scholarly journals LocalSTAR3D: a local stack-based RNA 3D structural alignment tool

2020 ◽  
Author(s):  
Xiaoli Chen ◽  
Nabila Shahnaz Khan ◽  
Shaojie Zhang
Keyword(s):  
Structural Alignment ◽  
Data Bank ◽  
Local Alignment ◽  
Global Alignment ◽  
Rna Structures ◽  
3D Structures ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Alignment Tool ◽  
Wide Range

Abstract A fast-growing number of non-coding RNA structures have been resolved and deposited in Protein Data Bank (PDB). In contrast to the wide range of global alignment and motif search tools, there is still a lack of local alignment tools. Among all the global alignment tools for RNA 3D structures, STAR3D has become a valuable tool for its unprecedented speed and accuracy. STAR3D compares the 3D structures of RNA molecules using consecutive base-pairs (stacks) as anchors and generates an optimal global alignment. In this article, we developed a local RNA 3D structural alignment tool, named LocalSTAR3D, which was extended from STAR3D and designed to report multiple local alignments between two RNAs. The benchmarking results show that LocalSTAR3D has better accuracy and coverage than other local alignment tools. Furthermore, the utility of this tool has been demonstrated by rediscovering kink-turn motif instances, conserved domains in group II intron RNAs, and the tRNA mimicry of IRES RNAs.

Chinese Herbal Medicine-Based Cancer Therapy: Novel Anticancer Agents Targeting MicroRNAs to Regulate Tumor Growth and Metastasis

2019 ◽  
Vol 47 (08) ◽  
pp. 1711-1735 ◽  
Author(s):  
Fu Peng ◽  
Xiaofang Xie ◽  
Cheng Peng
Keyword(s):  
Herbal Medicine ◽  
Chinese Herbal Medicine ◽  
Anticancer Agents ◽  
Biologically Active ◽  
Active Components ◽  
Rna Molecules ◽  
Chinese Herbal ◽  
Non Coding Rna ◽  
Wide Range ◽  
Tumor Growth And Metastasis

MicroRNAs, small non-coding RNA molecules, have gained a reputation of the most substantial regulators in gene network with the ability to down-regulate their targets. Accumulating evidence shifted insight toward microRNAs regulation as the key element of cancer initiation, development, and aggression. Recent studies have attached the importance of traditional Chinese medicine (TCM) to the treatment of various cancers, and the functional natural compounds have been considered as novel anticancer agents to directly inhibit tumor progression. In more recent decades, a wide range of biologically active components of TCM has gained increasing attention to their applications in the modulation of microRNAs. This review is on the purpose of demonstrating the significance of TCM bioactive ingredients in microRNAs regulation for cancer treatment according to the reports mainly in the recent six years, providing the evidence of efficient Chinese herbal medicine-based therapy and effective pro-diagnosis focusing on microRNAs expression of cancer patients.

scholarly journals NEAT1 and Paraspeckles in Cancer Development and Chemoresistance

2020 ◽  
Vol 6 (4) ◽  
pp. 43
Author(s):  
Gabriel Pisani ◽  
Byron Baron
Keyword(s):  
Cancer Progression ◽  
Drug Targets ◽  
Cellular Biology ◽  
Diverse Range ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Wide Range ◽  
Protein Research ◽  
The Stability ◽  
Abundant Transcript

Non-coding RNA were previously thought to be biologically useless molecules arising from simple transcriptional noise. These are now known to be an integral part of cellular biology and pathology. The wide range of RNA molecules have a diverse range of structures, functions, and mechanisms of action. However, structural long non-coding RNAs (lncRNAs) are a particular class of ncRNA that are proving themselves more and more important in cellular biology, as the exact structures that such RNAs form and stabilise become more understood. Nuclear Enriched Abundant Transcript 1 (NEAT1) is a specific structural RNA emerging as a critical component in the progress and development of cancer. NEAT1 forms part of multiple biological pathways, acting through a diverse group of mechanisms. The most important of these is the formation of the paraspeckle, through which it can influence the stability of a tumour to develop resistance to drugs. This review will thus cover the range of effects by which NEAT1 interacts with cancer progression in order to describe the various roles of NEAT1 in chemoresistance, as well as to identify drug targets that protein research alone could not provide.

scholarly journals Absence of knots in known RNA structures

2015 ◽  
Vol 112 (7) ◽  
pp. 2052-2057 ◽  
Author(s):  
Cristian Micheletti ◽  
Marco Di Stefano ◽  
Henri Orland
Keyword(s):  
Data Bank ◽  
General Strategy ◽  
Rna Structures ◽  
Structural Comparison ◽  
Viral Dna ◽  
Rna Sequences ◽  
Rna Molecules ◽  
Evolutionary Selection ◽  
Ongoing Effort ◽  
Physical Entanglement

The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also, abound in viral DNA packaged inside bacteriophages. RNA molecules, however, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the several thousand RNA structures present in the Protein Data Bank (PDB). The search identified no more than three deeply knotted RNA molecules. These entries are rRNAs of about 3,000 nt solved by cryo-EM. Their genuine knotted state is, however, doubtful based on the detailed structural comparison with homologs of higher resolution, which are all unknotted. Compared with the case of proteins and viral DNA, the observed incidence of knots in available RNA structures is, therefore, practically negligible. This fact suggests that either evolutionary selection or thermodynamic and kinetic folding mechanisms act toward minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. A possible general strategy for designing synthetic RNA sequences capable of self-tying in a twist-knot fold is finally proposed.

scholarly journals RNAmountAlign: efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment

2018 ◽  
Author(s):  
Amir H Bayegan ◽  
Peter Clote
Keyword(s):  
Optimal Algorithm ◽  
Structural Information ◽  
Structural Similarity ◽  
Structure Alignment ◽  
Local Alignment ◽  
Global Alignment ◽  
Sequence Structure ◽  
Rna Sequence ◽  
Wide Range ◽  
Run Time

AbstractAlignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for structural homology identification. A number of successful alignment programs are heuristic versions of Sankoff’s optimal algorithm. Most of them require O(n4) run time. This paper describes C++ software, RNAmountAlign, for RNA sequence/structure alignment that runs in O(n3) time and O(n2) space; moreover, our software returns a p-value (transformable to expect value E) based on Karlin-Altschul statistics for local alignment, as well as parameter fitting for local and global alignment. Using incremental mountain height, a representation of structural information computable in cubic time, RNAmountAlign implements quadratic time pairwise local, global and global/semiglobal (query search) alignment using a weighted combination of sequence and structural similarity. RNAmountAlign is capable of performing progressive multiple alignment as well. Benchmarking of RNAmountAlign against LocARNA, LARA, FOLDALIGN, DYNALIGN and STRAL shows that RNAmountAlign has reasonably good accuracy and much faster run time supporting all alignment types.AvailabilityRNAmountAlign is publicly available at http://bioinformatics.bc.edu/clotelab/RNAmountAlign.

scholarly journals MicroRNAs as Biomarkers for Animal Health and Welfare in Livestock

2020 ◽  
Vol 7 ◽  
Author(s):  
Silvia Miretti ◽  
Cristina Lecchi ◽  
Fabrizio Ceciliani ◽  
Mario Baratta
Keyword(s):  
Current Knowledge ◽  
Animal Health ◽  
Regulation Of Gene Expression ◽  
Cell Communication ◽  
Rna Molecules ◽  
Non Invasive ◽  
Non Coding Rna ◽  
Wide Range ◽  
Post Transcriptional Regulation ◽  
Extracellular Environment

MicroRNAs (miRNAs) are small and highly conserved non-coding RNA molecules that orchestrate a wide range of biological processes through the post-transcriptional regulation of gene expression. An intriguing aspect in identifying these molecules as biomarkers is derived from their role in cell-to-cell communication, their active secretion from cells into the extracellular environment, their high stability in body fluids, and their ease of collection. All these features confer on miRNAs the potential to become a non-invasive tool to score animal welfare. There is growing interest in the importance of miRNAs as biomarkers for assessing the welfare of livestock during metabolic, environmental, and management stress, particularly in ruminants, pigs, and poultry. This review provides an overview of the current knowledge regarding the potential use of tissue and/or circulating miRNAs as biomarkers for the assessment of the health and welfare status in these livestock species.

scholarly journals MicroRNAs: An Important Players in Breast Cancer Angiogenesis and Therapeutic Targets

2021 ◽  
Vol 8 ◽  
Author(s):  
Bashdar Mahmud Hussen ◽  
Sara Tharwat Abdullah ◽  
Mohammed Fatih Rasul ◽  
Abbas Salihi ◽  
Soudeh Ghafouri-Fard ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Tumor Development ◽  
Therapeutic Targets ◽  
Cellular Targets ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Wide Range ◽  
High Incidence ◽  
Different Types ◽  
Angiogenesis Process

The high incidence of breast cancer (BC) is linked to metastasis, facilitated by tumor angiogenesis. MicroRNAs (miRNAs or miRs) are small non-coding RNA molecules that have an essential role in gene expression and are significantly linked to the tumor development and angiogenesis process in different types of cancer, including BC. There’s increasing evidence showed that various miRNAs play a significant role in disease processes; specifically, they are observed and over-expressed in a wide range of diseases linked to the angiogenesis process. However, more studies are required to reach the best findings and identify the link among miRNA expression, angiogenic pathways, and immune response-related genes to find new therapeutic targets. Here, we summarized the recent updates on miRNA signatures and their cellular targets in the development of breast tumor angiogenetic and discussed the strategies associated with miRNA-based therapeutic targets as anti-angiogenic response.

scholarly journals RNA force field with accuracy comparable to state-of-the-art protein force fields

2018 ◽  
Vol 115 (7) ◽  
pp. E1346-E1355 ◽  
Author(s):  
Dazhi Tan ◽  
Stefano Piana ◽  
Robert M. Dirks ◽  
David E. Shaw
Keyword(s):  
Force Field ◽  
Md Simulation ◽  
State Of The Art ◽  
Force Fields ◽  
Md Simulations ◽  
Physical Models ◽  
Rna Structures ◽  
Rna Molecules ◽  
Wide Range ◽  
Protein Force Fields

Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an atomic level of detail the conformational changes undergone by proteins. The application of such simulations to RNA structures, however, has proven more challenging, due in large part to the fact that the physical models (“force fields”) available for MD simulations of RNA molecules are substantially less accurate in many respects than those currently available for proteins. Here, we introduce an extensive revision of a widely used RNA force field in which the parameters have been modified, based on quantum mechanical calculations and existing experimental information, to more accurately reflect the fundamental forces that stabilize RNA structures. We evaluate these revised parameters through long-timescale MD simulations of a set of RNA molecules that covers a wide range of structural complexity, including single-stranded RNAs, RNA duplexes, RNA hairpins, and riboswitches. The structural and thermodynamic properties measured in these simulations exhibited dramatically improved agreement with experimentally determined values. Based on the comparisons we performed, this RNA force field appears to achieve a level of accuracy comparable to that of state-of-the-art protein force fields, thus significantly advancing the utility of MD simulation as a tool for elucidating the structural dynamics and function of RNA molecules and RNA-containing biological assemblies.

scholarly journals Comparing “parallel passages” in digital archives

2019 ◽  
Vol 76 (1) ◽  
pp. 271-289
Author(s):  
Martyn Harris ◽  
Mark Levene ◽  
Dell Zhang ◽  
Dan Levene
Keyword(s):  
Character Recognition ◽  
Optical Character Recognition ◽  
Language Change ◽  
Language Model ◽  
Local Alignment ◽  
Digital Archives ◽  
Content Type ◽  
Alignment Tool ◽  
Wide Range ◽  
Recognition Errors

Purpose The purpose of this paper is to present a language-agnostic approach to facilitate the discovery of “parallel passages” stored in historic and cultural heritage digital archives. Design/methodology/approach The authors explore a novel, and relatively simple approach, using a character-based statistical language model combined with a tailored version of the Basic Local Alignment Tool to extract exact and approximate string patterns shared between groups of documents. Findings The approach is applicable to a wide range of languages, and compensates for variability in the text of the documents as a result of differences in dialect, authorship, language change over time and errors due to inaccurate transcriptions and optical character recognition errors as a result of the digitisation process. Research limitations/implications A number of case studies demonstrate that the approach is practical and generalisable to a wide range of archives with documents in different languages, domains and of varying quality. Practical implications The approach described can be applied to any digital archive of modern and contemporary texts. This makes the approach applicable to digital archives recording historic texts, but also those composed of more recent news articles, for example. Social implications The analysis of “parallel passages” enables researchers to quantify the presence and extent of text-reuse in a collection of documents, which can provide useful data on author style, text genres and cultural contexts. Originality/value The approach is novel and addresses a need by humanities researchers for tools that can identify similar documents and local similarities represented by shared text sequences in a potentially vast large archive of documents. As far as the authors are aware, there are no tools currently exist that provide the same level of tolerance to the language of the documents.

scholarly journals Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals

Crystals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 952
Author(s):  
Narsimha Pujari ◽  
Stephanie L. Saundh ◽  
Francis A. Acquah ◽  
Blaine H. M. Mooers ◽  
Adrian R. Ferré-D’Amaré ◽  
...  
Keyword(s):  
Crystal Packing ◽  
Rna Stability ◽  
Data Bank ◽  
Future Research ◽  
Rna Structures ◽  
Rna Molecules ◽  
X Ray Crystallography ◽  
Crystal Contacts ◽  
Rna Crystallography ◽  
Regulatory Functions

X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop–tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.

scholarly journals R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types

2020 ◽  
Author(s):  
Blake A. Sweeney ◽  
David Hoksza ◽  
Eric P. Nawrocki ◽  
Carlos Eduardo Ribas ◽  
Fábio Madeira ◽  
...  
Keyword(s):  
Large Subunit ◽  
3D Structure ◽  
Rna Structures ◽  
Computational Framework ◽  
Link Type ◽  
Comprehensive Method ◽  
Non Coding Rna ◽  
Wide Range ◽  
2D Structure ◽  
Non Coding Rnas

AbstractNon-coding RNAs (ncRNA) are essential for all life, and the functions of many ncRNAs depend on their secondary (2D) and tertiary (3D) structure. Despite proliferation of 2D visualisation software, there is a lack of methods for automatically generating 2D representations in consistent, reproducible, and recognisable layouts, making them difficult to construct, compare and analyse. Here we present R2DT, a comprehensive method for visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,632 templates representing the majority of known structured RNAs, from small RNAs to the large subunit ribosomal RNA. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world’s largest RNA 2D structure dataset. The software is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt.

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