scholarly journals RNA Structures Required for Production of Subgenomic Flavivirus RNA

2010 ◽  
Vol 84 (21) ◽  
pp. 11407-11417 ◽  
Author(s):  
Anneke Funk ◽  
Katherine Truong ◽  
Tomoko Nagasaki ◽  
Shessy Torres ◽  
Nadia Floden ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Noncoding Rna ◽  
Secondary Structures ◽  
Vital Role ◽  
Rna Structures ◽  
Stem Loop ◽  
Small Noncoding Rna ◽  
Positive Sense ◽  
Cell Host Microbe ◽  
Nuclease Degradation

ABSTRACT Flaviviruses are a group of single-stranded, positive-sense RNA viruses causing ∼100 million infections per year. We have recently shown that flaviviruses produce a unique, small, noncoding RNA (∼0.5 kb) derived from the 3′ untranslated region (UTR) of the genomic RNA (gRNA), which is required for flavivirus-induced cytopathicity and pathogenicity (G. P. Pijlman et al., Cell Host Microbe, 4: 579-591, 2008). This RNA (subgenomic flavivirus RNA [sfRNA]) is a product of incomplete degradation of gRNA presumably by the cellular 5′-3′ exoribonuclease XRN1, which stalls on the rigid secondary structure stem-loop II (SL-II) located at the beginning of the 3′ UTR. Mutations or deletions of various secondary structures in the 3′ UTR resulted in the loss of full-length sfRNA (sfRNA1) and production of smaller and less abundant sfRNAs (sfRNA2 and sfRNA3). Here, we investigated in detail the importance of West Nile virus Kunjin (WNVKUN) 3′ UTR secondary structures as well as tertiary interactions for sfRNA formation. We show that secondary structures SL-IV and dumbbell 1 (DB1) downstream of SL-II are able to prevent further degradation of gRNA when the SL-II structure is deleted, leading to production of sfRNA2 and sfRNA3, respectively. We also show that a number of pseudoknot (PK) interactions, in particular PK1 stabilizing SL-II and PK3 stabilizing DB1, are required for protection of gRNA from nuclease degradation and production of sfRNA. Our results show that PK interactions play a vital role in the production of nuclease-resistant sfRNA, which is essential for viral cytopathicity in cells and pathogenicity in mice.

The role of microRNA in degeneration of the intervertebral disc

2020 ◽  
Vol 27 (2) ◽  
pp. 66-71
Author(s):  
Ozal Arzuman Beylerli ◽  
Ilgiz F. Gareev ◽  
Valentin N. Pavlov
Keyword(s):  
Intervertebral Disc ◽  
Noncoding Rna ◽  
Structural Changes ◽  
Vital Role ◽  
Chronic Lower Back Pain ◽  
Rna Molecules ◽  
Small Noncoding Rna ◽  
Clinical Biomarkers ◽  
Matrix Cell

MicroRNAs (miRNAs) are a class of small noncoding RNA molecules that negatively regulate gene expression at posttranscriptional levels. MiRNAs regulate many normal physiological processes, and also play an important role in the development of most disorders. The expression levels of miRNAs are characterized by endogenous properties and tissue specificity. These characteristics increase the likelihood that miRNAs can serve as useful clinical biomarkers in the diagnosis of certain diseases. Chronic lower back pain is usually associated with degeneration of the intervertebral disc (IDD), which is closely associated with apoptosis, impaired extracellular matrix, cell proliferation, and an inflammatory response. This process is characterized by a cascade of molecular, cellular, biochemical, and structural changes. Currently, there is no clinical therapy that shows the pathophysiology of disk degeneration. The presence of unregulated expression of miRNA in patients with degenerative disk disease indicates a vital role of miRNAs in the pathogenesis of IDD. It becomes apparent that epigenetic processes affect the evolution of IDD as much as the genetic background. Deregulated phenotypes of pulp nucleus cells, including differentiation, migration, proliferation, and apoptosis, are involved in all stages of the progression of human IDD. In this review, we will focus on the role and therapeutic value of miRNAs in IDD.

scholarly journals Identification of a cis-Acting Replication Element within the Poliovirus Coding Region

2000 ◽  
Vol 74 (10) ◽  
pp. 4590-4600 ◽  
Author(s):  
Ian Goodfellow ◽  
Yasmin Chaudhry ◽  
Andrew Richardson ◽  
Janet Meredith ◽  
Jeffrey W. Almond ◽  
...  
Keyword(s):  
Rna Virus ◽  
Site Directed Mutagenesis ◽  
Evolutionary Significance ◽  
Rna Structures ◽  
Coding Region ◽  
Rna Sequences ◽  
Stem Loop ◽  
Cis Acting ◽  
Function Recovery ◽  
Positive Sense

ABSTRACT The replication of poliovirus, a positive-stranded RNA virus, requires translation of the infecting genome followed by virus-encoded VPg and 3D polymerase-primed synthesis of a negative-stranded template. RNA sequences involved in the latter process are poorly defined. Since many sequences involved in picornavirus replication form RNA structures, we searched the genome, other than the untranslated regions, for predicted local secondary structural elements and identified a 61-nucleotide (nt) stem-loop in the region encoding the 2C protein. Covariance analysis suggested the structure was well conserved in the Enterovirus genus of the Picornaviridae. Site-directed mutagenesis, disrupting the structure without affecting the 2C product, destroyed genome viability and suggested that the structure was required in the positive sense for function. Recovery of revertant viruses suggested that integrity of the structure was critical for function, and analysis of replication demonstrated that nonviable mutants did not synthesize negative strands. Our conclusion, that this RNA secondary structure constitutes a novel polioviruscis-acting replication element (CRE), is supported by the demonstration that subgenomic replicons bearing lethal mutations in the native structure can be restored to replication competence by the addition of a second copy of the 61-nt wild-type sequence at another location within the genome. This poliovirus CRE functionally resembles an element identified in rhinovirus type 14 (K. L. McKnight and S. M. Lemon, RNA 4:1569–1584, 1998) and the cardioviruses (P. E. Lobert, N. Escriou, J. Ruelle, and T. Michiels, Proc. Natl. Acad. Sci. USA 96:11560–11565, 1999) but differs in sequence, structure, and location. The functional role and evolutionary significance of CREs in the replication of positive-sense RNA viruses is discussed.

scholarly journals Small cis-Acting Sequences That Specify Secondary Structures in a Chloroplast mRNA Are Essential for RNA Stability and Translation

1999 ◽  
Vol 19 (12) ◽  
pp. 8479-8491 ◽  
Author(s):  
David C. Higgs ◽  
Risa S. Shapiro ◽  
Karen L. Kindle ◽  
David B. Stern
Keyword(s):  
Untranslated Region ◽  
Rna Stability ◽  
Dimethyl Sulfate ◽  
Secondary Structures ◽  
Rna Modification ◽  
Range Interaction ◽  
Stem Loop ◽  
Chloroplast Mrna

ABSTRACT Nucleus-encoded proteins interact with cis-acting elements in chloroplast transcripts to promote RNA stability and translation. We have analyzed the structure and function of three such elements within the Chlamydomonas petD 5′ untranslated region; petD encodes subunit IV of the cytochromeb 6/f complex. These elements were delineated by linker-scanning mutagenesis, and RNA secondary structures were investigated by mapping nuclease-sensitive sites in vitro and by in vivo dimethyl sulfate RNA modification. Element I spans a maximum of 8 nucleotides (nt) at the 5′ end of the mRNA; it is essential for RNA stability and plays a role in translation. This element appears to form a small stem-loop that may interact with a previously described nucleus-encoded factor to block 5′→3′ exoribonucleolytic degradation. Elements II and III, located in the center and near the 3′ end of the 5′ untranslated region, respectively, are essential for translation, but mutations in these elements do not affect mRNA stability. Element II is a maximum of 16 nt in length, does not form an obvious secondary structure, and appears to bind proteins that protect it from dimethyl sulfate modification. Element III spans a maximum of 14 nt and appears to form a stem-loop in vivo, based on dimethyl sulfate modification and the sequences of intragenic suppressors of element III mutations. Furthermore, mutations in element II result in changes in the RNA structure near element III, consistent with a long-range interaction that may promote translation.

MicroRNA29a regulates the expression of the nuclear oncogene Ski

Blood ◽  
2011 ◽  
Vol 118 (7) ◽  
pp. 1899-1902 ◽  
Author(s):  
Sabine Teichler ◽  
Thomas Illmer ◽  
Josephine Roemhild ◽  
Dmitriy Ovcharenko ◽  
Thorsten Stiewe ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Myeloid Leukemia ◽  
Noncoding Rna ◽  
Target Gene ◽  
Inverse Correlation ◽  
Fragile Sites ◽  
Rna Molecules ◽  
Small Noncoding Rna ◽  
Chromosome 7Q ◽  
Acute Myeloid

Abstract MicroRNAs (miRNAs) are small, noncoding RNA molecules that regulate growth and differentiation. miRNAs are frequently located at cancer-specific fragile sites in the human genome, such as chromosome 7q. The nuclear oncogene SKI is up-regulated in acute myeloid leukemia (AML) with −7/del7q. Here we asked whether loss of miRNAs on chromosome 7q may explain this up-regulation. miR-29a expression was found to be down-regulated in AML with −7/del7q. Forced expression of miR-29a down-regulated Ski and its target gene, Nr-CAM, whereas miR-29a inhibition induced Ski expression. Luciferase assays validated a functional binding site for miR-29a in the 3′ untranslated region of SKI. Finally, in samples of AML patients, we observed an inverse correlation of Ski and miR-29a expression, respectively. In conclusion, up-regulation of Ski in AML with −7/del7q is caused by loss of miR-29a. miR-29a may therefore function as an important tumor suppressor in AML by restraining expression of the SKI oncogene.

scholarly journals CrfA, a Small Noncoding RNA Regulator of Adaptation to Carbon Starvation in Caulobacter crescentus

2010 ◽  
Vol 192 (18) ◽  
pp. 4763-4775 ◽  
Author(s):  
Stephen G. Landt ◽  
Joseph A. Lesley ◽  
Leticia Britos ◽  
Lucy Shapiro
Keyword(s):  
Posttranscriptional Regulation ◽  
Noncoding Rna ◽  
Target Genes ◽  
Caulobacter Crescentus ◽  
Gene Activation ◽  
Carbon Starvation ◽  
Base Substitution ◽  
Complementary Sequence ◽  
Stem Loop ◽  
Small Noncoding Rna

ABSTRACT Small noncoding regulatory RNAs (sRNAs) play a key role in the posttranscriptional regulation of many bacterial genes. The genome of Caulobacter crescentus encodes at least 31 sRNAs, and 27 of these sRNAs are of unknown function. An overexpression screen for sRNA-induced growth inhibition along with sequence conservation in a related Caulobacter species led to the identification of a novel sRNA, CrfA, that is specifically induced upon carbon starvation. Twenty-seven genes were found to be strongly activated by CrfA accumulation. One-third of these target genes encode putative TonB-dependent receptors, suggesting CrfA plays a role in the surface modification of C. crescentus, facilitating the uptake of nutrients during periods of carbon starvation. The mechanism of CrfA-mediated gene activation was investigated for one of the genes predicted to encode a TonB-dependent receptor, CC3461. CrfA functions to stabilize the CC3461 transcript. Complementarity between a region of CrfA and the terminal region of the CC3461 5′-untranslated region (5′-UTR) and also the behavior of a deletion of this region and a site-specific base substitution and a 3-base deletion in the CrfA complementary sequence suggest that CrfA binds to a stem-loop structure upstream of the CC3461 Shine-Dalgarno sequence and stabilizes the transcript.

scholarly journals Spatiotemporal Expression and Molecular Characterization ofmiR-344bandmiR-344cin the Developing Mouse Brain

2016 ◽  
Vol 2016 ◽  
pp. 1-16 ◽  
Author(s):  
Jia-Wen Leong ◽  
Syahril Abdullah ◽  
King-Hwa Ling ◽  
Pike-See Cheah
Keyword(s):  
Mouse Brain ◽  
Noncoding Rna ◽  
Granular Layer ◽  
Developmental Stages ◽  
Adult Brain ◽  
Stem Loop ◽  
Small Noncoding Rna ◽  
Spatiotemporal Expression ◽  
Developing Mouse Brain

MicroRNAs (miRNAs) are small noncoding RNA known to regulate brain development. The expression of two novel miRNAs, namely,miR-344bandmiR-344c, was characterized during mouse brain developmental stages in this study.In situhybridization analysis showed thatmiR-344bandmiR-344cwere expressed in the germinal layer during embryonic brain developmental stages. In contrast,miR-344bwas not detectable in the adult brain whilemiR-344cwas expressed exclusively in the adult olfactory bulb and cerebellar granular layer. Stem-loop RT-qPCR analysis of whole brain RNAs showed that expression of themiR-344bandmiR-344cwas increased as brain developed throughout the embryonic stage and maintained at adulthood. Further investigation showed that these miRNAs were expressed in adult organs, wheremiR-344bandmiR-344cwere highly expressed in pancreas and brain, respectively. Bioinformatics analysis suggestedmiR-344bandmiR-344ctargetedOlig2andOtx2mRNAs, respectively. However, luciferase experiments demonstrated that these miRNAs did not targetOlig2andOtx2mRNAs. Further investigation on the locality ofmiR-344bandmiR-344cshowed that both miRNAs were localized in nuclei of immature neurons. In conclusion,miR-344bandmiR-344cwere expressed spatiotemporally during mouse brain developmental stages.

scholarly journals 1H, 13C and 15N chemical shift assignment of the stem-loop 5a from the 5′-UTR of SARS-CoV-2

2021 ◽  
Author(s):  
Robbin Schnieders ◽  
Stephen A. Peter ◽  
Elnaz Banijamali ◽  
Magdalena Riad ◽  
Nadide Altincekic ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Drug Targets ◽  
Antiviral Drug ◽  
Chemical Shift Assignment ◽  
Solution Nmr ◽  
Structural Studies ◽  
Stem Loop ◽  
Rna Translation ◽  
Positive Sense ◽  
Shift Assignment

AbstractThe SARS-CoV-2 (SCoV-2) virus is the causative agent of the ongoing COVID-19 pandemic. It contains a positive sense single-stranded RNA genome and belongs to the genus of Betacoronaviruses. The 5′- and 3′-genomic ends of the 30 kb SCoV-2 genome are potential antiviral drug targets. Major parts of these sequences are highly conserved among Betacoronaviruses and contain cis-acting RNA elements that affect RNA translation and replication. The 31 nucleotide (nt) long highly conserved stem-loop 5a (SL5a) is located within the 5′-untranslated region (5′-UTR) important for viral replication. SL5a features a U-rich asymmetric bulge and is capped with a 5′-UUUCGU-3′ hexaloop, which is also found in stem-loop 5b (SL5b). We herein report the extensive 1H, 13C and 15N resonance assignment of SL5a as basis for in-depth structural studies by solution NMR spectroscopy.

scholarly journals COT-04 Circulating biomarker for glioblastoma and primary central nervous system lymphoma -Next Generation Sequencing of small noncoding RNA-

2020 ◽  
Vol 2 (Supplement_3) ◽  
pp. ii21-ii21
Author(s):  
Shumpei Onishi ◽  
Fumiyuki Yamasaki ◽  
Motoki Takano ◽  
Ushio Yonezawa ◽  
Kazuhiko Sugiyama ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Noncoding Rna ◽  
Central Nervous System Lymphoma ◽  
Serum Samples ◽  
Small Noncoding Rna ◽  
Non Invasive ◽  
Diagnostic Models ◽  
Healthy Control ◽  
Generation Sequencing

Abstract Objective: Glioblastoma (GBM) and Primary Central Nervous System Lymphoma (PCNSL) are common intracranial malignant tumors. They sometimes present similar radiological findings and diagnoses could be difficult without surgical biopsy. For improving the current management, development of non-invasive biomarkers are desired. In this study, we explored the differently expressed circulating small noncoding RNA (sncRNA) in serum for specific diagnostic tool of GBM and PCNSL. Material & Methods: Serum samples were obtained from three groups: 1) GBM patients (N=26), 2) PCNSL patients (N=14) 3) healthy control (N=114). The total small RNAs were extracted from serum. The whole expression profiles of serum sncRNAs were measured using Next-Generation Sequencing System. We analyzed serum levels of sncRNAs (15–55 nt) in each serum samples. The difference of sncRNAs expression profile among three groups were compared. Data analysis was performed by logistic regression analysis followed by leave-one-out cross-validation (LOOCV). The accuracy of diagnostic models of sncRNAs combination were evaluated by receiver operating characteristic (ROC) analysis. Results: We created the combination models using three sncRNA in each models based on the logistic regression analysis. The model 1 (based on sncRNA-X1, X2 and X3) enabled to differentiate GBM patients form healthy control with a sensitivity of 92.3% and a specificity of 99.2% (AUC: 0.993). The model 2 (based on sncRNA-Y1, Y2 and Y3) enabled to differentiate PCNSL patients form healthy control with a sensitivity of 100% and a specificity of 93.9% (AUC: 0.984). The model 3 (based on sncRNA-Z1, Z2 and Z3) enabled to differentiate GBM patients form PCNSL patients with a sensitivity of 92.3% and a specificity of 78.6% (AUC: 0.920). Conclusion: We found three diagnostic models of serum sncRNAs as non-invasive biomarkers potentially useful for detection of GBM and PCNSL from healthy control, and for differentiation GBM from PCNSL.

scholarly journals The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1473
Author(s):  
Junxing Zhao ◽  
Jianming Qiu ◽  
Sadikshya Aryal ◽  
Jennifer L. Hackett ◽  
Jingxin Wang
Keyword(s):  
Untranslated Region ◽  
Dimethyl Sulfate ◽  
Nonstructural Proteins ◽  
Stem Loop ◽  
Cis Acting ◽  
Chemical Probing ◽  
Mutational Profiling ◽  
Genome Transcription ◽  
Polymerase Binding ◽  
Transcription And Replication

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. The 3′ untranslated region (UTR) of this β-CoV contains essential cis-acting RNA elements for the viral genome transcription and replication. These elements include an equilibrium between an extended bulged stem-loop (BSL) and a pseudoknot. The existence of such an equilibrium is supported by reverse genetic studies and phylogenetic covariation analysis and is further proposed as a molecular switch essential for the control of the viral RNA polymerase binding. Here, we report the SARS-CoV-2 3′ UTR structures in cells that transcribe the viral UTRs harbored in a minigene plasmid and isolated infectious virions using a chemical probing technique, namely dimethyl sulfate (DMS)-mutational profiling with sequencing (MaPseq). Interestingly, the putative pseudoknotted conformation was not observed, indicating that its abundance in our systems is low in the absence of the viral nonstructural proteins (nsps). Similarly, our results also suggest that another functional cis-acting element, the three-helix junction, cannot stably form. The overall architectures of the viral 3′ UTRs in the infectious virions and the minigene-transfected cells are almost identical.

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