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        <title>Frontiers in RNA Research | Non-coding RNA section | New and Recent Articles</title>
        <link>https://www.frontiersin.org/journals/rna-research/sections/non-coding-rna</link>
        <description>RSS Feed for Non-coding RNA section in the Frontiers in RNA Research journal | New and Recent Articles</description>
        <language>en-us</language>
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        <pubDate>2026-05-13T20:07:31.92+00:00</pubDate>
        <ttl>60</ttl>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2026.1793780</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2026.1793780</link>
        <title><![CDATA[How pertinent is the RIN for validating RNA quality isolated from cell-free biological fluids?]]></title>
        <pubdate>2026-03-09T00:00:00Z</pubdate>
        <category>Opinion</category>
        <author>Vivek Ambastha</author><author>Yuval Nevo</author><author>Yehoram Leshem</author>
        <description></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2025.1679653</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2025.1679653</link>
        <title><![CDATA[Y RNA and Y RNA-derived ysRNA associations with viral pathogens]]></title>
        <pubdate>2025-09-19T00:00:00Z</pubdate>
        <category>Mini Review</category>
        <author>Nathaniel S. Olliff</author><author>Alexandria A. Mabien</author><author>Grayson M. Cole</author><author>Glen M. Borchert</author>
        <description><![CDATA[Y RNAs are a poorly-studied class of small non-coding RNAs (sncRNAs) which have previously been implicated in the pathogenesis of different human diseases, including cardiac and autoimmune conditions, as well as certain cancers. In recent years, however, multiple studies have reported correlations between Y RNA expressions and disease outcomes in viral infections (e.g., IAV, HIV, HPV, and SARS-CoV-2) as well as potential mechanistic roles that Y RNAs may play in host anti-viral defense. These studies suggest that Y RNAs may be associated with upregulation of viral defense proteins as well as altered cell-cell communication during viral infections. In this review, current literature detailing Y RNA effects on human viral infection will be summarized and future directions in the study of these relationships discussed.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2025.1566829</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2025.1566829</link>
        <title><![CDATA[microRNA-4488 is differentially regulated during dengue virus infection and clearance of the virus]]></title>
        <pubdate>2025-04-16T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Roxana Filip</author><author>Parrish Evers</author><author>Spencer M. Uguccioni</author><author>Rhea C. Alonzi</author><author>Nadine Ahmed</author><author>Noreen Ahmed</author><author>John P. Pezacki</author>
        <description><![CDATA[Dengue virus (DENV) is a zoonotic disease transmitted to humans via mosquito bites. Viral infection is systemic in humans and can lead to organ failure including in the liver. Since there are many molecular changes that precede liver failure, identification of progress at the molecular level is informative. As an RNA virus, DENV perturbs non-coding RNAs including microRNAs. Here we examine microRNA profiles in hepatoma cells using small molecule–mediated annotation of miRNA targets. It was previously shown that treatment with the broadly antiviral oxysterol 25-hydroxycholesterol (25HC) induces the expression of antiviral microRNAs in the liver. Herein, we show that 25HC is potently antiviral against Dengue virus and identify miR-4488 as a microRNA which is overexpressed during infection and downregulated with oxysterol treatment. We also show that miR-4488 is downregulated when the viral levels are lowered using siRNA, suggesting that this microRNA is involved in the host-response to infection. Since miR-4488 levels closely correlate with DENV levels in the liver, it serves as a biomarker for virus infection in the liver and may contribute the overall effects of DENV in this organ.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2025.1555885</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2025.1555885</link>
        <title><![CDATA[Identification of long noncoding RNAs (lncRNAs) and co-transcriptional analysis of mRNAs and lncRNAs in transcriptomes of Anopheles gambiae]]></title>
        <pubdate>2025-04-15T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Jiannong Xu</author><author>Kai Hu</author><author>Michelle M. Riehle</author><author>Vedbar S. Khadka</author>
        <description><![CDATA[IntroductionAnopheles gambiae is a primary malaria vector mosquito in Africa. RNA-seq based transcriptome analysis has been widely used to study gene expression underlying mosquito life traits such as development, reproduction, immunity, metabolism, and behavior. While it is widely appreciated that long non-coding RNAs (lncRNAs) are expressed ubiquitously in transcriptomes across metazoans, lncRNAs remain relatively underexplored in An. gambiae, including their identity, expression profiles, and biological functions. The lncRNA genes were poorly annotated in the current reference of the PEST genome of An. gambiae. In this study, a set of publicly available RNA-seq datasets was leveraged to identify lncRNAs across diverse contexts, including whole mosquitoes, mosquito cells and tissues (such as hemocytes, midguts, and salivary glands), as well as under various physiological conditions (e.g., sugar-feeding, blood-feeding, bacterial challenges, and Plasmodium infections).MethodsA Transcript Discovery module implemented in the CLC genomics workbench was used to identify lncRNAs from selected published RNA-seq datasets.ResultsAcross this pool of transcriptomes, 2684 unique lncRNA genes, comprising 4082 transcripts, were identified. Following their identification, these lncRNA genes were integrated into the mosquito transcriptome annotation, which served as a reference for analyzing both mRNAs and lncRNAs for transcriptional dynamics under various conditions. Unsurprisingly, and similar to what has been reported for mRNAs, lncRNAs exhibited context-dependent expression patterns. Co-expression networks constructed using weighted gene co-expression network analysis (WGCNA) highlighted the interconnections among lncRNAs and mRNAs, which provide potential functional networks in which these lncRNAs are involved. Furthermore, we identified polysome-associated lncRNAs within polysome-captured transcripts, suggesting that lncRNAs are likely involved in translation regulation and contribute to coding capacity for micropeptides. The analysis of a ChIP-seq dataset revealed a correlation between transcriptional activities of lncRNAs and observed epigenetic signatures.DiscussionOverall, our study demonstrated that lncRNAs are transcribed alongside mRNAs in various biological contexts. The genome-wide annotation of lncRNA genes and integration into the PEST reference genome enable the simultaneous co-analysis of mRNA and lncRNA, which will enhance our understanding of their functions and shed light on their regulatory roles in An. gambiae biology.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2024.1473293</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2024.1473293</link>
        <title><![CDATA[Predicting conserved functional interactions for long noncoding RNAs via deep learning]]></title>
        <pubdate>2024-10-01T00:00:00Z</pubdate>
        <category>Brief Research Report</category>
        <author>Megan B. Kratz</author><author>Keriayn N. Smith</author>
        <description><![CDATA[Long noncoding RNA (lncRNA) genes outnumber protein coding genes in the human genome and the majority remain uncharacterized. A major difficulty in generalizing understanding of lncRNA function is the dearth of gross sequence conservation, both for lncRNAs across species and for lncRNAs that perform similar functions within a species. Machine learning based methods which harness vast amounts of information on RNAs are increasingly used to impute certain biological characteristics. This includes interactions with proteins that are important mediators of RNA function, thus enabling the generation of knowledge in contexts for which experimental data are lacking. Here, we applied a natural language-based machine learning approach that enabled us to identify RNA binding protein interactions in lncRNA transcripts, using only RNA sequence as an input. We found that this predictive method is a powerful approach to infer conserved binding across species as distant as human and opossum, even in the absence of sequence conservation, thus informing on sequence-function relationships for these poorly understood RNAs.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2024.1419979</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2024.1419979</link>
        <title><![CDATA[Compilation of resources on subcellular localization of lncRNA]]></title>
        <pubdate>2024-06-06T00:00:00Z</pubdate>
        <category>Systematic Review</category>
        <author>Shubham Choudhury</author><author>Anand Singh Rathore</author><author>Gajendra P. S. Raghava</author>
        <description><![CDATA[Long non-coding RNAs (lncRNAs) play a vital role in biological processes, and their dysfunctions lead to a wide range of diseases. Due to advancements in sequencing technology, more than 20,000 lncRNA transcripts have been identified in humans, almost equivalent to coding transcripts. One crucial aspect in annotating lncRNA function is predicting their subcellular localization, which often determines their functional roles within cells. This review aims to cover the experimental techniques, databases, and in silico tools developed for identifying subcellular localization. Firstly, we discuss the experimental methods employed to determine the subcellular localization of lncRNAs. These techniques provide valuable insights into the precise cellular compartments where lncRNAs reside. Secondly, we explore the available computational resources and databases contributing to our understanding of lncRNAs, including information on their subcellular localization. These computational methods utilize algorithms and machine learning approaches to predict lncRNA subcellular locations using sequence and structural features. Lastly, we discuss the limitations of existing methodologies, future challenges, and potential applications of subcellular localization prediction for lncRNAs. We highlight the need for further advancements in computational methods and experimental validation to enhance the accuracy and reliability of subcellular localization predictions. To support the scientific community, we have developed a platform called LncInfo, which offers comprehensive information on lncRNAs, including their subcellular localization. This platform aims to consolidate and provide accessible resources to researchers studying lncRNAs and their functional roles (http://webs.iiitd.edu.in/raghava/lncinfo).]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2024.1334464</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2024.1334464</link>
        <title><![CDATA[Long non-coding RNAs: emerging functional players in the pathobiology and progression of myeloid leukemia]]></title>
        <pubdate>2024-05-31T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Sangeeta Dutta</author><author>Vijay Suresh Akhade</author><author>Subhendu Roy Choudhury</author><author>Manchanahalli Rangaswamy Satyanarayana Rao</author>
        <description><![CDATA[Advancements and innovations in transcriptomics and computational biology have revealed long non-coding RNAs (lncRNAs) as some of the major regulators of essential biological processes. Their restricted spatial and temporal expressions as well as ability to interact with nucleic acids (DNA and RNA) and proteins make them key players in chromosome integrity, genomic architecture, and transcriptional and post-transcriptional regulation. Their dysregulation has been associated with numerous diseases and pathological conditions, including cancers. Myeloid leukemia is a malignancy of the hematopoietic system, and its pathobiology has been found to have increasing number of lncRNAs with functional significance. This comprehensive review summarizes a majority of the reported lncRNAs in acute myeloid leukemia (AML) and chronic myeloid leukemia (CML), focusing on the regulatory mechanisms by which they modulate the disease progression and pathogenesis, their potential as diagnostics and prognostic markers, and their feasibility as novel therapeutic targets. We also highlight our recent work on the significance of the lncRNA Hmrhl in CML, which has been found to regulate gene transcription at the chromatin level.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2023.1331185</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2023.1331185</link>
        <title><![CDATA[Roles of ribosomal RNA in health and disease]]></title>
        <pubdate>2024-01-19T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Ryan Johnston</author><author>Anne Aldrich</author><author>Shawn M. Lyons</author>
        <description><![CDATA[Ribosomes are amongst the most ancient molecular machines in cells, showing conservation from the simplest prokaryotes to humans. Ribosomes are an assembly of ribosomal (r)RNA and ribosomal proteins, but the rRNA comprises most of the mass of the ribosome and performs key enzymatic tasks. In humans, rRNA undergoes a laborious maturation that involves multiple processing steps and the deposition of chemical modifications. The correct processing and modification of rRNA ensures the proper function of the mature ribosome. Disturbance of these processes may lead to human disease. Understanding the role of rRNA in protein synthesis and the consequences of its dysregulation is key to deciphering and mitigating the emergence of pathological states in human biology.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2023.1257775</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2023.1257775</link>
        <title><![CDATA[SINE-derived short noncoding RNAs: their evolutionary origins, molecular mechanisms, and physiological significance]]></title>
        <pubdate>2023-08-10T00:00:00Z</pubdate>
        <category>Mini Review</category>
        <author>Rei Yoshimoto</author><author>Shinichi Nakagawa</author>
        <description><![CDATA[Short Interspersed Elements (SINEs) comprise a significant portion of the genomes of higher eukaryotes, including humans and mice. This review focuses on SINE-derived noncoding RNAs (ncRNAs), particularly BC1, BC200, and 4.5SH RNA, which are expressed abundantly and in a species-specific manner. These ncRNAs seem to have independently evolved their functions during evolutionary processes: BC1 and BC200 have become cytoplasmic translation inhibitors, while 4.5SH RNA has developed into a nuclear ncRNA that regulates splicing. This review delves into the unique roles of these ncRNAs, with a special emphasis on the recently discovered splicing regulation function of 4.5SH RNA. Furthermore, we discuss their evolutionary trajectories and potential implications for understanding the complexities of gene regulation.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2023.1240954</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2023.1240954</link>
        <title><![CDATA[Dynamic redistribution and inheritance of chromatin:RNA interactions during cell division]]></title>
        <pubdate>2023-08-03T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Emily Sparago</author><author>Reito Watanabe</author><author>Judith A. Sharp</author><author>Michael D. Blower</author>
        <description><![CDATA[During interphase, the nucleus contains a multitude of transcripts that influence the function of chromatin and global structure of the nucleus. Nuclear transcripts include nascent mRNAs in the process of transcription and mRNA processing, spliceosomal RNAs which catalyze mRNA processing, rRNAs that are being transcribed and processed to assemble functional ribosomes, and sno- and scaRNAs that participate in rRNA processing and modification. In addition, there are long noncoding RNAs (lncRNA) that associate with chromatin to control gene expression, or can even influence locus function in the case of centromeres and telomeres. Most of our knowledge of the functions of nuclear RNAs come from studies of interphase cells when the nuclear envelope separates nuclear and cytoplasmic contents. However, during mitosis the nuclear envelope breaks down, resulting in the mixing of nuclear and cytoplasmic components. Much less is known about the regulation and function of nuclear RNAs during mitosis. In this review, we discuss the cell cycle-dependent localization of different categories of RNAs, how the trans-acting factors SAF-A and Ki-67 regulate mitotic RNA localization, and describe how select categories of RNAs are inherited from the previous cell cycle in G1.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2023.1194526</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2023.1194526</link>
        <title><![CDATA[Enhancers are genes that express organizational RNAs]]></title>
        <pubdate>2023-06-01T00:00:00Z</pubdate>
        <category>Perspective</category>
        <author>John S. Mattick</author>
        <description><![CDATA[A longstanding enigma in molecular biology is the lack of scaling of protein-coding genes with developmental complexity, referred to as the g-value paradox. On the other hand, a feature of the evolution of multicellular organisms is the emergence of genetic loci termed “enhancers,” which control the spatiotemporal patterns of gene expression during development. Enhancer action has been widely interpreted in terms of an early model that postulated that transcription factors bound at enhancers are brought into juxtaposition with the promoters of target genes. This model tacitly assumed that there is no trans-acting gene product of enhancers, but subsequent studies have shown that enhancers are transcribed in the cells in which they are active. Like protein-coding genes, enhancers produce short bidirectional transcripts and long alternatively spliced RNAs, albeit at lower levels due to their transitory and cell-specific regulatory functions. The evidence indicates that long noncoding RNAs (lncRNAs) expressed from enhancers (elncRNAs) guide the formation of phase-separated transcriptional hubs and the epigenetic modifications to direct cell fate decisions during animal and plant ontogeny. Many, and likely most, lncRNAs are elncRNAs, which should be recognized as a bona fide class of gene products alongside mRNAs, rRNAs, tRNAs, snoRNAs, miRNAs and others of established function, with sequences specifying elncRNAs comprising an increasing fraction of genomic information as developmental complexity increases.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2023.1152146</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2023.1152146</link>
        <title><![CDATA[Current frontiers in RNA research]]></title>
        <pubdate>2023-05-22T00:00:00Z</pubdate>
        <category>Perspective</category>
        <author>Thomas R. Gingeras</author>
        <description><![CDATA[The biological importance of RNA has expanded as our appreciation of the complexity of its multiple types, structures, chemical compositions and biological roles. Research in RNA has been instrumental in revealing insights into fundamental biological processes including: the organization of information within genomes, the mechanisms of control of gene expression at the transcriptional (providing scaffolds for transcription factors and chromatin-modifying proteins) and post-transcriptional (RNA editing and modifications, translation, sponging) levels, spatiotemporal localization of elements involved in developmental and cell biology, and the evolution of first RNA genomes. Most recently, studies of RNA have expanded their clinical roles as diagnostics to the realm of therapeutic treatment for detected diseases. Finally, advances in RNA studies have been prompted by and contributed to the development of many novel methodological and computational approaches. The future of RNA research will add even more to our understanding of the origins of endophenotypes and these findings will be the focus of the Frontiers in RNA Research.]]></description>
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