A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer

We recently implemented a bioinformatics pipeline that can uncover novel, but rare, riboswitch candidates as well as other noncoding RNA structures in bacteria. A prominent candidate revealed by our initial search efforts was called the ‘thiS motif’ because of its frequent association with a gene coding for the ThiS protein, which delivers sulfur to form the thiazole moiety of the thiamin precursor HET-P. In the current report, we describe biochemical and genetic data demonstrating that thiS motif RNAs function as sensors of the thiamin precursor HMP-PP, which is fused with HET-P ultimately to form the final active coenzyme thiamin pyrophosphate (TPP). HMP-PP riboswitches exhibit a distinctive architecture wherein an unusually small ligand-sensing aptamer is almost entirely embedded within an otherwise classic intrinsic transcription terminator stem. This arrangement yields remarkably compact genetic switches that bacteria use to tune the levels of thiamin precursors during the biosynthesis of this universally distributed coenzyme.

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Secondary Structural Model of Human MALAT1 Reveals Multiple Structure–Function Relationships

International Journal of Molecular Sciences ◽

10.3390/ijms20225610 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5610 ◽

Cited By ~ 10

Author(s):

Phillip J. McCown ◽

Matthew C. Wang ◽

Luc Jaeger ◽

Jessica A. Brown

Keyword(s):

Structure Function ◽

Noncoding Rna ◽

Structural Model ◽

Dynamic Structure ◽

Nucleotide Polymorphisms ◽

Rna Structures ◽

Rna Modifications ◽

Functional Roles ◽

Conserved Core

Human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is an abundant nuclear-localized long noncoding RNA (lncRNA) that has significant roles in cancer. While the interacting partners and evolutionary sequence conservation of MALAT1 have been examined, much of the structure of MALAT1 is unknown. Here, we propose a hypothetical secondary structural model for 8425 nucleotides of human MALAT1 using three experimental datasets that probed RNA structures in vitro and in various human cell lines. Our model indicates that approximately half of human MALAT1 is structured, forming 194 helices, 13 pseudoknots, five structured tetraloops, nine structured internal loops, and 13 intramolecular long-range interactions that give rise to several multiway junctions. Evolutionary conservation and covariation analyses support 153 of 194 helices in 51 mammalian MALAT1 homologs and 42 of 194 helices in 53 vertebrate MALAT1 homologs, thereby identifying an evolutionarily conserved core that likely has important functional roles in mammals and vertebrates. Data mining revealed that RNA modifications, somatic cancer-associated mutations, and single-nucleotide polymorphisms may induce structural rearrangements that sequester or expose binding sites for several cancer-associated microRNAs. Our findings reveal new mechanistic leads into the roles of MALAT1 by identifying several intriguing structure–function relationships in which the dynamic structure of MALAT1 underlies its biological functions.

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Cooperativity and Interdependency between RNA Structure and RNA–RNA Interactions

Non-Coding RNA ◽

10.3390/ncrna7040081 ◽

2021 ◽

Vol 7 (4) ◽

pp. 81

Author(s):

Ilias Skeparnias ◽

Jinwei Zhang

Keyword(s):

Rna Structure ◽

Noncoding Rna ◽

Quaternary Structure ◽

Reciprocal Relationship ◽

Rna Structures ◽

Granule Formation ◽

Expression Control ◽

Gene Expression Control ◽

Transcription Complexes ◽

Rna Complexes

Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation. By contrast, the nature of these interactions and characteristics of their interfaces, especially those that involve partially or wholly structured RNAs, remain elusive. Herein, we discuss different modalities of RNA–RNA interactions with an emphasis on those that depend on secondary, tertiary, or quaternary structure. We dissect recently structurally elucidated RNA–RNA complexes including RNA triplexes, riboswitches, ribozymes, and reverse transcription complexes. These analyses highlight a reciprocal relationship that intimately links RNA structure formation with RNA–RNA interactions. The interactions not only shape and sculpt RNA structures but also are enabled and modulated by the structures they create. Understanding this two-way relationship between RNA structure and interactions provides mechanistic insights into the expanding repertoire of noncoding RNA functions, and may inform the design of novel therapeutics that target RNA structures or interactions.

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RNA Structures Required for Production of Subgenomic Flavivirus RNA

Journal of Virology ◽

10.1128/jvi.01159-10 ◽

2010 ◽

Vol 84 (21) ◽

pp. 11407-11417 ◽

Cited By ~ 139

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.

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RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA

eLife ◽

10.7554/elife.01892 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 122

Author(s):

Erich G Chapman ◽

Stephanie L Moon ◽

Jeffrey Wilusz ◽

Jeffrey S Kieft

Keyword(s):

Dengue Virus ◽

Rna Structure ◽

Noncoding Rna ◽

Rna Folding ◽

Rna Degradation ◽

Rna Structures ◽

Genomic Rna ◽

Virus Rna ◽

Folded Rna ◽

Viral Genomic Rna

Dengue virus is a growing global health threat. Dengue and other flaviviruses commandeer the host cell’s RNA degradation machinery to generate the small flaviviral RNA (sfRNA), a noncoding RNA that induces cytopathicity and pathogenesis. Host cell exonuclease Xrn1 likely loads on the 5′ end of viral genomic RNA and degrades processively through ∼10 kB of RNA, halting near the 3′ end of the viral RNA. The surviving RNA is the sfRNA. We interrogated the architecture of the complete Dengue 2 sfRNA, identifying five independently-folded RNA structures, two of which quantitatively confer Xrn1 resistance. We developed an assay for real-time monitoring of Xrn1 resistance that we used with mutagenesis and RNA folding experiments to show that Xrn1-resistant RNAs adopt a specific fold organized around a three-way junction. Disrupting the junction’s fold eliminates the buildup of disease-related sfRNAs in human cells infected with a flavivirus, directly linking RNA structure to sfRNA production.

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Systematic Identification and Molecular Characteristics of Long Noncoding RNAs in Pig Tissues

BioMed Research International ◽

10.1155/2017/6152582 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 9

Author(s):

Yalan Yang ◽

Rong Zhou ◽

Shiyun Zhu ◽

Xunbi Li ◽

Hua Li ◽

...

Keyword(s):

Noncoding Rna ◽

Noncoding Rnas ◽

Gc Content ◽

Long Noncoding Rnas ◽

Molecular Characteristics ◽

Characteristic Analysis ◽

Bioinformatics Pipeline ◽

Protein Coding ◽

A Genome ◽

Systematic Identification

Long noncoding RNAs (lncRNAs) are non-protein-coding RNAs that are involved in a variety of biological processes. The pig is an important farm animal and an ideal biomedical model. In this study, we performed a genome-wide scan for lncRNAs in multiple tissue types from pigs. A total of 118 million paired-end 90 nt clean reads were obtained via strand-specific RNA sequencing, 80.4% of which were aligned to the pig reference genome. We developed a stringent bioinformatics pipeline to identify 2,139 high-quality multiexonic lncRNAs. The characteristic analysis revealed that the novel lncRNAs showed relatively shorter transcript length, fewer exons, and lower expression levels in comparison with protein-coding genes (PCGs). The guanine-cytosine (GC) content of the protein-coding exons and introns was significantly higher than that of the lncRNAs. Moreover, the single nucleotide polymorphism (SNP) density of lncRNAs was significantly higher than that of PCGs. Conservation analysis revealed that most lncRNAs were evolutionarily conserved among pigs, humans, and mice, such as CUFF.253988.1, which shares homology with human long noncoding RNA MALAT1. The findings of our study significantly increase the number of known lncRNAs in pigs.

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Banded aggregates containing fibrillin are present in the cartilage matrix adjacent to chondrocytes in individuals affected with scoliosis

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100124860 ◽

1992 ◽

Vol 50 (1) ◽

pp. 892-893

Author(s):

Douglas R. Keene ◽

Magaret Fairhurst ◽

Catherine C. Ridgway ◽

Lynn Y. Sakai

Keyword(s):

Connective Tissue ◽

Marfan Syndrome ◽

Cross Section ◽

Immunoelectron Microscopy ◽

Cartilage Matrix ◽

Negative Stain ◽

Gene Coding ◽

Rotary Shadowing

Matrix microfibrils are present in the connective tissue matrices of all tissues. Following standard TEM processing, they appear in cross section as cylindrical fibrils 8-10 nm in diameter, often associated with amorphous elastin. They are also seen in the absence of amorphous elastin, for example in the shallow papillary layer of skin, and also in cartilage matrix (Figure 1). Negative stain and rotary shadowing studies suggest that microfibrils are composed of laterally associated globular structures connected by fine filamentous strands (“ beaded strings”), and that they are extendable. Immunoelectron microscopy has demonstrated that fibrillin, a 350 Kd glycoprotein, is distributed along all microfibrils with a relaxed periodicity of about 54 nm The gene coding for fibrillin has recently been identified and is defective in the Marfan syndrome.

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