scholarly journals In silico discovery and modeling of non-coding RNA structure in viruses

Methods ◽  
2015 ◽  
Vol 91 ◽  
pp. 48-56 ◽  
Author(s):  
Walter N. Moss ◽  
Joan A. Steitz
Keyword(s):  
In Silico ◽  
Rna Structure ◽  
Non Coding Rna

scholarly journals Aberrant expression of long non-coding RNA in thyroid neoplasms

2019 ◽  
pp. 17-25
Author(s):  
В.Д. Якушина ◽  
А.С. Танас ◽  
А.В. Лавров
Keyword(s):  
Thyroid Cancer ◽  
Signaling Pathway ◽  
In Silico ◽  
Thyroid Nodules ◽  
Differentially Expressed ◽  
Follicular Variant ◽  
Aberrant Expression ◽  
Lncrna Expression ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Актуальность. Длинные некодирующие РНК (днРНК) при раке щитовидной железы плохо изучены; не известны днРНК, общие и специфичные для фолликулярного и классического вариантов папиллярного рака, не установлены днРНК, аберрантно экспрессированные при других основных субтипах злокачественных новообразований щитовидной железы, а также при доброкачественных новообразованиях. Цель исследования - определить днРНК, аберрантно экспрессированные при фолликулярной аденоме (ФА), фолликулярном раке (ФРЩЖ), фолликулярном и классическом вариантах папиллярного рака (ПРЩЖ), анапластическом раке (АРЩЖ) щитовидной железы. Методы. Проанализирована экспрессия днРНК по данным исследований на микрочипах (8 независимых экспериментов, доступных в GEO) и секвенирования РНК (PRJEB11591 и TCGA-THCA). Исследованы 246 образцов нормальной ткани щитовидной железы, 26 - ФА, 30 - ФРЩЖ, 181 - фолликулярного варианта ПРЩЖ, 481 - классического варианта ПРЩЖ и 49 - АРЩЖ. Для классического и фолликулярного вариантов ПРЩЖ выполнена валидация дифференциальной экспрессии in silico. Потенциальные биологические функции были оценены в результате анализа обогащения коэкспрессированных генов. Результаты. Определены днРНК, дифференциально экспрессированные при ФА, ФРЩЖ, фолликулярном и классическом вариантах ПРЩЖ и АРЩЖ. Выявлены 8 днРНК, экспрессия которых изменена во всех субтипах новообразований щитовидной железы, 22 - общих для ПРЩЖ, 32 - специфичных для классического варианта ПРЩЖ, 1 - специфичная для фолликулярного варианта ПРЩЖ, и 177 - специфичных для АРЩЖ. Статистически значимо дифференциально экспрессированных днРНК в ФРЩ по сравнению с ФА не выявлено. Ранее известные онкогенные и супрессорные днРНК NR2F1-AS1, LINC00511, SLC26A4-AS1, CRNDE, RMST впервые обнаружены в новообразованиях щитовидной железы. Выявленные днРНК предположительно вовлечены в клеточную адгезию, организацию экстрацеллюлярного матрикса, образование эндодермы, регуляцию клеточного цикла и митоза, полярности клеток, сигнальные пути VEGF и WNT. Выводы. Установлены общие и специфичные паттерны экспрессии днРНК в доброкачественных и злокачественных новообразованиях щитовидной железы. Background. Long non-coding RNA (lncRNA) in thyroid cancer are poorly investigated; no lncRNAs common and specific for the follicular and classical variants of papillary cancer, as well as no lncRNAs aberrantly expressed in benign nodules or other subtypes of thyroid cancer are established. The objective of the study is to determine long noncoding RNAs aberrantly expressed in follicular adenoma (FA), follicular carcinoma (FTC), follicular and classical variants of papillary carcinoma (PTC), anaplastic carcinoma (ATC). Methods. lncRNA expression was analyzed in dataset of Microarray (8 independent experiments available in GEO) and RNA-seq studies (PRJEB11591 and TCGA-THCA). In total, 246 samples of normal thyroid tissue, 26 FAs, 30 FTCs, 181 follicular variant PTCs, 481 classic variant PTCs and 49 ATCs were examined. In silico validation was performed. Potential biological functions were assessed by enrichment analysis of coexpressed genes. Results. LncRNAs differentially expressed in FA, FTC, follicular, and classical variants of PTC, and ATC are identified. There are 8 lncRNAs common for all investigated thyroid nodules, 22 common for PTC, 32 specific for classical PTC, 1 specific for follicular variant of PTC, and 177 specific for ATC. No lncRNA significantly differentially expressed in FTC compared to FA is identified. The previously described oncogenic and suppressor lncRNAs NR2F1-AS1, LINC00511, SLC26A4-AS1, CRNDE, RMST are detected in thyroid carcinomas for the first time. Identified lncRNA are putatively involved in cell adhesion, extracellular matrix organization, endoderm formation, VEGF signaling pathway, WNT signaling pathway and cell polarity, cell cycle and mitosis. Conclusion. The general and specific patterns of lncRNA expression in benign and malignant thyroid nodules are established.

scholarly journals The global and local distribution of RNA structure throughout the SARS-CoV-2 genome

2020 ◽  
Author(s):  
Rafael de Cesaris Araujo Tavares ◽  
Gandhar Mahadeshwar ◽  
Han Wan ◽  
Nicholas C. Huston ◽  
Anna Marie Pyle
Keyword(s):  
In Silico ◽  
Rna Structure ◽  
Drug Targets ◽  
Rna Folding ◽  
Rna Viruses ◽  
Viral Agent ◽  
Rna Structures ◽  
Viral Rnas ◽  
Viral Genomes ◽  
Rna Genome

SARS-CoV-2 is the causative viral agent of COVID-19, the disease at the center of the current global pandemic. While knowledge of highly structured regions is integral for mechanistic insights into the viral infection cycle, very little is known about the location and folding stability of functional elements within the massive, ∼30kb SARS-CoV-2 RNA genome. In this study, we analyze the folding stability of this RNA genome relative to the structural landscape of other well-known viral RNAs. We present an in-silico pipeline to predict regions of high base pair content across long genomes and to pinpoint hotspots of well-defined RNA structures, a method that allows for direct comparisons of RNA structural complexity within the several domains in SARS-CoV-2 genome. We report that the SARS-CoV-2 genomic propensity for stable RNA folding is exceptional among RNA viruses, superseding even that of HCV, one of the most structured viral RNAs in nature. Furthermore, our analysis suggests varying levels of RNA structure across genomic functional regions, with accessory and structural ORFs containing the highest structural density in the viral genome. Finally, we take a step further to examine how individual RNA structures formed by these ORFs are affected by the differences in genomic and subgenomic contexts, which given the technical difficulty of experimentally separating cellular mixtures of sgRNA from gRNA, is a unique advantage of our in-silico pipeline. The resulting findings provide a useful roadmap for planning focused empirical studies of SARS-CoV-2 RNA biology, and a preliminary guide for exploring potential SARS-CoV-2 RNA drug targets. Importance The RNA genome of SARS-CoV-2 is among the largest and most complex viral genomes, and yet its RNA structural features remain relatively unexplored. Since RNA elements guide function in most RNA viruses, and they represent potential drug targets, it is essential to chart the architectural features of SARS-CoV-2 and pinpoint regions that merit focused study. Here we show that RNA folding stability of SARS-CoV-2 genome is exceptional among viral genomes and we develop a method to directly compare levels of predicted secondary structure across SARS-CoV-2 domains. Remarkably, we find that coding regions display the highest structural propensity in the genome, forming motifs that differ between the genomic and subgenomic contexts. Our approach provides an attractive strategy to rapidly screen for candidate structured regions based on base pairing potential and provides a readily interpretable roadmap to guide functional studies of RNA viruses and other pharmacologically relevant RNA transcripts.

scholarly journals KARAKTERISASI MICRORNA TRIPLE HELIX MELALUI METODE HYDROGEL SCAFFOLD SPESIFIK TERHADAP MICRORNA-26A DAN HSA-MICRORNA-15A: MODALITAS KURATIF MUTAKHIR PADA PENYAKIT KATARAK

2019 ◽  
Vol 2 (1) ◽  
pp. 50-62
Author(s):  
Nisrina Hanifa Afnan ◽  
Endah Sari R.Kumala ◽  
Mochammad Afifuddin
Keyword(s):  
Rna Structure ◽  
Triple Helix ◽  
Review Literature ◽  
World Health ◽  
Eye Drops ◽  
Hydrogel Scaffold ◽  
Non Coding Rna ◽  
Specific Target Gene ◽  
Antioxidant Proteins ◽  
Health Organization

Cataract is an eye disease that is marked by it decrease in lens transparency. Cataract is a major cause of blindness. Data The World Health Organization (WHO) in 2010 showed that there were 285 million people have visual impairments worldwide, 39 million of them blindness where 33% of them are caused by cataracts. Governance cataracts are currently limited to surgical efforts and administration of eye drops as antioxidant. But both have flaws because of the risk of complications limited ocular and lens penetrating ability. Therefore, the author reviewed the potential for triple helix microRNA characterization through specific Hydrogel Scaffold methods against microRNA-26a and hsa-microRNA-15a as the latest curative modalities on cataract disease. microRNA is a non coding RNA molecule consisting of 22 nucleotide. microRNA is known to have a specific target gene so it will increase the effectiveness of therapy in cataracts. The method used in this writing is a study of literature. The author reviews various sources, the majority come from a global journal. The author enters several keywords such as cataract, microRNA, triplex nanoparticle, and Hydrogel Scaffold. The website is used including nature, sciencedirect, pubmed, and ebsco. After extraction based on the inclusion and exclusion criteria that have been determined, the journal is then analyzed and synthesized whose results are written in this review literature. based on literature obtained, microRNA-26a has decreased expression in cataract cases. So that when microRNA-26a is transfected, there will be an increase in regulation which can increase the positive effect on inhibiting the process of fibrosis oncataract pathomechanism mediated by Notch / Jagged-1. Meanwhile, microRNA- 15a overexpresses, so that when transfected antagomir microRNA-15a, then this microRNA will decrease and give negative feedback so the expression of bcl-2 and mcl-1 as antiapoptotic and antioxidant proteins will be increased. To increase its stability, both microRNA-26a and antagomir microRNA-15a will be formed into a triple helix RNA structure through addition dendrimer with the Hydogel Scaffold method. This allows the microRNA become more stable in circulation and can be released in specific genes. By therefore, through the triple helix RNA characterization specific to microRNA-15a and microRNA-26a, cataract therapy is expected to be more effective and efficient. Keywords : cataracts, triple helix microRNA, microRNA-15a, microRNA-2

scholarly journals In silico study on RNA structures of intronic mutations of beta-globin gene

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 49
Author(s):  
Nur Imaniati Sumantri ◽  
Kenny Lischer ◽  
Dian Rachma Wijayanti ◽  
Tomy Abuzairi
Keyword(s):  
In Silico ◽  
Rna Structure ◽  
Tertiary Structure ◽  
Globin Gene ◽  
Thalassemia Major ◽  
Beta Thalassemia ◽  
Beta Globin ◽  
Rna Structures ◽  
Beta Globin Gene ◽  
Mrna Structure

Background: Mutation of the beta-globin gene (HBB) interferes with primary mRNA transcription, leading to beta-thalassemia disease. The IVS1nt1 and IVS1nt5 mutations were reported as two of the most prevalent intronic mutations associated with beta-thalassemia major. These mutations may affect the mRNA structure of the human beta-globin (HBB) gene. However, the mechanism by which variation in HBB alters the mRNA structure remains unclear. The objective of this study was to unveil the secondary and tertiary conformation difference of the mutants compared to the wildtype using in silico analysis. Methods: The sequence of HBB was obtained from Ensemble database and mutated manually at nucleotides 143 (IVS1nt1G>T) and 147 (IVS1nt5G>C). The RNA secondary and tertiary structure were performed by ViennaRNA Web Services and 3dRNA v2.0, respectively. Results and Discussion: The results revealed the unique folding characteristics of each mutations for the secondary and tertiary structures. Based on the structure, unwanted folding occurred in the IVS1nt1G>T and IVS1nt5G>C mRNA structures compared to the wild-type structure. This finding was supported by the results of centroid-based analysis and RNA structure analysis, indicating that the larger loops in IVS1nt1 and IVS1nt5 result in an unstable structure. Our study found that intronic mutations affect the mRNA structure of HBB by altering its folding mechanism.

scholarly journals HOTAIR Long Non-coding RNA: Characterizing the Locus Features by the In Silico Approaches

2017 ◽  
Vol 15 (4) ◽  
pp. 170-177 ◽  
Author(s):  
Mohammadreza Hajjari ◽  
Saghar Rahnama
Keyword(s):  
In Silico ◽  
Non Coding Rna ◽  
Long Non Coding Rna

scholarly journals Analysis of RNA sequence and structure in key genes of Mycobacterium ulcerans reveals conserved structural motifs and regions with apparent pressure to remain unstructured

2021 ◽  
Author(s):  
Warren B. Rouse ◽  
Jessica Gart ◽  
Lauren Peysakhova ◽  
Walter Moss
Keyword(s):  
In Silico ◽  
Rna Structure ◽  
Buruli Ulcer ◽  
In Silico Analysis ◽  
Geographic Area ◽  
Mycobacterium Ulcerans ◽  
Surgical Removal ◽  
Basic Biology ◽  
Sequence Study ◽  
Silico Analysis

Buruli Ulcer is a neglected tropical disease that results in disfiguring and potentially dangerous lesions in affected persons across a wide geographic area, which includes much of West Africa. The causative agent of Buruli Ulcer is Mycobacterium ulcerans, a relative of the bacterium that causes tuberculosis and leprosy. Few therapeutic options exist for the treatment of this disease beyond the main approach, surgical removal, which is frequently ineffective. In this study we analyze six genes in Mycobacterium ulcerans that have high potential of therapeutic targeting. We focus our analysis on a combined in silico and comparative sequence study of potential RNA secondary structure across these genes. The end result of this work was the comprehensive local RNA structural landscape across each of these significant genes. This revealed multiple sites of ordered and evolved RNA structure interspersed between sequences that either have no bias for structure or, indeed, appear to be ordered to be unstructured and (potentially) accessible. In addition to providing data that could be of interest to basic biology, our results provide guides for efforts aimed at targeting this pathogen at the RNA level. We explore this latter possibility through the in silico analysis of antisense oligonucleotides that could be used to target pathogen RNA.

scholarly journals In silico study on RNA structures of intronic mutations of beta-globin gene

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 49
Author(s):  
Nur Imaniati Sumantri ◽  
Kenny Lischer ◽  
Dian Rachma Wijayanti ◽  
Tomy Abuzairi
Keyword(s):  
In Silico ◽  
Rna Structure ◽  
Tertiary Structure ◽  
Globin Gene ◽  
Thalassemia Major ◽  
Beta Thalassemia ◽  
Beta Globin ◽  
Rna Structures ◽  
Beta Globin Gene ◽  
Mrna Structure

Background: Mutation of the beta-globin gene (HBB) interferes with primary mRNA transcription, leading to beta-thalassemia disease. The IVS1nt1 and IVS1nt5 mutations were reported as two of the most prevalent intronic mutations associated with beta-thalassemia major. These mutations may affect the mRNA structure of the human beta-globin (HBB) gene. However, the mechanism by which variation in HBB alters the mRNA structure remains unclear. The objective of this study was to unveil the secondary and tertiary conformation difference of the mutants compared to the wildtype using in silico analysis. Methods: The sequence of HBB was obtained from Ensemble database and mutated manually at nucleotides 143 (IVS1nt1G>T) and 147 (IVS1nt5G>C). The RNA secondary and tertiary structure were performed by ViennaRNA Web Services and RNA Composer, respectively. Results and Discussion: The results revealed the unique folding characteristics of each mutations for the secondary and tertiary structures. Based on the structure, unwanted folding occurred in the IVS1nt1G>T and IVS1nt5G>C mRNA structures compared to the wild-type structure. This finding was supported by the results of centroid-based analysis and RNA structure analysis, indicating that the larger loops in IVS1nt1 and IVS1nt5 result in an unstable structure. Our study found that intronic mutations affect the mRNA structure of HBB by altering its folding mechanism.

scholarly journals In silico study on RNA structures of intronic mutations of beta-globin gene

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 49
Author(s):  
Nur Imaniati Sumantri ◽  
Kenny Lischer ◽  
Dian Rachma Wijayanti ◽  
Tomy Abuzairi
Keyword(s):  
In Silico ◽  
Rna Structure ◽  
Tertiary Structure ◽  
Globin Gene ◽  
Thalassemia Major ◽  
Beta Thalassemia ◽  
Beta Globin ◽  
Rna Structures ◽  
Beta Globin Gene ◽  
Mrna Structure

Background: Mutation of the beta-globin gene (HBB) interferes with primary mRNA transcription, leading to beta-thalassemia disease. The IVS1nt1 and IVS1nt5 mutations were reported as two of the most prevalent intronic mutations associated with beta-thalassemia major. These mutations may affect the mRNA structure of the human beta-globin (HBB) gene. However, the mechanism by which variation in HBB alters the mRNA structure remains unclear. The objective of this study was to unveil the secondary and tertiary conformation difference of the mutants compared to the wildtype using in silico analysis. Methods: The sequence of HBB was obtained from Ensemble database and mutated manually at nucleotides 143 (IVS1nt1G>T) and 147 (IVS1nt5G>C). The RNA secondary and tertiary structure were performed by ViennaRNA Web Services and RNA Composer, respectively. Results and Discussion: The results revealed the unique folding characteristics of each mutations for the secondary and tertiary structures. Based on the structure, unwanted folding occurred in the IVS1nt1G>T and IVS1nt5G>C mRNA structures compared to the wild-type structure. This finding was supported by the results of centroid-based analysis and RNA structure analysis, indicating that the larger loops in IVS1nt1 and IVS1nt5 result in an unstable structure. Our study found that intronic mutations affect the mRNA structure of HBB by altering its folding mechanism.

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