scholarly journals Consistent global structures of complex RNA states through multidimensional chemical mapping

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Clarence Yu Cheng ◽  
Fang-Chieh Chou ◽  
Wipapat Kladwang ◽  
Siqi Tian ◽  
Pablo Cordero ◽  
...  
Keyword(s):  
Secondary Structure ◽  
3D Structure ◽  
Three Dimensions ◽  
Biological Processes ◽  
Chemical Mapping ◽  
Entry Site ◽  
Tertiary Structures ◽  
Internal Ribosome Entry ◽  
Non Coding Rna ◽  
Paired End Sequencing

Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.

scholarly journals Out-of-Plane Aptamer Functionalization of RNA Three-Helix Tiles

Nanomaterials ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 507 ◽  
Author(s):  
Aradhana Chopra ◽  
Sandra Sagredo ◽  
Guido Grossi ◽  
Ebbe Andersen ◽  
Friedrich Simmel
Keyword(s):  
Small Molecules ◽  
Internal Ribosome Entry Site ◽  
Hybrid Nanostructures ◽  
Three Dimensions ◽  
Rna Structures ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Double Helices ◽  
Out Of Plane ◽  
Rna Motif

Co-transcriptionally folding RNA nanostructures have great potential as biomolecular scaffolds, which can be used to organize small molecules or proteins into spatially ordered assemblies. Here, we develop an RNA tile composed of three parallel RNA double helices, which can associate into small hexagonal assemblies via kissing loop interactions between its two outer helices. The inner RNA helix is modified with an RNA motif found in the internal ribosome entry site (IRES) of the hepatitis C virus (HCV), which provides a 90° bend. This modification is used to functionalize the RNA structures with aptamers pointing perpendicularly away from the tile plane. We demonstrate modifications with the fluorogenic malachite green and Spinach aptamers as well with the protein-binding PP7 and streptavidin aptamers. The modified structures retain the ability to associate into larger assemblies, representing a step towards RNA hybrid nanostructures extending in three dimensions.

scholarly journals The 5′ untranslated region of GB virus B shows functional similarity to the internal ribosome entry site of hepatitis C virus

1999 ◽  
Vol 80 (9) ◽  
pp. 2337-2341 ◽  
Author(s):  
Ken Grace ◽  
Margaret Gartland ◽  
Peter Karayiannis ◽  
Michael J. McGarvey ◽  
Berwyn Clarke
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Secondary Structure ◽  
Internal Ribosome Entry Site ◽  
Mutational Analysis ◽  
Sequence Similarity ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Close Phylogenetic Relationship

Since its characterization in 1995, there has been increasing interest in the significance of GB virus B (GBV-B) due to its close phylogenetic relationship to hepatitis C virus (HCV). The genome of GBV-B is similar in length and organization to that of HCV and the two viruses share sequence similarity in their 5′ untranslated regions (5′UTR). A secondary structure model of the GBV-B 5′UTR has been proposed by comparative sequence analysis with HCV. The highly conserved secondary structure, present in HCV and the pestiviruses, is also present in the 5′UTR of GBV-B. Translation of the HCV polyprotein initiates via an internal ribosome entry site (IRES) and it is proposed that the GBV-B UTR may function in a similar manner. Dicistronic reporter constructs were made to investigate the function of the GBV-B 5′UTR. Mutational analysis and in vitro translation experiments demonstrate that GBV-B initiates translation via an IRES.

scholarly journals Selective destabilization of short-lived mRNAs with the granulocyte-macrophage colony-stimulating factor AU-rich 3' noncoding region is mediated by a cotranslational mechanism.

1993 ◽  
Vol 13 (3) ◽  
pp. 1971-1980 ◽  
Author(s):  
T Aharon ◽  
R J Schneider
Keyword(s):  
Secondary Structure ◽  
Noncoding Region ◽  
Protein Synthesis Inhibitors ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Ribosome Binding ◽  
Selective Degradation ◽  
Cellular Mrnas ◽  
Potential Link ◽  
Macrophage Colony

The 3' noncoding region element (AUUUA)n specifically targets many short-lived mRNAs for degradation. Although the mechanism by which this sequence functions is not yet understood, a potential link between facilitated mRNA turnover and translation has been implied by the stabilization of cellular mRNAs in the presence of protein synthesis inhibitors. We therefore directly investigated the role of translation on mRNA stability. We demonstrate that mRNAs which are poorly translated through the introduction of stable secondary structure in the 5' noncoding region are not efficiently targeted for selective destabilization by the (AUUUA)n element. These results suggest that AUUUA-mediated degradation involves either a 5'-->3' exonuclease or is coupled to ongoing translation of the mRNA. To distinguish between these two possibilities, we inserted the poliovirus internal ribosome entry site, which promotes internal ribosome initiation, downstream of the 5' secondary structure. Translation directed by internal ribosome binding was found to fully restore targeted destabilization of AUUUA-containing mRNAs despite the presence of 5' secondary structure. This study therefore demonstrates that selective degradation mediated by the (AUUUA)n element is coupled to ribosome binding or ongoing translation of the mRNA and does not involve 5'-to-3' exonuclease activity.

scholarly journals Sequence and secondary structure requirements in a highly conserved element for foot-and-mouth disease virus internal ribosome entry site activity and eIF4G binding

2004 ◽  
Vol 85 (9) ◽  
pp. 2555-2565 ◽  
Author(s):  
Gergis Bassili ◽  
Eleni Tzima ◽  
Yutong Song ◽  
Lanja Saleh ◽  
Kerstin Ochs ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Disease Virus ◽  
Internal Ribosome Entry Site ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Primary Sequence ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Mouth Disease Virus ◽  
Foot And Mouth

Foot-and-mouth disease virus (FMDV) and other picornaviruses initiate translation of their positive-strand RNA genomes at the highly structured internal ribosome entry site (IRES), which mediates ribosome recruitment to an internal site of the virus RNA. This process is facilitated by eukaryotic translation initiation factors (eIFs), such as eIF4G and eIF4B. In the eIF4G-binding site, a characteristic, discontinuous sequence element is highly conserved within the cardio- and aphthovirus subgroup (including FMDV) of the picornaviruses. This conserved element was mutated in order to investigate its primary sequence and secondary structure requirements for IRES function. Both binding of eIF4G to the IRES and IRES-directed translation are seriously impaired by mutations in two unpaired dinucleotide stretches that are exposed from the double-stranded (ds)RNA. In the base-paired regions of the conserved element, maintenance of the double-stranded secondary structure is essential, whilst in some cases, the primary sequence within the dsRNA regions is also important for IRES function. Extra eIF4F added to the translation reaction does not restore full IRES activity or eIF4G binding, indicating that disturbances in the structure of this conserved element cannot be overcome by increased initiation factor concentrations.

scholarly journals Long non-coding RNA NR2F1-AS1 induces breast cancer lung metastatic dormancy by regulating NR2F1 and ΔNp63

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yingjie Liu ◽  
Peiyuan Zhang ◽  
Qiuyao Wu ◽  
Houqin Fang ◽  
Yuan Wang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Rna Binding ◽  
Epithelial Mesenchymal Transition ◽  
Disseminated Tumor Cells ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Mesenchymal Transition ◽  
Non Coding Rna ◽  
Tumor Dissemination ◽  
Long Non Coding Rna

AbstractDisseminated tumor cells often fall into a long term of dormant stage, characterized by decreased proliferation but sustained survival, in distant organs before awakening for metastatic growth. However, the regulatory mechanism of metastatic dormancy and awakening is largely unknown. Here, we show that the epithelial-like and mesenchymal-like subpopulations of breast cancer stem-like cells (BCSCs) demonstrate different levels of dormancy and tumorigenicity in lungs. The long non-coding RNA (lncRNA) NR2F1-AS1 (NAS1) is up-regulated in the dormant mesenchymal-like BCSCs, and functionally promotes tumor dissemination but reduces proliferation in lungs. Mechanistically, NAS1 binds to NR2F1 mRNA and recruits the RNA-binding protein PTBP1 to promote internal ribosome entry site (IRES)-mediated NR2F1 translation, thus leading to suppression of ΔNp63 transcription by NR2F1. Furthermore, ΔNp63 downregulation results in epithelial-mesenchymal transition, reduced tumorigenicity and enhanced dormancy of cancer cells in lungs. Overall, the study links BCSC plasticity with metastatic dormancy, and reveals the lncRNA as an important regulator of both processes.

scholarly journals The Picornavirus Avian Encephalomyelitis Virus Possesses a Hepatitis C Virus-Like Internal Ribosome Entry Site Element

2007 ◽  
Vol 82 (4) ◽  
pp. 1993-2003 ◽  
Author(s):  
Mehran Bakhshesh ◽  
Elisabetta Groppelli ◽  
Margaret M. Willcocks ◽  
Elizabeth Royall ◽  
Graham J. Belsham ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Secondary Structure ◽  
Internal Ribosome Entry Site ◽  
Mammalian Cells ◽  
Hepatitis A Virus ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Encephalomyelitis Virus ◽  
Ires Element

ABSTRACT Avian encephalomyelitis virus (AEV) is a picornavirus that causes disease in poultry worldwide, and flocks must be vaccinated for protection. AEV is currently classified within the hepatovirus genus, since its proteins are most closely related to those of hepatitis A virus (HAV). We now provide evidence that the 494-nucleotide-long 5′ untranslated region of the AEV genome contains an internal ribosome entry site (IRES) element that functions efficiently in vitro and in mammalian cells. Unlike the HAV IRES, the AEV IRES is relatively short and functions in the presence of cleaved eIF4G and it is also resistant to an inhibitor of eIF4A. These properties are reminiscent of the recently discovered class of IRES elements within certain other picornaviruses, such as porcine teschovirus 1 (PTV-1). Like the PTV-1 IRES, the AEV IRES shows significant similarity to the hepatitis C virus (HCV) IRES in sequence, function, and predicted secondary structure. Furthermore, mutational analysis of the predicted pseudoknot structure at the 3′ end of the AEV IRES lends support to the secondary structure we present. AEV is therefore another example of a picornavirus harboring an HCV-like IRES element within its genome, and thus, its classification within the hepatovirus genus may need to be reassessed in light of these findings.

Selective destabilization of short-lived mRNAs with the granulocyte-macrophage colony-stimulating factor AU-rich 3' noncoding region is mediated by a cotranslational mechanism

1993 ◽  
Vol 13 (3) ◽  
pp. 1971-1980
Author(s):  
T Aharon ◽  
R J Schneider
Keyword(s):  
Secondary Structure ◽  
Noncoding Region ◽  
Protein Synthesis Inhibitors ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Ribosome Binding ◽  
Selective Degradation ◽  
Cellular Mrnas ◽  
Potential Link ◽  
Macrophage Colony

The 3' noncoding region element (AUUUA)n specifically targets many short-lived mRNAs for degradation. Although the mechanism by which this sequence functions is not yet understood, a potential link between facilitated mRNA turnover and translation has been implied by the stabilization of cellular mRNAs in the presence of protein synthesis inhibitors. We therefore directly investigated the role of translation on mRNA stability. We demonstrate that mRNAs which are poorly translated through the introduction of stable secondary structure in the 5' noncoding region are not efficiently targeted for selective destabilization by the (AUUUA)n element. These results suggest that AUUUA-mediated degradation involves either a 5'-->3' exonuclease or is coupled to ongoing translation of the mRNA. To distinguish between these two possibilities, we inserted the poliovirus internal ribosome entry site, which promotes internal ribosome initiation, downstream of the 5' secondary structure. Translation directed by internal ribosome binding was found to fully restore targeted destabilization of AUUUA-containing mRNAs despite the presence of 5' secondary structure. This study therefore demonstrates that selective degradation mediated by the (AUUUA)n element is coupled to ribosome binding or ongoing translation of the mRNA and does not involve 5'-to-3' exonuclease activity.

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