An efficient algorithm for planar drawing of RNA structures with pseudoknots of any type

2016 ◽  
Vol 14 (03) ◽  
pp. 1650009 ◽  
Author(s):  
Yanga Byun ◽  
Kyungsook Han
Keyword(s):  
Rna Structure ◽  
Large Scale ◽  
Structural Elements ◽  
Rna Structures ◽  
Structural Element ◽  
Rna Pseudoknots ◽  
Number Of Stems ◽  
Rna Pseudoknot ◽  
Aesthetic Structure ◽  
Planar Drawing

An RNA pseudoknot is a tertiary structural element in which bases of a loop pair with complementary bases are outside the loop. A drawing of RNA secondary structures is a tree, but a drawing of RNA pseudoknots is a graph that has an inner cycle within a pseudoknot and possibly outer cycles formed between the pseudoknot and other structural elements. Visualizing a large-scale RNA structure with pseudoknots as a planar drawing is challenging because a planar drawing of an RNA structure requires both pseudoknots and an entire structure enclosing the pseudoknots to be embedded into a plane without overlapping or crossing. This paper presents an efficient heuristic algorithm for visualizing a pseudoknotted RNA structure as a planar drawing. The algorithm consists of several parts for finding crossing stems and page mapping the stems, for the layout of stem-loops and pseudoknots, and for overlap detection between structural elements and resolving it. Unlike previous algorithms, our algorithm generates a planar drawing for a large RNA structure with pseudoknots of any type and provides a bracket view of the structure. It generates a compact and aesthetic structure graph for a large pseudoknotted RNA structure in O([Formula: see text]) time, where n is the number of stems of the RNA structure.

scholarly journals Repurposing Ribo-Seq to provide insights into structured RNAs

2020 ◽  
Author(s):  
Brayon J. Fremin ◽  
Ami S. Bhatt
Keyword(s):  
Secondary Structure ◽  
Rna Structure ◽  
Large Scale ◽  
Structural Information ◽  
Ribosome Profiling ◽  
Rna Structures ◽  
Size Selection ◽  
Bacterial Ribosome ◽  
Powerful Approach

AbstractRibosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, this method can enrich RNAs that are not bound by ribosomes, but rather, are protected from degradation in another way. For example, Escherichia coli Ribo-Seq libraries also capture reads from most non-coding RNAs (ncRNAs). These fragments of ncRNAs pass all size selection steps of the Ribo-Seq protocol and survive hours of MNase treatment, presumably without protection from the ribosome or other macromolecules or proteins. Since bacterial ribosome profiling does not directly isolate ribosomes, but instead uses broad size range cutoffs to fractionate actively translated RNAs, it is understandable that some ncRNAs are retained after size selection. However, how these ‘contaminants’ survive MNase treatment is unclear. Through analyzing metaRibo-Seq reads across ssrS, a well established structured RNA in E. coli, and structured direct repeats from Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays in Ruminococcus lactaris, we observed that these RNAs are protected from MNase treatment by virtue of their secondary structure. Therefore, large volumes of data previously discarded as contaminants in bacterial Ribo-Seq experiments can, in fact, be used to gain information regarding the in vivo secondary structure of ncRNAs, providing unique insight into their native functional structures.ImportanceWe observe that ‘contaminant’ signals in bacterial Ribo-Seq experiments that are often disregarded and discarded, in fact, strongly overlap with structured regions of ncRNAs. Structured ncRNAs are pivotal mediators of bioregulation in bacteria and their functions are often reliant on their specific structures. We present an approach to access important RNA structural information through merely repurposing ‘contaminant’ signals in bacterial Ribo-Seq experiments. This powerful approach enables us to partially resolve RNA structures, identify novel structured RNAs, and elucidate RNA structure-function relationships in bacteria at a large-scale and in vivo.

scholarly journals Structured RNA Contaminants in Bacterial Ribo-Seq

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Brayon J. Fremin ◽  
Ami S. Bhatt
Keyword(s):  
Rna Structure ◽  
Large Scale ◽  
Partial Information ◽  
Ribosome Profiling ◽  
Micrococcal Nuclease ◽  
Data Sets ◽  
Rna Structures ◽  
Content Type ◽  
Sequencing Library

ABSTRACT Ribosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, Ribo-Seq signal can be observed across RNAs that one would not expect to be bound by ribosomes. For example, Escherichia coli Ribo-Seq libraries also capture reads from most noncoding RNAs (ncRNAs). While some of these ncRNAs may overlap coding regions, this alone does not explain the majority of observed signal across ncRNAs. These fragments of ncRNAs in Ribo-Seq data pass all size selection steps of the Ribo-Seq protocol and survive hours of micrococcal nuclease (MNase) treatment. In this work, we specifically focus on Ribo-Seq signal across ncRNAs and provide evidence to suggest that RNA structure, as opposed to ribosome binding, protects them from degradation and allows them to persist in the Ribo-Seq sequencing library preparation. By inspecting these “contaminant reads” in bacterial Ribo-Seq, we show that data previously disregarded in bacterial Ribo-Seq experiments may, in fact, be used to gain partial information regarding the in vivo secondary structure of ncRNAs. IMPORTANCE Structured ncRNAs are pivotal mediators of bioregulation in bacteria, and their functions are often reliant on their specific structures. Here, we first inspect Ribo-Seq reads across noncoding regions, identifying contaminant reads in these libraries. We observe that contaminant reads in bacterial Ribo-Seq experiments that are often disregarded, in fact, strongly overlap with structured regions of ncRNAs. We then perform several bioinformatic analyses to determine why these contaminant reads may persist in Ribo-Seq libraries. Finally, we highlight some structured RNA contaminants in Ribo-Seq and support the hypothesis that structures in the RNA protect them from MNase digestion. We conclude that researchers should be cautious when interpreting Ribo-Seq signal as coding without considering signal distribution. These findings also may enable us to partially resolve RNA structures, identify novel structured RNAs, and elucidate RNA structure-function relationships in bacteria at a large scale and in vivo through the reanalysis of existing Ribo-Seq data sets.

scholarly journals A Genome-Wide Analysis of RNA Pseudoknots That Stimulate Efficient −1 Ribosomal Frameshifting or Readthrough in Animal Viruses

2013 ◽  
Vol 2013 ◽  
pp. 1-15 ◽  
Author(s):  
Xiaolan Huang ◽  
Qiang Cheng ◽  
Zhihua Du
Keyword(s):  
Large Scale ◽  
Stop Codon ◽  
Ribosomal Frameshifting ◽  
Viral Genomes ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Rna Pseudoknots ◽  
Rna Pseudoknot ◽  
Stop Codon Readthrough

Programmed −1 ribosomal frameshifting (PRF) and stop codon readthrough are two translational recoding mechanisms utilized by some RNA viruses to express their structural and enzymatic proteins at a defined ratio. Efficient recoding usually requires an RNA pseudoknot located several nucleotides downstream from the recoding site. To assess the strategic importance of the recoding pseudoknots, we have carried out a large scale genome-wide analysis in which we used an in-house developed program to detect all possible H-type pseudoknots within the genomic mRNAs of 81 animal viruses. Pseudoknots are detected downstream from ~85% of the recoding sites, including many previously unknown pseudoknots. ~78% of the recoding pseudoknots are the most stable pseudoknot within the viral genomes. However, they are not as strong as some designed pseudoknots that exhibit roadblocking effect on the translating ribosome. Strong roadblocking pseudoknots are not detected within the viral genomes. These results indicate that the decoding pseudoknots have evolved to possess optimal stability for efficient recoding. We also found that the sequence at thegag-polframeshift junction of HIV1 harbors potential elaborated pseudoknots encompassing the frameshift site. A novel mechanism is proposed for possible involvement of the elaborated pseudoknots in the HIV1 PRF event.

scholarly journals RNA structure-wide discovery of functional interactions with multiplexed RNA motif library

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kaoru R. Komatsu ◽  
Toshiki Taya ◽  
Sora Matsumoto ◽  
Emi Miyashita ◽  
Shunnichi Kashida ◽  
...  
Keyword(s):  
Rna Structure ◽  
Large Scale ◽  
Regulatory Elements ◽  
Rna Structures ◽  
Rna Sequences ◽  
Functional Interactions ◽  
Affinity Enrichment ◽  
Target Binding ◽  
Rna Motif ◽  
Computational Analyses

AbstractBiochemical assays and computational analyses have discovered RNA structures throughout various transcripts. However, the roles of these structures are mostly unknown. Here we develop folded RNA element profiling with structure library (FOREST), a multiplexed affinity assay system to identify functional interactions from transcriptome-wide RNA structure datasets. We generate an RNA structure library by extracting validated or predicted RNA motifs from gene-annotated RNA regions. The RNA structure library with an affinity enrichment assay allows for the comprehensive identification of target-binding RNA sequences and structures in a high-throughput manner. As a proof-of-concept, FOREST discovers multiple RNA-protein interaction networks with quantitative scores, including translational regulatory elements that function in living cells. Moreover, FOREST reveals different binding landscapes of RNA G-quadruplex (rG4) structures-binding proteins and discovers rG4 structures in the terminal loops of precursor microRNAs. Overall, FOREST serves as a versatile platform to investigate RNA structure-function relationships on a large scale.

scholarly journals Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures

2020 ◽  
Author(s):  
Ilaria Manfredonia ◽  
Chandran Nithin ◽  
Almudena Ponce-Salvatierra ◽  
Pritha Ghosh ◽  
Tomasz K. Wirecki ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Structure ◽  
Therapeutic Strategies ◽  
Structural Elements ◽  
Rna Structures ◽  
Structure Probing ◽  
Genome Wide ◽  
Positive Sense ◽  
High Sequence Conservation ◽  
Single Base Resolution

SummarySARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome of ∼30 kb, whose outbreak caused the still ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally conserved structural elements within coronavirus RNA genomes have been identified to date.Here, we performed RNA structure probing by SHAPE-MaP to obtain a single-base resolution secondary structure map of the full SARS-CoV-2 coronavirus genome. The SHAPE-MaP probing data recapitulate the previously described coronavirus RNA elements (5′ UTR, ribosomal frameshifting element, and 3′ UTR), and reveal new structures. Secondary structure-restrained 3D modeling of highly-structured regions across the SARS-CoV-2 genome allowed for the identification of several putative druggable pockets. Furthermore, ∼8% of the identified structure elements show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. In addition, we identify a set of persistently single-stranded regions having high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics.Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.

STRUCTURAL RELIABILITY ANALYSIS BASED ON P-BOXES

2020 ◽  
Vol 92 (6) ◽  
pp. 51-58
Author(s):  
S.A. SOLOVYEV ◽  
Keyword(s):  
Probability Distribution ◽  
Reliability Analysis ◽  
Structural Reliability ◽  
Epistemic Uncertainty ◽  
Random Variable ◽  
Strength Criterion ◽  
Structural Elements ◽  
Structural Element ◽  
Limit States ◽  
Distribution Shape

The article describes a method for reliability (probability of non-failure) analysis of structural elements based on p-boxes. An algorithm for constructing two p-blocks is shown. First p-box is used in the absence of information about the probability distribution shape of a random variable. Second p-box is used for a certain probability distribution function but with inaccurate (interval) function parameters. The algorithm for reliability analysis is presented on a numerical example of the reliability analysis for a flexural wooden beam by wood strength criterion. The result of the reliability analysis is an interval of the non-failure probability boundaries. Recommendations are given for narrowing the reliability boundaries which can reduce epistemic uncertainty. On the basis of the proposed approach, particular methods for reliability analysis for any structural elements can be developed. Design equations are given for a comprehensive assessment of the structural element reliability as a system taking into account all the criteria of limit states.

scholarly journals RNA thermoswitches modulate Staphylococcus aureus adaptation to ambient temperatures

2021 ◽  
Vol 49 (6) ◽  
pp. 3409-3426
Author(s):  
Arancha Catalan-Moreno ◽  
Marta Cela ◽  
Pilar Menendez-Gil ◽  
Naiara Irurzun ◽  
Carlos J Caballero ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Rna Structure ◽  
Cold Shock ◽  
Mrna Translation ◽  
Site Directed Mutagenesis ◽  
Rna Structures ◽  
Double Stranded Rna ◽  
Ambient Temperatures ◽  
Shock Proteins ◽  
Rna Hairpin

Abstract Thermoregulation of virulence genes in bacterial pathogens is essential for environment-to-host transition. However, the mechanisms governing cold adaptation when outside the host remain poorly understood. Here, we found that the production of cold shock proteins CspB and CspC from Staphylococcus aureus is controlled by two paralogous RNA thermoswitches. Through in silico prediction, enzymatic probing and site-directed mutagenesis, we demonstrated that cspB and cspC 5′UTRs adopt alternative RNA structures that shift from one another upon temperature shifts. The open (O) conformation that facilitates mRNA translation is favoured at ambient temperatures (22°C). Conversely, the alternative locked (L) conformation, where the ribosome binding site (RBS) is sequestered in a double-stranded RNA structure, is folded at host-related temperatures (37°C). These structural rearrangements depend on a long RNA hairpin found in the O conformation that sequesters the anti-RBS sequence. Notably, the remaining S. aureus CSP, CspA, may interact with a UUUGUUU motif located in the loop of this long hairpin and favour the folding of the L conformation. This folding represses CspB and CspC production at 37°C. Simultaneous deletion of the cspB/cspC genes or their RNA thermoswitches significantly decreases S. aureus growth rate at ambient temperatures, highlighting the importance of CspB/CspC thermoregulation when S. aureus transitions from the host to the environment.

Projects Selection and Evaluation Tools for the of Non-Conventional Materials and Technologies (NOCMATS)

2012 ◽  
Vol 517 ◽  
pp. 13-19 ◽  
Author(s):  
P. Ohayon ◽  
Khosrow Ghavami
Keyword(s):  
Large Scale ◽  
Evaluation Criteria ◽  
Second World War ◽  
Structural Elements ◽  
Industrialized Countries ◽  
Governmental Agencies ◽  
Vegetable Fibers ◽  
Private Organizations ◽  
The Social ◽  
Second World

The results of many successfully realized Research and Development (R&D) concerned with non-conventional materials and technologies (NOCMAT) in developing countries including Brazil have not been used in large scale in practice. This is due to the lack of selection and evaluation criteria and concepts from planning and designing to implementation programs by governmental agencies and private organizations concerned with the newly developed sustainable materials and technologies. The problems of selecting and evaluating R&D innovation outputs and impacts for construction are complex and need scientific and systematic studies in order to avoid the social and environmental mistakes occurred in industrialized countries after the Second World War. This paper presents a logical framework for the implementation of pertinent indicators to be used as a tool in R&D of NOCMAT projects selection and evaluation concerned with materials, structural elements and technologies of bamboo and composites reinforced with vegetable fibers. Indicators, related to the efficiency, effectiveness, impact, relevance and sustainability of such projects are considered and discussed.

A Model of Seawater Structure Near the West Coast of Vancouver Island, British Columbia

1963 ◽  
Vol 20 (4) ◽  
pp. 939-967 ◽  
Author(s):  
Robert K. Lane
Keyword(s):  
British Columbia ◽  
West Coast ◽  
Large Scale ◽  
Coastal Region ◽  
Vancouver Island ◽  
Structural Elements ◽  
The West ◽  
Characteristic Structure ◽  
Oceanographic Data ◽  
Vertical Sections

Oceanographic data collected in a line of stations extending seaward of the west coast of Vancouver Island, British Columbia, were reviewed and analyzed. On the basis of these data and the large-scale meteorological processes of wind, insolation, and precipitation, the characteristic structure of temperature and salinity in the coastal region was denned in five temporal stages throughout the year. These stages are presented as vertical sections along the line with characteristic ranges of values to be found in each of the structural elements.

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