoholic steatohepatitis (NASH). We summarize the current research trend in lncRNAs and their potential as biomarkers and therapeutic targets for the treatment of HCC and NASH. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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Review
Changes in Non-Coding RNA in Depression and Bipolar Disorder: Can They Be Used as Diagnostic or Theranostic Biomarkers?
Non-Coding RNA 2020, 6(3), 33; https://doi.org/10.3390/ncrna6030033 - 24 Aug 2020
Cited by 3 | Viewed by 2765
Abstract
The similarities between the depressive symptoms of Major Depressive Disorders (MDD) and Bipolar Disorders (BD) suggest these disorders have some commonality in their molecular pathophysiologies, which is not apparent from the risk genes shared between MDD and BD. This is significant, given the [...] Read more.
The similarities between the depressive symptoms of Major Depressive Disorders (MDD) and Bipolar Disorders (BD) suggest these disorders have some commonality in their molecular pathophysiologies, which is not apparent from the risk genes shared between MDD and BD. This is significant, given the growing literature suggesting that changes in non-coding RNA may be important in both MDD and BD, because they are causing dysfunctions in the control of biochemical pathways that are affected in both disorders. Therefore, understanding the changes in non-coding RNA in MDD and BD will lead to a better understanding of how and why these disorders develop. Furthermore, as a significant number of individuals suffering with MDD and BD do not respond to medication, identifying non-coding RNA that are altered by the drugs used to treat these disorders offer the potential to identify biomarkers that could predict medication response. Such biomarkers offer the potential to quickly identify patients who are unlikely to respond to traditional medications so clinicians can refocus treatment strategies to ensure more effective outcomes for the patient. This review will focus on the evidence supporting the involvement of non-coding RNA in MDD and BD and their potential use as biomarkers for treatment response. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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Article
Comparison of Poly-A+ Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq
Non-Coding RNA 2020, 6(3), 32; https://doi.org/10.3390/ncrna6030032 - 21 Aug 2020
Cited by 3 | Viewed by 2637
Abstract
Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A+ selection. In the past 10 years, [...] Read more.
Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A+ selection. In the past 10 years, methods to perform ribosomal RNA (rRNA) depletion of total RNA have been developed as an alternative, aiming for better coverage of whole transcriptomic RNA, both polyadenylated and non-polyadenylated transcripts. The purpose of this study was to determine which library preparation method is optimal for lncRNA investigations in the horse. Using liver and cerebral parietal lobe tissues from two healthy Thoroughbred mares, RNA-seq libraries were prepared using standard poly-A+ selection and rRNA-depletion methods. Averaging the two biologic replicates, poly-A+ selection yielded 327 and 773 more unique lncRNA transcripts for liver and parietal lobe, respectively. More lncRNA were found to be unique to poly-A+ selected libraries, and rRNA-depletion identified small nucleolar RNA (snoRNA) to have a higher relative expression than in the poly-A+ selected libraries. Overall, poly-A+ selection provides a more thorough identification of total lncRNA in equine tissues while rRNA-depletion may allow for easier detection of snoRNAs. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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Retraction
Retraction: Verheijen, B.M. Expression Profile of Long Non-Coding RNAs during Early Postnatal Development of Mouse Spinal Cord. Non-Coding RNA 2020, 6, 18
Non-Coding RNA 2020, 6(3), 31; https://doi.org/10.3390/ncrna6030031 - 10 Aug 2020
Viewed by 2447
Abstract
The paper by Dr [...] Full article
Review
Emerging Insights on the Biological Impact of Extracellular Vesicle-Associated ncRNAs in Multiple Myeloma
Non-Coding RNA 2020, 6(3), 30; https://doi.org/10.3390/ncrna6030030 - 05 Aug 2020
Cited by 5 | Viewed by 3030
Abstract
Increasing evidence indicates that extracellular vesicles (EVs) released from both tumor cells and the cells of the bone marrow microenvironment contribute to the pathobiology of multiple myeloma (MM). Recent studies on the mechanisms by which EVs exert their biological activity have indicated that [...] Read more.
Increasing evidence indicates that extracellular vesicles (EVs) released from both tumor cells and the cells of the bone marrow microenvironment contribute to the pathobiology of multiple myeloma (MM). Recent studies on the mechanisms by which EVs exert their biological activity have indicated that the non-coding RNA (ncRNA) cargo is key in mediating their effect on MM development and progression. In this review, we will first discuss the role of EV-associated ncRNAs in different aspects of MM pathobiology, including proliferation, angiogenesis, bone disease development, and drug resistance. Finally, since ncRNAs carried by MM vesicles have also emerged as a promising tool for early diagnosis and therapy response prediction, we will report evidence of their potential use as clinical biomarkers. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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Review
Potential miRNAs for miRNA-Based Therapeutics in Breast Cancer
Non-Coding RNA 2020, 6(3), 29; https://doi.org/10.3390/ncrna6030029 - 13 Jul 2020
Cited by 5 | Viewed by 3242
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that can post-transcriptionally regulate the genes involved in critical cellular processes. The aberrant expressions of oncogenic or tumor suppressor miRNAs have been associated with cancer progression and malignancies. This resulted in the dysregulation of signaling pathways involved [...] Read more.
MicroRNAs (miRNAs) are small non-coding RNAs that can post-transcriptionally regulate the genes involved in critical cellular processes. The aberrant expressions of oncogenic or tumor suppressor miRNAs have been associated with cancer progression and malignancies. This resulted in the dysregulation of signaling pathways involved in cell proliferation, apoptosis and survival, metastasis, cancer recurrence and chemoresistance. In this review, we will first (i) provide an overview of the miRNA biogenesis pathways, and in vitro and in vivo models for research, (ii) summarize the most recent findings on the roles of microRNAs (miRNAs) that could potentially be used for miRNA-based therapy in the treatment of breast cancer and (iii) discuss the various therapeutic applications. Full article
(This article belongs to the Special Issue Non-Coding RNAs as Therapeutic Targets)
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Review
Macrophage Long Non-Coding RNAs in Pathogenesis of Cardiovascular Disease
Non-Coding RNA 2020, 6(3), 28; https://doi.org/10.3390/ncrna6030028 - 11 Jul 2020
Cited by 2 | Viewed by 2943
Abstract
Chronic inflammation is inextricably linked to cardiovascular disease (CVD). Macrophages themselves play important roles in atherosclerosis, as well as acute and chronic heart failure. Although the role of macrophages in CVD pathophysiology is well-recognized, little is known regarding the precise mechanisms influencing their [...] Read more.
Chronic inflammation is inextricably linked to cardiovascular disease (CVD). Macrophages themselves play important roles in atherosclerosis, as well as acute and chronic heart failure. Although the role of macrophages in CVD pathophysiology is well-recognized, little is known regarding the precise mechanisms influencing their function in these contexts. Long non-coding RNAs (lncRNAs) have emerged as significant regulators of macrophage function; as such, there is rising interest in understanding how these nucleic acids influence macrophage signaling, cell fate decisions, and activity in health and disease. In this review, we summarize current knowledge regarding lncRNAs in directing various aspects of macrophage function in CVD. These include foam cell formation, Toll-like receptor (TLR) and NF-kβ signaling, and macrophage phenotype switching. This review will provide a comprehensive understanding concerning previous, ongoing, and future studies of lncRNAs in macrophage functions and their importance in CVD. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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Review
Long-Noncoding RNA (lncRNA) in the Regulation of Hypoxia-Inducible Factor (HIF) in Cancer
Non-Coding RNA 2020, 6(3), 27; https://doi.org/10.3390/ncrna6030027 - 06 Jul 2020
Cited by 12 | Viewed by 3819
Abstract
Hypoxia is dangerous for oxygen-dependent cells, therefore, physiological adaption to cellular hypoxic conditions is essential. The transcription factor hypoxia-inducible factor (HIF) is the main regulator of hypoxic metabolic adaption reducing oxygen consumption and is regulated by gradual von Hippel-Lindau (VHL)-dependent proteasomal degradation. Beyond [...] Read more.
Hypoxia is dangerous for oxygen-dependent cells, therefore, physiological adaption to cellular hypoxic conditions is essential. The transcription factor hypoxia-inducible factor (HIF) is the main regulator of hypoxic metabolic adaption reducing oxygen consumption and is regulated by gradual von Hippel-Lindau (VHL)-dependent proteasomal degradation. Beyond physiology, hypoxia is frequently encountered within solid tumors and first drugs are in clinical trials to tackle this pathway in cancer. Besides hypoxia, cancer cells may promote HIF expression under normoxic conditions by altering various upstream regulators, cumulating in HIF upregulation and enhanced glycolysis and angiogenesis, altogether promoting tumor proliferation and progression. Therefore, understanding the underlying molecular mechanisms is crucial to discover potential future therapeutic targets to evolve cancer therapy. Long non-coding RNAs (lncRNA) are a class of non-protein coding RNA molecules with a length of over 200 nucleotides. They participate in cancer development and progression and might act as either oncogenic or tumor suppressive factors. Additionally, a growing body of evidence supports the role of lncRNAs in the hypoxic and normoxic regulation of HIF and its subunits HIF-1α and HIF-2α in cancer. This review provides a comprehensive update and overview of lncRNAs as regulators of HIFs expression and activation and discusses and highlights potential involved pathways. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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Review
LncRNA NEAT1 in Paraspeckles: A Structural Scaffold for Cellular DNA Damage Response Systems?
Non-Coding RNA 2020, 6(3), 26; https://doi.org/10.3390/ncrna6030026 - 01 Jul 2020
Cited by 10 | Viewed by 3969
Abstract
Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) reported to be frequently deregulated in various types of cancers and neurodegenerative processes. NEAT1 is an indispensable structural component of paraspeckles (PSs), which are dynamic and membraneless nuclear bodies that affect [...] Read more.
Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) reported to be frequently deregulated in various types of cancers and neurodegenerative processes. NEAT1 is an indispensable structural component of paraspeckles (PSs), which are dynamic and membraneless nuclear bodies that affect different cellular functions, including stress response. Furthermore, increasing evidence supports the crucial role of NEAT1 and essential structural proteins of PSs (PSPs) in the regulation of the DNA damage repair (DDR) system. This review aims to provide an overview of the current knowledge on the involvement of NEAT1 and PSPs in DDR, which might strengthen the rationale underlying future NEAT1-based therapeutic options in tumor and neurodegenerative diseases. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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Review
LncRNAs in Non-Small-Cell Lung Cancer
Non-Coding RNA 2020, 6(3), 25; https://doi.org/10.3390/ncrna6030025 - 30 Jun 2020
Cited by 15 | Viewed by 3224
Abstract
Lung cancer is associated with a high mortality, with around 1.8 million deaths worldwide in 2018. Non-small-cell lung cancer (NSCLC) accounts for around 85% of cases and, despite improvement in the management of NSCLC, most patients are diagnosed at advanced stage and the [...] Read more.
Lung cancer is associated with a high mortality, with around 1.8 million deaths worldwide in 2018. Non-small-cell lung cancer (NSCLC) accounts for around 85% of cases and, despite improvement in the management of NSCLC, most patients are diagnosed at advanced stage and the five-year survival remains around 15%. This highlights a need to identify novel ways to treat the disease to reduce the burden of NSCLC. Long non-coding RNAs (lncRNAs) are non-coding RNA molecules longer than 200 nucleotides in length which play important roles in gene expression and signaling pathways. Recently, lncRNAs were implicated in cancer, where their expression is dysregulated resulting in aberrant functions. LncRNAs were shown to function as both tumor suppressors and oncogenes in a variety of cancer types. Although there are a few well characterized lncRNAs in NSCLC, many lncRNAs remain un-characterized and their mechanisms of action largely unknown. LncRNAs have success as therapies in neurodegenerative diseases, and having a detailed understanding of their function in NSCLC may guide novel therapeutic approaches and strategies. This review discusses the role of lncRNAs in NSCLC tumorigenesis, highlighting their mechanisms of action and their clinical potential. Full article
(This article belongs to the Collection Feature Papers in Non-coding RNA)
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