Journal articles: 'Cellular RNAs'

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Hema, M., K. Gopinath, and C. Kao. "Repair of the tRNA-Like CCA Sequence in a Multipartite Positive-Strand RNA Virus." Journal of Virology 79, no. 3 (February 1, 2005): 1417–27. http://dx.doi.org/10.1128/jvi.79.3.1417-1427.2005.

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ABSTRACT The 3′ portions of plus-strand brome mosaic virus (BMV) RNAs mimic cellular tRNAs. Nucleotide substitutions or deletions in the 3′ CCA of the tRNA-like sequence (TLS) affect minus-strand initiation unless repaired. We observed that 2-nucleotide deletions involving the CCA 3′ sequence in one or all BMV RNAs still allowed RNA accumulation in barley protoplasts at significant levels. Alterations of CCA to GGA in only BMV RNA3 also allowed RNA accumulation at wild-type levels. However, substitutions in all three BMV RNAs severely reduced RNA accumulation, demonstrating that substitutions have different repair requirements than do small deletions. Furthermore, wild-type BMV RNA1 was required for the repair and replication of RNAs with nucleotide substitutions. Results from sequencing of progeny viral RNA from mutant input RNAs demonstrated that RNA1 did not contribute its sequence to the mutant RNAs. Instead, the repaired ends were heterogeneous, with one-third having a restored CCA and others having sequences with the only commonality being the restoration of one cytidylate. The role of BMV RNA1 in increased repair was examined.

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Pak, Julia, and Andrew Fire. "Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans." Science 315, no. 5809 (November 23, 2006): 241–44. http://dx.doi.org/10.1126/science.1132839.

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RNA interference (RNAi) is a phylogenetically widespread gene-silencing process triggered by double-stranded RNA. In plants and Caenorhabditis elegans, two distinct populations of small RNAs have been proposed to participate in RNAi: “Primary siRNAs” (derived from DICER nuclease-mediated cleavage of the original trigger) and “secondary siRNAs” [additional small RNAs whose synthesis requires an RNA-directed RNA polymerase (RdRP)]. Analyzing small RNAs associated with ongoing RNAi in C. elegans, we found that secondary siRNAs constitute the vast majority. The bulk of secondary siRNAs exhibited structure and sequence indicative of a biosynthetic mode whereby each molecule derives from an independent de novo initiation by RdRP. Analysis of endogenous small RNAs indicated that a fraction derive from a biosynthetic mechanism that is similar to that of secondary siRNAs formed during RNAi, suggesting that small antisense transcripts derived from cellular messenger RNAs by RdRP activity may have key roles in cellular regulation.

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Macias, Sara, Ross A. Cordiner, and Javier F. Cáceres. "Cellular functions of the microprocessor." Biochemical Society Transactions 41, no. 4 (July 18, 2013): 838–43. http://dx.doi.org/10.1042/bst20130011.

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The microprocessor is a complex comprising the RNase III enzyme Drosha and the double-stranded RNA-binding protein DGCR8 (DiGeorge syndrome critical region 8 gene) that catalyses the nuclear step of miRNA (microRNA) biogenesis. DGCR8 recognizes the RNA substrate, whereas Drosha functions as an endonuclease. Recent global analyses of microprocessor and Dicer proteins have suggested novel functions for these components independent of their role in miRNA biogenesis. A HITS-CLIP (high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation) experiment designed to identify novel substrates of the microprocessor revealed that this complex binds and regulates a large variety of cellular RNAs. The microprocessor-mediated cleavage of several classes of RNAs not only regulates transcript levels, but also modulates alternative splicing events, independently of miRNA function. Importantly, DGCR8 can also associate with other nucleases, suggesting the existence of alternative DGCR8 complexes that may regulate the fate of a subset of cellular RNAs. The aim of the present review is to provide an overview of the diverse functional roles of the microprocessor.

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Jiang, Di. "Cellular RNAs guide CRISPR-Cas9." Science 372, no. 6545 (May 27, 2021): 929.10–929. http://dx.doi.org/10.1126/science.372.6545.929-j.

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Hopper, Anita K. "Cellular Dynamics of Small RNAs." Critical Reviews in Biochemistry and Molecular Biology 41, no. 1 (January 2006): 3–19. http://dx.doi.org/10.1080/10409230500405237.

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Cooper, Daphne A., Shuvojit Banerjee, Arindam Chakrabarti, Adolfo García-Sastre, Jay R. Hesselberth, Robert H. Silverman, and David J. Barton. "RNase L Targets Distinct Sites in Influenza A Virus RNAs." Journal of Virology 89, no. 5 (December 24, 2014): 2764–76. http://dx.doi.org/10.1128/jvi.02953-14.

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ABSTRACTInfluenza A virus (IAV) infections are influenced by type 1 interferon-mediated antiviral defenses and by viral countermeasures to these defenses. When IAV NS1 protein is disabled, RNase L restricts virus replication; however, the RNAs targeted for cleavage by RNase L under these conditions have not been defined. In this study, we used deep-sequencing methods to identify RNase L cleavage sites within host and viral RNAs from IAV PR8ΔNS1-infected A549 cells. Short hairpin RNA knockdown of RNase L allowed us to distinguish between RNase L-dependent and RNase L-independent cleavage sites. RNase L-dependent cleavage sites were evident at discrete locations in IAV RNA segments (both positive and negative strands). Cleavage in PB2, PB1, and PA genomic RNAs suggests that viral RNPs are susceptible to cleavage by RNase L. Prominent amounts of cleavage mapped to specific regions within IAV RNAs, including some areas of increased synonymous-site conservation. Among cellular RNAs, RNase L-dependent cleavage was most frequent at precise locations in rRNAs. Our data show that RNase L targets specific sites in both host and viral RNAs to restrict influenza virus replication when NS1 protein is disabled.IMPORTANCERNase L is a critical component of interferon-regulated and double-stranded-RNA-activated antiviral host responses. We sought to determine how RNase L exerts its antiviral activity during influenza virus infection. We enhanced the antiviral activity of RNase L by disabling a viral protein, NS1, that inhibits the activation of RNase L. Then, using deep-sequencing methods, we identified the host and viral RNAs targeted by RNase L. We found that RNase L cleaved viral RNAs and rRNAs at very precise locations. The direct cleavage of IAV RNAs by RNase L highlights an intimate battle between viral RNAs and an antiviral endonuclease.

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Riddihough, Guy. "RNA editing helps identify cellular RNAs." Science Signaling 8, no. 393 (September 8, 2015): ec260-ec260. http://dx.doi.org/10.1126/scisignal.aad3741.

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Yao, Run-Wen, Yang Wang, and Ling-Ling Chen. "Cellular functions of long noncoding RNAs." Nature Cell Biology 21, no. 5 (May 2019): 542–51. http://dx.doi.org/10.1038/s41556-019-0311-8.

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Riddihough, G. "RNA editing helps identify cellular RNAs." Science 349, no. 6252 (September 3, 2015): 1066–68. http://dx.doi.org/10.1126/science.349.6252.1066-q.

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Xu, Ning, Bo Segerman, Xiaofu Zhou, and Göran Akusjärvi. "Adenovirus Virus-Associated RNAII-Derived Small RNAs Are Efficiently Incorporated into the RNA-Induced Silencing Complex and Associate with Polyribosomes." Journal of Virology 81, no. 19 (July 25, 2007): 10540–49. http://dx.doi.org/10.1128/jvi.00885-07.

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ABSTRACT Adenovirus type 5 encodes two highly structured short RNAs, the virus-associated (VA) RNAI and RNAII. Both are processed by Dicer into small RNAs that are incorporated into the RNA-induced silencing complex (RISC). We show here, by cloning of small RNAs, that approximately 80% of Ago2-containing RISC immunopurified from late-infected cells is associated with VA RNA-derived small RNAs (mivaRNAs). Most surprisingly, VA RNAII, which is expressed at 20-fold lower levels compared to that of VA RNAI, appears to be the preferred substrate for Dicer and accounts for approximately 60% of all small RNAs in RISC. The mivaRNAs are derived from the 3′ strand of the terminal stems of the VA RNAs, with the major fraction of VA RNAII starting at position 138. The small RNAs derived from VA RNAI were more heterogeneous in size, with the two predominant small RNAs starting at positions 137 and 138. Collectively, our results suggest that the mivaRNAs are efficiently used for RISC assembly in late-infected cells. Potentially, they function as miRNAs, regulating translation of cellular mRNAs. In support of this hypothesis, we detected a fraction of the VA RNAII-derived mivaRNAs on polyribosomes.

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Wolin, Sandra L., and Lynne E. Maquat. "Cellular RNA surveillance in health and disease." Science 366, no. 6467 (November 14, 2019): 822–27. http://dx.doi.org/10.1126/science.aax2957.

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The numerous quality control pathways that target defective ribonucleic acids (RNAs) for degradation play key roles in shaping mammalian transcriptomes and preventing disease. These pathways monitor most steps in the biogenesis of both noncoding RNAs (ncRNAs) and protein-coding messenger RNAs (mRNAs), degrading ncRNAs that fail to form functional complexes with one or more proteins and eliminating mRNAs that encode abnormal, potentially toxic proteins. Mutations in components of diverse RNA surveillance pathways manifest as disease. Some mutations are characterized by increased interferon production, suggesting that a major role of these pathways is to prevent aberrant cellular RNAs from being recognized as “non-self.” Other mutations are common in cancer, or result in developmental defects, revealing the importance of RNA surveillance to cell and organismal function.

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Deng, Zhiqi, Liqun Ma, Peiyu Zhang, and Hongliang Zhu. "Small RNAs Participate in Plant–Virus Interaction and Their Application in Plant Viral Defense." International Journal of Molecular Sciences 23, no. 2 (January 8, 2022): 696. http://dx.doi.org/10.3390/ijms23020696.

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Small RNAs are significant regulators of gene expression, which play multiple roles in plant development, growth, reproductive and stress response. It is generally believed that the regulation of plants’ endogenous genes by small RNAs has evolved from a cellular defense mechanism for RNA viruses and transposons. Most small RNAs have well-established roles in the defense response, such as viral response. During viral infection, plant endogenous small RNAs can direct virus resistance by regulating the gene expression in the host defense pathway, while the small RNAs derived from viruses are the core of the conserved and effective RNAi resistance mechanism. As a counter strategy, viruses evolve suppressors of the RNAi pathway to disrupt host plant silencing against viruses. Currently, several studies have been published elucidating the mechanisms by which small RNAs regulate viral defense in different crops. This paper reviews the distinct pathways of small RNAs biogenesis and the molecular mechanisms of small RNAs mediating antiviral immunity in plants, as well as summarizes the coping strategies used by viruses to override this immune response. Finally, we discuss the current development state of the new applications in virus defense based on small RNA silencing.

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Liu, Chu-Xiao, and Ling-Ling Chen. "Circular RNAs: Characterization, cellular roles, and applications." Cell 185, no. 13 (June 2022): 2390. http://dx.doi.org/10.1016/j.cell.2022.06.001.

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14

Pennisi, E. "Lengthy RNAs earn respect as cellular players." Science 344, no. 6188 (June 5, 2014): 1072. http://dx.doi.org/10.1126/science.344.6188.1072.

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Charley, Phillida A., and Jeffrey Wilusz. "Sponging of cellular proteins by viral RNAs." Current Opinion in Virology 9 (December 2014): 14–18. http://dx.doi.org/10.1016/j.coviro.2014.09.001.

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Li, Xiao-Ling, John A. Blackford, and Bret A. Hassel. "RNase L Mediates the Antiviral Effect of Interferon through a Selective Reduction in Viral RNA during Encephalomyocarditis Virus Infection." Journal of Virology 72, no. 4 (April 1, 1998): 2752–59. http://dx.doi.org/10.1128/jvi.72.4.2752-2759.1998.

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ABSTRACT The 2′,5′-oligoadenylate (2-5A) system is an RNA degradation pathway which plays an important role in the antipicornavirus effects of interferon (IFN). RNase L, the terminal component of the 2-5A system, is thought to mediate this antiviral activity through the degradation of viral RNA; however, the capacity of RNase L to selectively target viral RNA has not been carefully examined in intact cells. Therefore, the mechanism of RNase L-mediated antiviral activity was investigated following encephalomyocarditis virus (EMCV) infection of cell lines in which expression of transfected RNase L was induced or endogenous RNase L activity was inhibited. RNase L induction markedly enhanced the anti-EMCV activity of IFN via a reduction in EMCV RNA. Inhibition of endogenous RNase L activity inhibited this reduction in viral RNA. RNase L had no effect on IFN-mediated protection from vesicular stomatitis virus. RNase L induction reduced the rate of EMCV RNA synthesis, suggesting that RNase L may target viral RNAs involved in replication early in the virus life cycle. The RNase L-mediated reduction in viral RNA occurred in the absence of detectable effects on specific cellular mRNAs and without any global alteration in the cellular RNA profile. Extensive rRNA cleavage, indicative of high levels of 2-5A, was not observed in RNase L-induced, EMCV-infected cells; however, transfection of 2-5A into cells resulted in widespread degradation of cellular RNAs. These findings provide the first demonstration of the selective capacity of RNase L in intact cells and link this selective activity to cellular levels of 2-5A.

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Hall, Adam E., Carly Turnbull, and Tamas Dalmay. "Y RNAs: recent developments." BioMolecular Concepts 4, no. 2 (April 1, 2013): 103–10. http://dx.doi.org/10.1515/bmc-2012-0050.

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AbstractNon-coding RNAs have emerged as key regulators in diverse cellular processes. Y RNAs are ∼100-nucleotide-long non-coding RNAs that show high conservation in metazoans. Human Y RNAs are known to bind to the Ro60 and La proteins to form the Ro ribonucleoprotein complex. Their main biological function appears to be in mediating the initiation of chromosomal DNA replication, regulating the autoimmune protein Ro60, and generating smaller RNA fragments following cellular stress, although the precise molecular mechanisms underlying these functions remain elusive. Here, we aim to review the most recent literature on Y RNAs and gain insight into the function of these intriguing molecules.

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Casella, Gabriel, Rachel Munk, Kyoung Mi Kim, Yulan Piao, Supriyo De, Kotb Abdelmohsen, and Myriam Gorospe. "Transcriptome signature of cellular senescence." Nucleic Acids Research 47, no. 14 (June 28, 2019): 7294–305. http://dx.doi.org/10.1093/nar/gkz555.

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Abstract Cellular senescence, an integral component of aging and cancer, arises in response to diverse triggers, including telomere attrition, macromolecular damage and signaling from activated oncogenes. At present, senescent cells are identified by the combined presence of multiple traits, such as senescence-associated protein expression and secretion, DNA damage and β-galactosidase activity; unfortunately, these traits are neither exclusively nor universally present in senescent cells. To identify robust shared markers of senescence, we have performed RNA-sequencing analysis across eight diverse models of senescence triggered in human diploid fibroblasts (WI-38, IMR-90) and endothelial cells (HUVEC, HAEC) by replicative exhaustion, exposure to ionizing radiation or doxorubicin, and expression of the oncogene HRASG12V. The intersection of the altered transcriptomes revealed 50 RNAs consistently elevated and 18 RNAs consistently reduced across all senescence models, including many protein-coding mRNAs and some non-coding RNAs. We propose that these shared transcriptome profiles will enable the identification of senescent cells in vivo, the investigation of their roles in aging and malignancy and the development of strategies to target senescent cells therapeutically.

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Taliansky, Michael, Viktoria Samarskaya, Sergey K. Zavriev, Igor Fesenko, Natalia O. Kalinina, and Andrew J. Love. "RNA-Based Technologies for Engineering Plant Virus Resistance." Plants 10, no. 1 (January 2, 2021): 82. http://dx.doi.org/10.3390/plants10010082.

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In recent years, non-coding RNAs (ncRNAs) have gained unprecedented attention as new and crucial players in the regulation of numerous cellular processes and disease responses. In this review, we describe how diverse ncRNAs, including both small RNAs and long ncRNAs, may be used to engineer resistance against plant viruses. We discuss how double-stranded RNAs and small RNAs, such as artificial microRNAs and trans-acting small interfering RNAs, either produced in transgenic plants or delivered exogenously to non-transgenic plants, may constitute powerful RNA interference (RNAi)-based technology that can be exploited to control plant viruses. Additionally, we describe how RNA guided CRISPR-CAS gene-editing systems have been deployed to inhibit plant virus infections, and we provide a comparative analysis of RNAi approaches and CRISPR-Cas technology. The two main strategies for engineering virus resistance are also discussed, including direct targeting of viral DNA or RNA, or inactivation of plant host susceptibility genes. We also elaborate on the challenges that need to be overcome before such technologies can be broadly exploited for crop protection against viruses.

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Xiao, Mei-Sheng, and Jeremy E. Wilusz. "An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3′ ends." Nucleic Acids Research 47, no. 16 (July 3, 2019): 8755–69. http://dx.doi.org/10.1093/nar/gkz576.

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AbstractThousands of eukaryotic protein-coding genes generate circular RNAs that have covalently linked ends and are resistant to degradation by exonucleases. To prove their circularity as well as biochemically enrich these transcripts, it has become standard in the field to use the 3′-5′ exonuclease RNase R. Here, we demonstrate that standard protocols involving RNase R can fail to digest >20% of all highly expressed linear RNAs, but these shortcomings can largely be overcome. RNAs with highly structured 3′ ends, including snRNAs and histone mRNAs, are naturally resistant to RNase R, but can be efficiently degraded once a poly(A) tail has been added to their ends. In addition, RNase R stalls in the body of many polyadenylated mRNAs, especially at G-rich sequences that have been previously annotated as G-quadruplex (G4) structures. Upon replacing K+ (which stabilizes G4s) with Li+ in the reaction buffer, we find that RNase R is now able to proceed through these sequences and fully degrade the mRNAs in their entirety. In total, our results provide important improvements to the current methods used to isolate circular RNAs as well as a way to reveal RNA structures that may naturally inhibit degradation by cellular exonucleases.

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Dinman, Jonathan D. "Shapeshifting RNAs guide innate immunity." Journal of Biological Chemistry 293, no. 41 (October 12, 2018): 16125–26. http://dx.doi.org/10.1074/jbc.h118.005799.

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The innate immune system can distinguish between RNAs of viral and cellular origin, but the basis for this discrimination is not known. A new paper by Calderon and Conn demonstrates that conformational plasticity determines the ability of one RNA sequence to bind to and activate the pattern recognition receptor OAS1/RNase L. In identifying a novel mode through which the immune response is naturally controlled, this finding opens new avenues toward developing approaches for the management of a wide range of viral infections.

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Ciesielska, Sylwia, Izabella Slezak-Prochazka, Patryk Bil, and Joanna Rzeszowska-Wolny. "Micro RNAs in Regulation of Cellular Redox Homeostasis." International Journal of Molecular Sciences 22, no. 11 (June 2, 2021): 6022. http://dx.doi.org/10.3390/ijms22116022.

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In living cells Reactive Oxygen Species (ROS) participate in intra- and inter-cellular signaling and all cells contain specific systems that guard redox homeostasis. These systems contain both enzymes which may produce ROS such as NADPH-dependent and other oxidases or nitric oxide synthases, and ROS-neutralizing enzymes such as catalase, peroxiredoxins, thioredoxins, thioredoxin reductases, glutathione reductases, and many others. Most of the genes coding for these enzymes contain sequences targeted by micro RNAs (miRNAs), which are components of RNA-induced silencing complexes and play important roles in inhibiting translation of their targeted messenger RNAs (mRNAs). In this review we describe miRNAs that directly target and can influence enzymes responsible for scavenging of ROS and their possible role in cellular redox homeostasis. Regulation of antioxidant enzymes aims to adjust cells to survive in unstable oxidative environments; however, sometimes seemingly paradoxical phenomena appear where oxidative stress induces an increase in the levels of miRNAs which target genes which are supposed to neutralize ROS and therefore would be expected to decrease antioxidant levels. Here we show examples of such cellular behaviors and discuss the possible roles of miRNAs in redox regulatory circuits and further cell responses to stress.

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Henkin, T. M. "Riboswitch RNAs: using RNA to sense cellular metabolism." Genes & Development 22, no. 24 (December 15, 2008): 3383–90. http://dx.doi.org/10.1101/gad.1747308.

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Moon, Stephanie L., and Jeffrey Wilusz. "Viral RNAs versus the Cellular RNA Decay Machinery." Microbe Magazine 9, no. 3 (March 1, 2014): 105–10. http://dx.doi.org/10.1128/microbe.9.105.1.

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Kwok, Chun Kit, and Shankar Balasubramanian. "Targeted Detection of G-Quadruplexes in Cellular RNAs." Angewandte Chemie International Edition 54, no. 23 (April 23, 2015): 6751–54. http://dx.doi.org/10.1002/anie.201500891.

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Kwok, Chun Kit, and Shankar Balasubramanian. "Targeted Detection of G-Quadruplexes in Cellular RNAs." Angewandte Chemie 127, no. 23 (April 23, 2015): 6855–58. http://dx.doi.org/10.1002/ange.201500891.

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Singh, Khushwant, Chris Dardick, and Jiban Kumar Kundu. "RNAi-Mediated Resistance Against Viruses in Perennial Fruit Plants." Plants 8, no. 10 (September 22, 2019): 359. http://dx.doi.org/10.3390/plants8100359.

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Small RNAs (sRNAs) are 20–30-nucleotide-long, regulatory, noncoding RNAs that induce silencing of target genes at the transcriptional and posttranscriptional levels. They are key components for cellular functions during plant development, hormone signaling, and stress responses. Generated from the cleavage of double-stranded RNAs (dsRNAs) or RNAs with hairpin structures by Dicer-like proteins (DCLs), they are loaded onto Argonaute (AGO) protein complexes to induce gene silencing of their complementary targets by promoting messenger RNA (mRNA) cleavage or degradation, translation inhibition, DNA methylation, and/or histone modifications. This mechanism of regulating RNA activity, collectively referred to as RNA interference (RNAi), which is an evolutionarily conserved process in eukaryotes. Plant RNAi pathways play a fundamental role in plant immunity against viruses and have been exploited via genetic engineering to control disease. Plant viruses of RNA origin that contain double-stranded RNA are targeted by the RNA-silencing machinery to produce virus-derived small RNAs (vsRNAs). Some vsRNAs serve as an effector to repress host immunity by capturing host RNAi pathways. High-throughput sequencing (HTS) strategies have been used to identify endogenous sRNA profiles, the “sRNAome”, and analyze expression in various perennial plants. Therefore, the review examines the current knowledge of sRNAs in perennial plants and fruits, describes the development and implementation of RNA interference (RNAi) in providing resistance against economically important viruses, and explores sRNA targets that are important in regulating a variety of biological processes.

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Bellutti, Florian, Maximilian Kauer, Doris Kneidinger, Thomas Lion, and Reinhard Klein. "Identification of RISC-Associated Adenoviral MicroRNAs, a Subset of Their Direct Targets, and Global Changes in the Targetome upon Lytic Adenovirus 5 Infection." Journal of Virology 89, no. 3 (November 19, 2014): 1608–27. http://dx.doi.org/10.1128/jvi.02336-14.

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ABSTRACTAdenoviruses encode a set of highly abundant microRNAs (mivaRNAs), which are generated by Dicer-mediated cleavage of the larger noncoding virus-associated RNAs (VA RNAs) I and II. We performed deep RNA sequencing to thoroughly investigate the relative abundance of individual single strands of mivaRNA isoforms in human A549 cells lytically infected with human adenovirus 5 (Ad5) at physiologically relevant multiplicities of infection (MOIs). In addition, we investigated their relative abundance in the endogenous RNA-induced silencing complexes (RISCs). The occupation of endogenous RISCs by mivaRNAs turned out to be pronounced but not as dominant as previously inferred from experiments with AGO2-overexpressing cells infected at high MOIs. In parallel, levels of RISC-incorporated mRNAs were investigated as well. Analysis of mRNAs enriched in RISCs in Ad5-infected cells revealed that only mRNAs with complementarity to the seed sequences of mivaRNAs derived from VA RNAI but not VA RNAII were overrepresented among them, indicating that only mivaRNAs derived from VA RNAI are likely to contribute substantially to the posttranscriptional downregulation of host gene expression. Furthermore, to generate a comprehensive picture of the entire transcriptome/targetome in lytically infected cells, we determined changes in cellular miRNA levels in both total RNA and RISC RNA as well, and bioinformatical analysis of mRNAs of total RNA/RISC fractions revealed a general, genome-wide trend toward detargeting of cellular mRNAs upon infection. Lastly, we identified the direct targets of both single strands of a VA RNAI-derived mivaRNA that constituted one of the two most abundant isoforms in RISCs of lytically infected A549 cells.IMPORTANCEViral and cellular miRNAs have been recognized as important players in virus-host interactions. This work provides the currently most comprehensive picture of the entire mRNA/miRNA transcriptome and of the complete RISC targetome during lytic adenovirus infection and thus represents the basis for a deeper understanding of the interplay between the virus and the cellular RNA interference machinery. Our data suggest that, at least in the model system that was employed, lytic infection by Ad5 is accompanied by a measurable global net detargeting effect on cellular mRNAs, and analysis of RISC-associated viral small RNAs revealed that the VA RNAs are the only source of virus-encoded miRNAs. Moreover, this work allows to assess the power of individual viral miRNAs to regulate cellular gene expression and provides a list of proven and putative direct targets of these miRNAs, which is of importance, given the fact that information about validated targets of adenovirus-encoded miRNAs is scarce.

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Bohnsack, Katherine, Claudia Höbartner, and Markus Bohnsack. "Eukaryotic 5-methylcytosine (m5C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease." Genes 10, no. 2 (January 30, 2019): 102. http://dx.doi.org/10.3390/genes10020102.

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5-methylcytosine (m5C) is an abundant RNA modification that’s presence is reported in a wide variety of RNA species, including cytoplasmic and mitochondrial ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as messenger RNAs (mRNAs), enhancer RNAs (eRNAs) and a number of non-coding RNAs. In eukaryotes, C5 methylation of RNA cytosines is catalyzed by enzymes of the NOL1/NOP2/SUN domain (NSUN) family, as well as the DNA methyltransferase homologue DNMT2. In recent years, substrate RNAs and modification target nucleotides for each of these methyltransferases have been identified, and structural and biochemical analyses have provided the first insights into how each of these enzymes achieves target specificity. Functional characterizations of these proteins and the modifications they install have revealed important roles in diverse aspects of both mitochondrial and nuclear gene expression. Importantly, this knowledge has enabled a better understanding of the molecular basis of a number of diseases caused by mutations in the genes encoding m5C methyltransferases or changes in the expression level of these enzymes.

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Lettieri-Barbato, Daniele, Katia Aquilano, Carolina Punziano, Giuseppina Minopoli, and Raffaella Faraonio. "MicroRNAs, Long Non-Coding RNAs, and Circular RNAs in the Redox Control of Cell Senescence." Antioxidants 11, no. 3 (February 28, 2022): 480. http://dx.doi.org/10.3390/antiox11030480.

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Cell senescence is critical in diverse aspects of organism life. It is involved in tissue development and homeostasis, as well as in tumor suppression. Consequently, it is tightly integrated with basic physiological processes during life. On the other hand, senescence is gradually being considered as a major contributor of organismal aging and age-related diseases. Increased oxidative stress is one of the main risk factors for cellular damages, and thus a driver of senescence. In fact, there is an intimate link between cell senescence and response to different types of cellular stress. Oxidative stress occurs when the production of reactive oxygen species/reactive nitrogen species (ROS/RNS) is not adequately detoxified by the antioxidant defense systems. Non-coding RNAs are endogenous transcripts that govern gene regulatory networks, thus impacting both physiological and pathological events. Among these molecules, microRNAs, long non-coding RNAs, and more recently circular RNAs are considered crucial mediators of almost all cellular processes, including those implicated in oxidative stress responses. Here, we will describe recent data on the link between ROS/RNS-induced senescence and the current knowledge on the role of non-coding RNAs in the senescence program.

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Bejugam, Pruthvi Raj, Aniruddha Das, and Amaresh Chandra Panda. "Seeing Is Believing: Visualizing Circular RNAs." Non-Coding RNA 6, no. 4 (November 11, 2020): 45. http://dx.doi.org/10.3390/ncrna6040045.

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Advancement in the RNA sequencing techniques has discovered hundreds of thousands of circular RNAs (circRNAs) in humans. However, the physiological function of most of the identified circRNAs remains unexplored. Recent studies have established that spliceosomal machinery and RNA-binding proteins modulate circRNA biogenesis. Furthermore, circRNAs have been implicated in regulating crucial cellular processes by interacting with various proteins and microRNAs. However, there are several challenges in understanding the mechanism of circRNA biogenesis, transport, and their interaction with cellular factors to regulate cellular events because of their low abundance and sequence similarity with linear RNA. Addressing these challenges requires systematic studies that directly visualize the circRNAs in cells at single-molecule resolution along with the molecular regulators. In this review, we present the design, benefits, and weaknesses of RNA imaging techniques such as single-molecule RNA fluorescence in situ hybridization and BaseScope in fixed cells and fluorescent RNA aptamers in live-cell imaging of circRNAs. Furthermore, we propose the potential use of molecular beacons, multiply labeled tetravalent RNA imaging probes, and Cas-derived systems to visualize circRNAs.

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Shanthi, Keerthanaa Balasubramanian, Daniel Fischer, Abhishek Sharma, Antti Kiviniemi, Mika Kaakinen, Seppo J. Vainio, and Geneviève Bart. "Human Adult Astrocyte Extracellular Vesicle Transcriptomics Study Identifies Specific RNAs Which Are Preferentially Secreted as EV Luminal Cargo." Genes 14, no. 4 (March 31, 2023): 853. http://dx.doi.org/10.3390/genes14040853.

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Astrocytes are central nervous system (CNS)-restricted glial cells involved in synaptic function and CNS blood flow regulation. Astrocyte extracellular vesicles (EVs) participate in neuronal regulation. EVs carry RNAs, either surface-bound or luminal, which can be transferred to recipient cells. We characterized the secreted EVs and RNA cargo of human astrocytes derived from an adult brain. EVs were isolated by serial centrifugation and characterized with nanoparticle tracking analysis (NTA), Exoview, and immuno-transmission electron microscopy (TEM). RNA from cells, EVs, and proteinase K/RNase-treated EVs was analyzed by miRNA-seq. Human adult astrocyte EVs ranged in sizes from 50 to 200 nm, with CD81 as the main tetraspanin marker and larger EVs positive for integrin β1. Comparison of the RNA between the cells and EVs identified RNA preferentially secreted in the EVs. In the case of miRNAs, enrichment analysis of their mRNA targets indicates that they are good candidates for mediating EV effects on recipient cells. The most abundant cellular miRNAs were also abundant in EVs, and the majority of their mRNA targets were found to be downregulated in mRNA-seq data, but the enrichment analysis lacked neuronal specificity. Proteinase K/RNase treatment of EV-enriched preparations identified RNAs secreted independently of EVs. Comparing the distribution of cellular and secreted RNA identifies the RNAs involved in intercellular communication via EVs.

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Rosa, Cristina, Yen-Wen Kuo, Hada Wuriyanghan, and Bryce W. Falk. "RNA Interference Mechanisms and Applications in Plant Pathology." Annual Review of Phytopathology 56, no. 1 (August 25, 2018): 581–610. http://dx.doi.org/10.1146/annurev-phyto-080417-050044.

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The origin of RNA interference (RNAi), the cell sentinel system widely shared among eukaryotes that recognizes RNAs and specifically degrades or prevents their translation in cells, is suggested to predate the last eukaryote common ancestor ( 138 ). Of particular relevance to plant pathology is that in plants, but also in some fungi, insects, and lower eukaryotes, RNAi is a primary and effective antiviral defense, and recent studies have revealed that small RNAs (sRNAs) involved in RNAi play important roles in other plant diseases, including those caused by cellular plant pathogens. Because of this, and because RNAi can be manipulated to interfere with the expression of endogenous genes in an intra- or interspecific manner, RNAi has been used as a tool in studies of gene function but also for plant protection. Here, we review the discovery of RNAi, canonical mechanisms, experimental and translational applications, and new RNA-based technologies of importance to plant pathology.

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Hogg, J. Robert. "Viral Evasion and Manipulation of Host RNA Quality Control Pathways." Journal of Virology 90, no. 16 (May 25, 2016): 7010–18. http://dx.doi.org/10.1128/jvi.00607-16.

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Viruses have evolved diverse strategies to maximize the functional and coding capacities of their genetic material. Individual viral RNAs are often used as substrates for both replication and translation and can contain multiple, sometimes overlapping open reading frames. Further, viral RNAs engage in a wide variety of interactions with both host and viral proteins to modify the activities of important cellular factors and direct their own trafficking, packaging, localization, stability, and translation. However, adaptations increasing the information density of small viral genomes can have unintended consequences. In particular, viral RNAs have developed features that mark them as potential targets of host RNA quality control pathways. This minireview focuses on ways in which viral RNAs run afoul of the cellular mRNA quality control and decay machinery, as well as on strategies developed by viruses to circumvent or exploit cellular mRNA surveillance.

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Sadlak, Joanna, Ila Joshi, Tomasz J. Prószyński, and Anthony Kischel. "CircAMOTL1 RNA and AMOTL1 Protein: Complex Functions of AMOTL1 Gene Products." International Journal of Molecular Sciences 24, no. 3 (January 20, 2023): 2103. http://dx.doi.org/10.3390/ijms24032103.

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The complexity of the cellular proteome facilitates the control of a wide range of cellular processes. Non-coding RNAs, including microRNAs and long non-coding RNAs, greatly contribute to the repertoire of tools used by cells to orchestrate various functions. Circular RNAs (circRNAs) constitute a specific class of non-coding RNAs that have recently emerged as a widely generated class of molecules produced from many eukaryotic genes that play essential roles in regulating cellular processes in health and disease. This review summarizes current knowledge about circRNAs and focuses on the functions of AMOTL1 circRNAs and AMOTL1 protein. Both products from the AMOTL1 gene have well-known functions in physiology, cancer, and other disorders. Using AMOTL1 as an example, we illustrate how focusing on both circRNAs and proteins produced from the same gene contributes to a better understanding of gene functions.

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Lew, A. E., L. A. Jackson, and M. I. Bellgard. "Comparative genomic analysis of non-coding sequences and the application of RNA interference tools for bovine functional genomics." Australian Journal of Experimental Agriculture 45, no. 8 (2005): 995. http://dx.doi.org/10.1071/ea05057.

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Non-coding (nc) RNAs are important regulators of developmental genes, and essential for the modification of cellular DNA and chromatin through a process known as RNA interference (RNAi). The mediators of RNAi can be in the form of short double stranded (ds) RNAs, micro (mi) RNAs or small interfering (si) RNAs. miRNAs are involved in a translation repression pathway that inhibits protein translation in mRNA targets. Comparative genomic screens have revealed conserved regulatory non-coding sequences, which assist to predict the function of endogenous miRNAs. Only a few comparative studies include bovine genomic sequence, and RNAi has yet to be applied in bovine genome functional screens. siRNAs target homologous mRNAs for degradation, and thereby, silence specific genes. The use of synthetic siRNAs facilitates the elucidation of gene pathways by specific gene knockdown. A survey of the literature identifies a small number of reports using RNAi to examine immune pathways in bovine cell lines; however, they do not target genes involved in specific production traits. Applications of RNAi to elucidate bovine immune pathways for relevant bacterial and parasite diseases are yet to be reported. The inhibition of viral replication using RNAi has been demonstrated with bovine RNA viruses such as pestivirus and foot and mouth disease virus signifying the potential of RNAi as an antiviral therapeutic. RNAi approaches combined with genome data for protozoan parasites, insects and nematodes, will expedite the identification of novel targets for the treatment and prevention of economically important parasitic infections. This review will examine the approaches used in mammalian RNAi research, the current status of its applications to livestock systems and will discuss potential applications in beef cattle programs.

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Gallois-Montbrun, Sarah, Rebecca K. Holmes, Chad M. Swanson, Mireia Fernández-Ocaña, Helen L. Byers, Malcolm A. Ward, and Michael H. Malim. "Comparison of Cellular Ribonucleoprotein Complexes Associated with the APOBEC3F and APOBEC3G Antiviral Proteins." Journal of Virology 82, no. 11 (March 26, 2008): 5636–42. http://dx.doi.org/10.1128/jvi.00287-08.

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ABSTRACT The human apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F (APOBEC3F [A3F]) and A3G proteins are effective inhibitors of infection by various retroelements and share ∼50% amino acid sequence identity. We therefore undertook comparative analyses of the protein and RNA compositions of A3F- and A3G-associated ribonucleoprotein complexes (RNPs). Like A3G, A3F is found associated with a complex array of cytoplasmic RNPs and can accumulate in RNA-rich cytoplasmic microdomains known as mRNA processing bodies or stress granules. While A3F RNPs display greater resistance to disruption by RNase digestion, the major protein difference is the absence of the Ro60 and La autoantigens. Consistent with this, A3F RNPs also lack a number of small polymerase III RNAs, including the RoRNP-associated Y RNAs, as well as 7SL RNA. Alu RNA is, however, present in A3F and A3G RNPs, and both proteins suppress Alu element retrotransposition. Thus, we define a number of subtle differences between the RNPs associated with A3F and A3G and speculate that these contribute to functional differences that have been described for these proteins.

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Gales, Jón Pol, Julie Kubina, Angèle Geldreich, and Maria Dimitrova. "Strength in Diversity: Nuclear Export of Viral RNAs." Viruses 12, no. 9 (September 11, 2020): 1014. http://dx.doi.org/10.3390/v12091014.

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The nuclear export of cellular mRNAs is a complex process that requires the orchestrated participation of many proteins that are recruited during the early steps of mRNA synthesis and processing. This strategy allows the cell to guarantee the conformity of the messengers accessing the cytoplasm and the translation machinery. Most transcripts are exported by the exportin dimer Nuclear RNA export factor 1 (NXF1)–NTF2-related export protein 1 (NXT1) and the transcription–export complex 1 (TREX1). Some mRNAs that do not possess all the common messenger characteristics use either variants of the NXF1–NXT1 pathway or CRM1, a different exportin. Viruses whose mRNAs are synthesized in the nucleus (retroviruses, the vast majority of DNA viruses, and influenza viruses) exploit both these cellular export pathways. Viral mRNAs hijack the cellular export machinery via complex secondary structures recognized by cellular export factors and/or viral adapter proteins. This way, the viral transcripts succeed in escaping the host surveillance system and are efficiently exported for translation, allowing the infectious cycle to proceed. This review gives an overview of the cellular mRNA nuclear export mechanisms and presents detailed insights into the most important strategies that viruses use to export the different forms of their RNAs from the nucleus to the cytoplasm.

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Kong, Kristen J., Xiaocen Lu, Elena Dolgosheina, Haruki Iino, Adam Cawte, David S. Rueda, and Peter J. Unrau. "Fluorogenic aptamers for imaging and manipulation of cellular RNAs." Biophysical Journal 121, no. 3 (February 2022): 318a—319a. http://dx.doi.org/10.1016/j.bpj.2021.11.1168.

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Mitkevich, Vladimir A., Nickolai A. Tchurikov, Pavel V. Zelenikhin, Irina Yu Petrushanko, Alexander A. Makarov, and Olga N. Ilinskaya. "Binase cleaves cellular noncoding RNAs and affects coding mRNAs." FEBS Journal 277, no. 1 (November 26, 2009): 186–96. http://dx.doi.org/10.1111/j.1742-4658.2009.07471.x.

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LEE, L. K., B. M. DUNHAM, Z. LI, and C. M. ROTH. "Cellular Dynamics of Antisense Oligonucleotides and Short Interfering RNAs." Annals of the New York Academy of Sciences 1082, no. 1 (October 1, 2006): 47–51. http://dx.doi.org/10.1196/annals.1348.061.

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Sesto, Nina, Mikael Koutero, and Pascale Cossart. "Bacterial and cellular RNAs at work during Listeria infection." Future Microbiology 9, no. 9 (September 2014): 1025–37. http://dx.doi.org/10.2217/fmb.14.79.

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Borghini, Andrea, and Maria Grazia Andreassi. "Non-coding RNAs in cellular response to ionizing radiation." Non-coding RNA Investigation 2 (2018): 42. http://dx.doi.org/10.21037/ncri.2018.06.10.

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Silverman, Adam P., and Eric T. Kool. "Quenched probes for highly specific detection of cellular RNAs." Trends in Biotechnology 23, no. 5 (May 2005): 225–30. http://dx.doi.org/10.1016/j.tibtech.2005.03.007.

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Sizova, D. V., and I. N. Shatsky. "Internal ribosome entry sites of viral and cellular RNAs." Molecular Biology 34, no. 2 (March 2000): 157–67. http://dx.doi.org/10.1007/bf02759634.

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Lakhotia, Subhash C. "Long non-coding RNAs coordinate cellular responses to stress." Wiley Interdisciplinary Reviews: RNA 3, no. 6 (September 13, 2012): 779–96. http://dx.doi.org/10.1002/wrna.1135.

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Park, Seongjin, Karine Prévost, Matt Reyer, Emily Heideman, Wei Liu, Eric Massé, and Jingyi Fei. "Cellular Distribution and Diffusivity of Hfq with Interacting RNAs." Biophysical Journal 116, no. 3 (February 2019): 501a. http://dx.doi.org/10.1016/j.bpj.2018.11.2705.

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Plawgo, Kinga, and Katarzyna Dorota Raczynska. "Context-Dependent Regulation of Gene Expression by Non-Canonical Small RNAs." Non-Coding RNA 8, no. 3 (April 29, 2022): 29. http://dx.doi.org/10.3390/ncrna8030029.

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In recent functional genomics studies, a large number of non-coding RNAs have been identified. It has become increasingly apparent that noncoding RNAs are crucial players in a wide range of cellular and physiological functions. They have been shown to modulate gene expression on different levels, including transcription, post-transcriptional processing, and translation. This review aims to highlight the diverse mechanisms of the regulation of gene expression by small noncoding RNAs in different conditions and different types of human cells. For this purpose, various cellular functions of microRNAs (miRNAs), circular RNAs (circRNAs), snoRNA-derived small RNAs (sdRNAs) and tRNA-derived fragments (tRFs) will be exemplified, with particular emphasis on the diversity of their occurrence and on the effects on gene expression in different stress conditions and diseased cell types. The synthesis and effect on gene expression of these noncoding RNAs varies in different cell types and may depend on environmental conditions such as different stresses. Moreover, noncoding RNAs play important roles in many diseases, including cancer, neurodegenerative disorders, and viral infections.

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Betti, Federico, Maria José Ladera-Carmona, Pierdomenico Perata, and Elena Loreti. "RNAi Mediated Hypoxia Stress Tolerance in Plants." International Journal of Molecular Sciences 21, no. 24 (December 10, 2020): 9394. http://dx.doi.org/10.3390/ijms21249394.

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Small RNAs regulate various biological process involved in genome stability, development, and adaptive responses to biotic or abiotic stresses. Small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs). MicroRNAs (miRNAs) are regulators of gene expression that affect the transcriptional and post-transcriptional regulation in plants and animals through RNA interference (RNAi). miRNAs are endogenous small RNAs that originate from the processing of non-coding primary miRNA transcripts folding into hairpin-like structures. The mature miRNAs are incorporated into the RNA-induced silencing complex (RISC) and drive the Argonaute (AGO) proteins towards their mRNA targets. siRNAs are generated from a double-stranded RNA (dsRNA) of cellular or exogenous origin. siRNAs are also involved in the adaptive response to biotic or abiotic stresses. The response of plants to hypoxia includes a genome-wide transcription reprogramming. However, little is known about the involvement of RNA signaling in gene regulation under low oxygen availability. Interestingly, miRNAs have been shown to play a role in the responses to hypoxia in animals, and recent evidence suggests that hypoxia modulates the expression of various miRNAs in plant systems. In this review, we describe recent discoveries on the impact of RNAi on plant responses to hypoxic stress in plants.

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Chen, Beibei, Bo Zhang, Huaxia Luo, Jiao Yuan, Geir Skogerbø, and Runsheng Chen. "Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells." International Journal of Cell Biology 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/672462.

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Introduction. Small noncoding RNAs have important regulatory functions in different cell pathways. It is believed that most of them mainly play role in gene post-transcriptional regulation in the cytoplasm. Recent evidence suggests miRNA and siRNA activity in the nucleus. Here, we show distinct genome-wide sub-cellular localization distribution profiles of small noncoding RNAs in human breast cancer cells.Methods. We separated breast cancer cell nuclei from cytoplasm, and identified small RNA sequences using a high-throughput sequencing platform. To determine the relationship between miRNA sub-cellular distribution and cancer progression, we used microarray analysis to examine the miRNA expression levels in nucleus and cytoplasm of three human cell lines, one normal breast cell line and two breast cancer cell lines. Logistic regression and SVM were used for further analysis.Results. The sub-cellular distribution of small noncoding RNAs shows that numerous miRNAs and their isoforms (isomiR) not only locate to the cytoplasm but also appeare in the nucleus. Subsequent microarray analyses indicated that the miRNA nuclear-cytoplasmic-ratio is a significant characteristic of different cancer cell lines.Conclusions. Our results indicate that the sub-cellular distribution is important for miRNA function, and that the characterization of the small RNAs sub-cellular localizome may contribute to cancer research and diagnosis.

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Journal articles on the topic 'Cellular RNAs'

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