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        <title>Frontiers in RNA Research | New and Recent Articles</title>
        <link>https://www.frontiersin.org/journals/rna-research</link>
        <description>RSS Feed for Frontiers in RNA Research | New and Recent Articles</description>
        <language>en-us</language>
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        <pubDate>2026-05-13T14:15:17.869+00:00</pubDate>
        <ttl>60</ttl>
        <item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2026.1779364</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2026.1779364</link>
        <title><![CDATA[Beyond mutations: personalising oncology via RNA-editing]]></title>
        <pubdate>2026-03-20T00:00:00Z</pubdate>
        <category>Mini Review</category>
        <author>Ivo Fierro-Monti</author>
        <description><![CDATA[Adenosine-to-inosine (A-to-I) RNA-editing, catalysed by ADAR enzymes, is a dynamic layer of post-transcriptional regulation that significantly diversifies the cancer transcriptome and proteome. A-to-I editing, the most frequent and well-established form of editing in human cancer, holds greater immediate relevance for personalised oncology than the less mapped C-to-U “editome” landscape. By recoding oncogenes and tumour suppressors (e.g., AZIN1, NEIL1), modulating drug response, and generating immunogenic RNA-editing-derived neoantigens, A-to-I events directly influence tumour progression, heterogeneity, and immune recognition. These roles establish RNA-editing profiles as promising biomarkers for patient stratification and prognosis. Furthermore, the integration of editing data with multi-omics and machine learning is accelerating the development of personalised therapeutic strategies. These include ADAR-guided RNA correction, mRNA vaccines encoding edited neoantigens, and RNA interference, offering reversible and tailored intervention points. Despite challenges in delivery, specificity, and clinical translation, A-to-I RNA-editing represents both a fundamental cancer mechanism and a versatile toolkit, driving the next generation of precision oncology beyond the constraints of the genomic blueprint.]]></description>
      </item><item>
        <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.2026.1757629</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2026.1757629</link>
        <title><![CDATA[The uORF–NMD axis and uPeptides: a new frontier in cancer therapy]]></title>
        <pubdate>2026-03-05T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Rafaela Lacerda</author><author>Samuel Silvestre</author><author>Verónica Vieira da Silva</author><author>Luísa Romão</author>
        <description><![CDATA[Nonsense-mediated decay (NMD) was first described as a surveillance mechanism that targets and rapidly degrades aberrant mRNAs carrying premature termination codons (PTCs). However, it is now known that NMD also degrades a significant number of physiological transcripts, including some containing upstream open reading frames (uORFs). uORFs are mRNA cis-acting elements defined by a translation start codon in the 5′ transcript leader sequence in frame with a stop codon located upstream or overlapped with the main coding sequence (mCDS). Besides inducing NMD, translation of uORFs often represses translation of the mCDS, thereby maintaining mCDS-encoded proteins at low levels. However, translation of uORFs can also generate uORF-encoded peptides (uPeptides). These uPeptides may regulate critical cellular pathways. Recent technological advances in ribosome profiling and mass spectrometry techniques have allowed the detection of numerous uPeptides in both healthy and malignantly transformed human cells. Cancer cells can exhibit altered transcriptional landscapes, some of which are due to altered NMD activity, leading to the production of new uPeptides with roles in different cellular pathways; some of these can act as neoantigens. In this review, we aim to provide insight into the latest research on uPeptides and their functional roles in cellular pathways and during tumorigenesis. We also wish to explore the importance of NMD in regulating uPeptides’ expression in normal and cancer cells. Furthermore, we intend to review how these uPeptides contribute to expand the immunopeptidome, offering new targets for personalised cancer vaccines. Altogether, the collected data may help design new therapeutic approaches towards personalised medicine to fight cancer onset and development.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2026.1749833</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2026.1749833</link>
        <title><![CDATA[Getting the message: low-plex detection of RNA in tissues]]></title>
        <pubdate>2026-02-20T00:00:00Z</pubdate>
        <category>Mini Review</category>
        <author>Bradley Spencer-Dene</author><author>Elena Miranda</author>
        <description><![CDATA[The rapidly emerging field of spatial transcriptomics is transforming developmental biology, oncology, and disease pathology, mapping intricate gene expression patterns within their native tissue contexts. Traditionally, the analysis of messenger RNA (mRNA) expression has been the main focus of this research. However, the eukaryotic cell transcriptome comprises a diverse array of dynamic RNA molecules. Therefore, spatial profiling of different RNA species throughout their life cycle is essential for comprehensively elucidating RNA biology in complex tissues. Formalin-fixed paraffin-embedded (FFPE) samples are widely used in research and clinical settings optimally preserving tissue morphology and cellular details over long periods. Pathology departments have accrued vast collections of FFPE blocks, creating a rich yet under-utilized array of materials that, accompanied by clinical data, stands as a treasure trove for human biology and translational research. Nevertheless, FFPE specimens present several challenges. The RNA within these samples is prone to fragmentation during processing and may further degrade if stored improperly. Additionally, chemical modifications can occur in the RNA, leading to fragmentation or resistance to enzymatic reactions essential for sequencing. The loss of poly-A tails adds another layer of complexity, limiting the effectiveness of oligo-dT primed reverse transcription. As a result, options for spatial profiling of RNA molecules in this tissue type are restricted. Commercial assays that are now available for both manual and automated detection of single to low-plex mRNA targets in tissues, including point mutations, miRNAs and even oligonucleotides have brought these applications into more mainstream workflows, and these will be the primary focus of this review.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2025.1722301</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2025.1722301</link>
        <title><![CDATA[A G-quadruplex structure in the SARS-CoV-2 RNA recruits human topoisomerase I]]></title>
        <pubdate>2026-01-07T00:00:00Z</pubdate>
        <category>Brief Research Report</category>
        <author>Maximilian Burghaus</author><author>Till Staschko</author><author>Marta Mendes</author><author>Larissa Filcenkova</author><author>Janina Gerhard</author><author>Gunnar Dittmar</author><author>Heiko Ihmels</author><author>Sybille Krauß</author>
        <description><![CDATA[The COVID-19 pandemic has led to millions of deaths. Although the pandemic state has been declared to have ended and the disease has become endemic, the number of circulating SARS-CoV-2 variants and the lack of decreasing trends around the world highlight the challenge the virus still poses. The viral RNA genome contains several structural elements including G-quadruplexes. These structures may facilitate the binding between an RNA and RNA-binding proteins. Herein, we investigated host cell proteins that get trapped by a G-quadruplex structure of the SARS-CoV-2 RNA. The identified proteins include the human DNA topoisomerase 1 (TOP1). The protein is known to interact with G-quadruplex-DNA, but here, we show an interaction with a G-quadruplex structure formed by the RNA of SARS-CoV-2, which has not been reported before. TOP1 may be recruited by the non-canonical secondary structure to resolve it, which may enhance viral replication. Interestingly, previous studies showed that TOP1 inhibition can suppress SARS-CoV-2-induced inflammation. Thus, after discovery of TOP1 as a binding partner of the SARS-CoV-2 G-quadruplex structure, we tested different compounds for their effect on the recruitment of TOP1 to the G-quadruplex. Notably, our data suggest that the known alkaloid berberine can stabilize the TOP1-G4-RNA-complex. Functionally, TOP1 is possibly recruited by the G-quadruplex to resolve this secondary structure, thereby enhancing viral replication. Thus, berberine is a promising lead compound that may inhibit viral replication.]]></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.2025.1531242</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2025.1531242</link>
        <title><![CDATA[The role of m6A RNA methylation in infectious diseases]]></title>
        <pubdate>2025-04-10T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Nidhi Yadav</author><author>Reshma Khan</author><author>Sandeep Goyal</author><author>Rajesh Kumari</author>
        <description><![CDATA[Among over 170 known RNA modifications, N6-methyladenosine (m6A) stands out as the most ubiquitous and extensively studied modification, found in different cellular RNA. The m6A plays a pivotal role in regulating RNA nuclear export, stability, secondary structure, translation, and degradation eventually determining the gene expression. The m6A modification is controlled by three classes of enzymes: “writers”, “erasers”, and “readers” which not only play a role in adding and removing the methyl group but also help in recognizing and interpreting the methylation marks. Although m6A has been widely studied in the context of metabolic diseases and cancers, its influence on infectious diseases remains under-explored. The infection cycle of several pathogens, including viruses, bacteria, and parasites is regulated by the m6A methylation machinery. In this review, we will not only explore the existing knowledge about m6A methylation but also its influence in shaping the pathogen life cycle paving our way to therapeutic aspects to mitigate infectious diseases.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2025.1556979</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2025.1556979</link>
        <title><![CDATA[TRMT112, a master activator of several methyltransferases modifying factors involved in RNA maturation and translation]]></title>
        <pubdate>2025-03-27T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Can Wang</author><author>Laurianne L. E. Tay</author><author>Wanwan Hu</author><author>Morgane Corre</author><author>Marc Graille</author>
        <description><![CDATA[Most RNAs and many protein factors involved in mRNA maturation and translation are decorated by numerous and diverse chemical modifications, which contribute to the efficiency, fidelity and regulation of these complex and essential cellular processes. Among those modifications, methylation catalyzed mainly by S-adenosyl-L-methionine (SAM) dependent methyltransferases (MTases) is the most common one. TRMT112 is a small protein acting as an allosteric regulator of several MTases. Initial studies focusing on TRMT112 and its associated MTases were performed in Saccharomyces cerevisiae whereas only few were expanded to human cells, leading to the identification and characterization of four TRMT112 partners in yeast (Trm11, Bud23, Mtq2 and Trm9) and five in human cells (TRMT11, BUD23, MTQ2/HemK2 and two Trm9 orthologues ALKBH8 and TRMT9B). Recent studies have identified several novel MTase partners of human TRMT112, namely METTL5, THUMPD2 and THUMPD3. Interestingly, all these TRMT112-MTase complexes modify factors (RNAs and proteins) involved in mRNA maturation and translation processes and growing evidence supports the importance of these MTases in cancer and correct brain development. In this review, we summarize the current knowledge on TRMT112 protein and its various MTase partners in eukaryotes and archaea.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2024.1526447</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2024.1526447</link>
        <title><![CDATA[Editorial: Ribonucleoprotein formation and regulation]]></title>
        <pubdate>2024-12-06T00:00:00Z</pubdate>
        <category>Editorial</category>
        <author>Michael D. Hebert</author><author>A. Gregory Matera</author>
        <description></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2024.1485307</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2024.1485307</link>
        <title><![CDATA[The expanding role of cap-adjacent modifications in animals]]></title>
        <pubdate>2024-10-01T00:00:00Z</pubdate>
        <category>Perspective</category>
        <author>Eleanor Bellows</author><author>Rupert G. Fray</author><author>Helen M. Knight</author><author>Nathan Archer</author>
        <description><![CDATA[Eukaryotic mRNA cap structures directly influence mRNA stability, translation, and immune recognition. While the significance of the mRNA cap itself has been well-established, recent research has revealed the intricate modifications to the nucleotides immediately adjacent to the cap. These include 2′-O-methylation (Cap1, Cap2) and N6-methyladenosine (m6Am), which recent work suggests may be dynamically regulated, interdependent, and vital for gene-regulation. This perspective explores the expanding role of cap-adjacent modifications. Cap1 is found on metazoan mRNA, viruses which infect metazoans, and the COVID-19 mRNA vaccines. We combined basic local alignment and 2D-TLC to track cap-adjacent modifying proteins and the modifications themselves to profile their prevalence throughout eukaryotes. We confirm that Cap1 is broadly metazoan specific, but surprisingly also in a brown algae. Additionally, we find genomic presence of the eraser, FTO more predictive of the occurrence of m6Am than the m6Am-writer, PCIF1. We then outline future directions to understand and exploit these enigmatic modifications.]]></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.2024.1460913</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2024.1460913</link>
        <title><![CDATA[N2-methylguanosine and N2, N2-dimethylguanosine in cytosolic and mitochondrial tRNAs]]></title>
        <pubdate>2024-09-25T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Jonny Petrosyan</author><author>Katherine E. Bohnsack</author>
        <description><![CDATA[Decoration of cellular RNAs with modified RNA nucleosides is an important layer of gene expression regulation. Throughout the transcriptome, RNA modifications influence the folding, stability and function of RNAs as well as their interactions with RNA-binding proteins. Although first detected more than 50 years ago, the modified nucleosides N2-methylguanosine (m2G) and N2,N2-dimethylguanosine (m22G) have recently come to the fore through the identification and characterization of the human methyltransferases (MTases) responsible for their installation. In tRNAs, m2G and m22G are present at the junctions between the acceptor stem and the D-arm, and the D-arm and the anticodon stem loop. Here, we review the current knowledge on the effects of mono- and di-methylation of N2 of guanosine on base-pairing and provide an overview of m2(2)G sites in cytosolic and mitochondrial tRNAs. We highlight key features of m2G and m22G MTases, and describe how these enzymes specifically recognize their RNA substrates and target nucleosides. We also discuss the impact of these modifications on tRNA functions, their dynamic regulation and their implications in disease.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2024.1448194</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2024.1448194</link>
        <title><![CDATA[Proteomic analysis of the SMN complex reveals conserved and etiologic connections to the proteostasis network]]></title>
        <pubdate>2024-09-18T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>A. Gregory Matera</author><author>Rebecca E. Steiner</author><author>C. Allie Mills</author><author>Benjamin D. McMichael</author><author>Laura E. Herring</author><author>Eric L. Garcia</author>
        <description><![CDATA[IntroductionMolecular chaperones and co-chaperones are highly conserved cellular components that perform a variety of duties related to the proper three-dimensional folding of the proteome. The web of factors that carries out this essential task is called the proteostasis network (PN). Ribonucleoproteins (RNPs) represent an underexplored area in terms of the connections they make with the PN. The Survival Motor Neuron (SMN) complex is an assembly chaperone and serves as a paradigm for studying how specific RNAs are identified and paired with their client substrate proteins to form RNPs. SMN is the eponymous component of a large complex, required for the biogenesis of uridine-rich small nuclear ribonucleoproteins (U-snRNPs), that localizes to distinct membraneless organelles in both the nucleus and cytoplasm of animal cells. SMN protein forms the oligomeric core of this complex, and missense mutations in the human SMN1 gene are known to cause Spinal Muscular Atrophy (SMA). The basic framework for understanding how snRNAs are assembled into U-snRNPs is known. However, the pathways and mechanisms used by cells to regulate their biogenesis are poorly understood.MethodsGiven the importance of these processes to normal development as well as neurodegenerative disease, we set out to identify and characterize novel SMN binding partners. We carried out affinity purification mass spectrometry (AP-MS) of Drosophila SMN complexes using fly lines exclusively expressing either wildtype or SMA-causing missense alleles.ResultsBioinformatic analyses of the pulldown data, along with comparisons to proximity labeling studies carried out in human cells, revealed conserved connections to at least two other major chaperone systems including heat shock folding chaperones (HSPs) and histone/nucleosome assembly chaperones. Notably, we found that heat shock cognate protein Hsc70-4 and other HspA family members preferentially associated with SMA-causing alleles of SMN.DiscussionHsc70-4 is particularly interesting because its mRNA is aberrantly sequestered by a mutant form of TDP-43 in mouse and Drosophila ALS (Amyotrophic Lateral Sclerosis) disease models. Most important, a missense allele of Hsc70-4 (HspA8 in mammals) was recently identified as a bypass suppressor of the SMA phenotype in mice. Collectively, these findings suggest that chaperone-related dysfunction lies at the etiological root of both ALS and SMA.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frnar.2024.1419833</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2024.1419833</link>
        <title><![CDATA[RNAseq-differentiated gene expression profile of people living with HTLV-1 in the Brazilian Amazon region: a pilot study]]></title>
        <pubdate>2024-08-26T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Leonn Mende Soares Pereira</author><author>Rafaella do Nascimento Ferreira</author><author>Vânia Nakauth Azevedo</author><author>Maria Alice Freitas Queiroz</author><author>Carlos Willian Dias Dantas</author><author>Rommel Thiago Jucá Ramos</author><author>Sandro Patroca da Silva</author><author>Carlos Araújo da Costa</author><author>Maisa Silva de Sousa</author><author>Izaura Maria Vieira Cayres Vallinoto</author><author>Ana Cecília Ribeiro Cruz</author><author>Antonio Carlos Rosário Vallinoto</author>
        <description><![CDATA[In this study, we aimed investigated the differential gene expression profiles of samples from uninfected individuals (control group) and study groups of asymptomatic human T-lymphotropic virus 1 (HTLV-1) carriers and patients with HTLV-1-associated myelopathy (HAM) by exploratory RNA sequencing (RNA-Seq) analysis. The gene expression profiles of individuals in the asymptomatic group were represented by 3 genes, most associated with cell cycle regulation. The gene expression profiles of individuals in the HAM group were represented by 12 genes, the majority of which are associated with the immune response. The HLA-A gene and the non-coding RNA LINC02470 were upregulated in the asymptomatic and HAM groups. The HLA-DQB1 and HLA-C genes were downregulated in the asymptomatic and HAM groups. In this pilot study, although limited in terms of methodological rigor, we showed differential gene expression profiles in different clinical groups of HTLV-1 infection. However, further studies are needed to confirm these findings.]]></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.2024.1415530</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2024.1415530</link>
        <title><![CDATA[High-throughput mutational analysis of a methyltransferase ribozyme]]></title>
        <pubdate>2024-06-03T00:00:00Z</pubdate>
        <category>Brief Research Report</category>
        <author>Ryota Yamagami</author><author>Hina Kubota</author><author>Emi Kohno</author><author>Hiroyuki Hori</author>
        <description><![CDATA[Methyltransferase ribozyme 1 (MTR1) is a catalytic RNA that has been isolated from a random RNA pool by in vitro selection. The ribozyme catalyzes site-specific formation of 1-methyl adenosine (m1A) using 6-methyl guanine (m6G) as a methyl group donor. The ribozyme has been extensively characterized by biochemical and structural analyses. Here, we describe high-throughput screening of single point mutants in the catalytic domain of MTR1 and determine their effect on ribozyme activity. Our mutational profiling method successfully assessed the activity of the 141 MTR1 variants tested in each experiment and revealed that the ribozyme is very sensitive to nucleotide substitutions in the catalytic core domain. Our technique can be applied to methyltransferase ribozymes that catalyze formation of different modifications such as 7-methylguanosine (m7G) or 3-methylcytidine (m3C).]]></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.2024.1389104</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frnar.2024.1389104</link>
        <title><![CDATA[SUMOylation regulation of ribosome biogenesis: Emerging roles for USP36]]></title>
        <pubdate>2024-04-03T00:00:00Z</pubdate>
        <category>Mini Review</category>
        <author>Yunhan Yang</author><author>Yanping Li</author><author>Rosalie C. Sears</author><author>Xiao-Xin Sun</author><author>Mu-Shui Dai</author>
        <description><![CDATA[Ribosome biogenesis is essential for cell growth, proliferation, and animal development. Its deregulation leads to various human disorders such as ribosomopathies and cancer. Thus, tight regulation of ribosome biogenesis is crucial for normal cell homeostasis. Emerging evidence suggests that posttranslational modifications such as ubiquitination and SUMOylation play a crucial role in regulating ribosome biogenesis. Our recent studies reveal that USP36, a nucleolar deubiquitinating enzyme (DUB), acts also as a SUMO ligase to regulate nucleolar protein group SUMOylation, thereby being essential for ribosome biogenesis. Here, we provide an overview of the current understanding of the SUMOylation regulation of ribosome biogenesis and discuss the role of USP36 in nucleolar SUMOylation.]]></description>
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