scholarly journals Computational approaches for the discovery of splicing regulatory RNA structures

2019 ◽  
Vol 1862 (11-12) ◽  
pp. 194380 ◽  
Author(s):  
Ryan J. Andrews ◽  
Walter N. Moss
Keyword(s):  
Regulatory Rna ◽  
Rna Structures ◽  
Computational Approaches

scholarly journals New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

2011 ◽  
Vol 21 (11) ◽  
pp. 1929-1943 ◽  
Author(s):  
B. J. Parker ◽  
I. Moltke ◽  
A. Roth ◽  
S. Washietl ◽  
J. Wen ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Regulatory Rna ◽  
Rna Structures

scholarly journals Search for 5′-leader regulatory RNA structures based on gene annotation aided by the RiboGap database

Methods ◽  
2017 ◽  
Vol 117 ◽  
pp. 3-13 ◽  
Author(s):  
Mohammad Reza Naghdi ◽  
Katia Smail ◽  
Joy X. Wang ◽  
Fallou Wade ◽  
Ronald R. Breaker ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Regulatory Rna ◽  
Rna Structures

scholarly journals The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures

2016 ◽  
Vol 62 (1) ◽  
pp. 111-120 ◽  
Author(s):  
Nathan Pirakitikulr ◽  
Andrew Kohlway ◽  
Brett D. Lindenbach ◽  
Anna M. Pyle
Keyword(s):  
Regulatory Rna ◽  
Rna Structures ◽  
Coding Region

Identification of conserved regulatory RNA structures in prokaryotic metabolic pathway genes

Biosystems ◽  
2005 ◽  
Vol 80 (2) ◽  
pp. 145-154 ◽  
Author(s):  
Elena A. Lesnik ◽  
Gary B. Fogel ◽  
Dana Weekes ◽  
Timothy J. Henderson ◽  
Harold B. Levene ◽  
...  
Keyword(s):  
Metabolic Pathway ◽  
Regulatory Rna ◽  
Rna Structures

scholarly journals Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Hannah Steinert ◽  
Florian Sochor ◽  
Anna Wacker ◽  
Janina Buck ◽  
Christina Helmling ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Messenger Rna ◽  
Regulation Of Gene Expression ◽  
Untranslated Regions ◽  
Structural Description ◽  
Regulatory Rna ◽  
Structural Elements ◽  
Rna Structures ◽  
Cis Acting ◽  
Aptamer Domain

In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element. Here, we show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of the full-length transcripts is static: it exclusively populates the functional off-state but cannot switch to the on-state, regardless of the presence or absence of ligand. We show that only the combined matching of transcription rates and ligand binding enables transcription intermediates to undergo ligand-dependent conformational refolding.

scholarly journals Mutation in position of 32 (G>U) of S2M differentiate human SARS-CoV2 from Bat Coronavirus

2020 ◽  
Author(s):  
Majid Vahed ◽  
Mohammad Vahed ◽  
Aaron Sweeney ◽  
Farshad H Shirazi ◽  
Mehdi Mirsaeidi
Keyword(s):  
Genomic Sequence ◽  
Therapeutic Agents ◽  
Regulatory Rna ◽  
Host Defenses ◽  
Rna Structures ◽  
Host Proteins ◽  
Tertiary Structures ◽  
Stem Loop ◽  
The Impact ◽  
Bat Coronavirus

ABSTRACTThe new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a zoonotic pathogen that has rapidly mutated and become transmissible to humans. There is little existing data on the mutations in SARS-CoV-2 and the impact of these polymorphisms on its transmission and viral load. In this study, the SARS-CoV-2 genomic sequence was analyzed to identify variants within the 3’UTR region of its cis-regulatory RNA elements. A 43-nucleotide genetic element with a highly conserved stem-loop II-like motif (S2M), was discovered. The research revealed 32 G>U and 16 G>U/A mutations located within the S2M sequence in human SARS-CoV-2 models. These polymorphisms appear to make the S2M secondary and tertiary structures in human SARS-CoV-2 models less stable when compared to the S2M structures of bat/pangolin models. This grants the RNA structures more flexibility, which could be one of its escape mechanisms from host defenses or facilitate its entry into host proteins and enzymes. While this S2M sequence may not be omnipresent across all human SARS-CoV-2 models, when present, its sequence is always highly conserved. It may be used as a potential target for the development of vaccines and therapeutic agents.

Bacterial cis-regulatory RNA structures

2006 ◽  
Vol 40 (4) ◽  
pp. 541-550 ◽  
Author(s):  
M. S. Gelfand
Keyword(s):  
Regulatory Rna ◽  
Rna Structures

scholarly journals Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa:Kinship to coliphages and conservation of regulatory RNA structures

Virology ◽  
1995 ◽  
Vol 206 (1) ◽  
pp. 611-625 ◽  
Author(s):  
R.C.L. Olsthoorn ◽  
G. Garde ◽  
T. Dayhuff ◽  
J.F. Atkins ◽  
J. Van Duin
Keyword(s):  
Nucleotide Sequence ◽  
Regulatory Rna ◽  
Rna Structures ◽  
Rna Phage

Computational approaches for alternative and transient secondary structures of ribonucleic acids

2018 ◽  
Vol 18 (3) ◽  
pp. 182-191
Author(s):  
Tsukasa Fukunaga ◽  
Michiaki Hamada
Keyword(s):  
Secondary Structures ◽  
Living Cells ◽  
Translation Regulation ◽  
Folding Pathway ◽  
Rna Structures ◽  
Computational Approaches ◽  
Rna Secondary Structures ◽  
Ribonucleic Acids ◽  
Alternative Structures ◽  
Regulatory Processes

Abstract Transient and alternative structures of ribonucleic acids (RNAs) play essential roles in various regulatory processes, such as translation regulation in living cells. Because experimental analyses for RNA structures are difficult and time-consuming, computational approaches based on RNA secondary structures are promising. In this article, we review computational methods for detecting and analyzing transient/alternative secondary structures of RNAs, including static approaches based on probabilistic distributions of RNA secondary structures and dynamic approaches such as kinetic folding and folding pathway predictions.

scholarly journals Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome

2020 ◽  
Author(s):  
Sean P. Ryder ◽  
Brittany R. Morgan ◽  
Francesca Massi
Keyword(s):  
High Throughput Sequencing ◽  
Hypervariable Region ◽  
Regulatory Elements ◽  
Regulatory Rna ◽  
Rna Structures ◽  
Stem Loop ◽  
Functional Relevance ◽  
The Stability ◽  
Genome Heterogeneity ◽  
A Minor

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has motivated a widespread effort to understand its epidemiology and pathogenic mechanisms. Modern high-throughput sequencing technology has led to the deposition of vast numbers of SARS-CoV-2 genome sequences in curated repositories, which have been useful in mapping the spread of the virus around the globe. They also provide a unique opportunity to observe virus evolution in real time. Here, we evaluate two cohorts of SARS-CoV-2 genomic sequences to identify rapidly emerging variants within structured cis-regulatory elements of the SARS-CoV-2 genome. Overall, twenty variants are present at a minor allele frequency of at least 0.5%. Several enhance the stability of Stem Loop 1 in the 5’UTR, including a set of co-occurring variants that extend its length. One appears to modulate the stability of the frameshifting pseudoknot between ORF1a and ORF1b, and another perturbs a bi-stable molecular switch in the 3’UTR. Finally, five variants destabilize structured elements within the 3’UTR hypervariable region, including the S2M stem loop, raising questions as to the functional relevance of these structures in viral replication. Two of the most abundant variants appear to be caused by RNA editing, suggesting host-viral defense contributes to SARS-CoV-2 genome heterogeneity. This analysis has implications for the development of therapeutics that target viral cis-regulatory RNA structures or sequences, as rapidly emerging variations in these regions could lead to drug resistance.

Sign in / Sign up

Export Citation Format

Share Document