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 Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

2019 ◽  
Author(s):  
Roman Ochsenreiter ◽  
Ivo L. Hofacker ◽  
Michael T. Wolfinger
Keyword(s):  
Life Cycle ◽  
Comparative Genomics ◽  
In Silico ◽  
Wide Distribution ◽  
Viral Life Cycle ◽  
Untranslated Regions ◽  
Structural Elements ◽  
Rna Structures ◽  
Evolutionarily Conserved ◽  
To Come

Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3'UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs xrRNAs within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3'UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs

scholarly journals Functional RNA Structures in the 3’UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

2019 ◽  
Author(s):  
Roman Ochsenreiter ◽  
Ivo L. Hofacker ◽  
Michael T. Wolfinger
Keyword(s):  
Life Cycle ◽  
Comparative Genomics ◽  
In Silico ◽  
Wide Distribution ◽  
Viral Life Cycle ◽  
Untranslated Regions ◽  
Structural Elements ◽  
Rna Structures ◽  
Evolutionarily Conserved ◽  
To Come

AbstractUntranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3’UTR of tick-borne, insect-specific and no-known-vector flavivirusesin silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs (xrRNAs) within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3’UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs.

scholarly journals Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 298 ◽  
Author(s):  
Roman Ochsenreiter ◽  
Ivo Hofacker ◽  
Michael Wolfinger
Keyword(s):  
Life Cycle ◽  
Comparative Genomics ◽  
In Silico ◽  
Wide Distribution ◽  
Viral Life Cycle ◽  
Untranslated Regions ◽  
Structural Elements ◽  
Rna Structures ◽  
Evolutionarily Conserved ◽  
To Come

Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3 ′ UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs (xrRNAs) within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3 ′ UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs.

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

Bioinformatics Methods for Studying MicroRNA and ARE-Mediated Regulation of Post-Transcriptional Gene Expression

2010 ◽  
Vol 1 (3) ◽  
pp. 97-112 ◽  
Author(s):  
Richipal Singh Bindra ◽  
Jason T. L. Wang ◽  
Paramjeet Singh Bagga
Keyword(s):  
Mirna Target ◽  
Target Prediction ◽  
Untranslated Regions ◽  
Regulatory Rna ◽  
Rna Motifs ◽  
Protein Coding ◽  
Rna Molecules ◽  
Cellular Processes ◽  
Target Sites ◽  
Transcriptional Gene Regulation

MicroRNAs (miRNAs) are short single-stranded RNA molecules with 21-22 nucleotides known to regulate post-transcriptional expression of protein-coding genes involved in most of the cellular processes. Prediction of miRNA targets is a challenging bioinformatics problem. AU-rich elements (AREs) are regulatory RNA motifs found in the 3’ untranslated regions (UTRs) of mRNAs, and they play dominant roles in the regulated decay of short-lived human mRNAs via specific interactions with proteins. In this paper, the authors review several miRNA target prediction tools and data sources, as well as computational methods used for the prediction of AREs. The authors discuss the connection between miRNA and ARE-mediated post-transcriptional gene regulation. Finally, a data mining method for identifying the co-occurrences of miRNA target sites in ARE containing genes is presented.

scholarly journals Intron and Its Splicing Mechanism and Their Connection with Human Disease

2016 ◽  
Vol 15 (3) ◽  
pp. 307-312
Author(s):  
Mine Dosay-Akbulut
Keyword(s):  
Human Genome ◽  
Human Disease ◽  
Rna Splicing ◽  
Messenger Rna ◽  
Developmental Disorders ◽  
Regulation Of Gene Expression ◽  
Medical Science ◽  
Intronless Genes ◽  
Different Types ◽  
Extra Difficulty

In the maturation mechanism of a messenger RNA, splicing play an important role with removing the noncoding introns and ligating the coding exons. Alternative splicing (AS) gives an extra difficulty to this mechanism and to the regulation of gene expression. The possible disturbing in the alternative RNA splicing mechanism can be a reason to several diseases like cancers and neurodegenerative disorders. Intronless genes (IGs) are seen in almost 3% of the human genome. Functionality of IGs has an important role in signal transduction genes and related regulatory proteins. This diversity can be reason to IG-associated diseases, especially neuropathies, developmental disorders, and cancer. The retroelements can be seen in almost half of the human genome. The known informations indicate that insertion of retroelement into exons and introns of genes promote different types of genetic disease, including cancer. The retroelement connected mutagenesis cause to fifty different types of human disease. The molecular informations and bioinformatic analyses can be used to explain the connection with splicing mutations and genetic mechanisms of several different human disease and understanding of this mechanism play an important role in the formation of treatment programme against to these diseases.Bangladesh Journal of Medical Science Vol.15(3) 2016 p.307-312

scholarly journals Genome-Wide Analysis of LIM Family Genes in Foxtail Millet (Setaria italica L.) and Characterization of the Role of SiWLIM2b in Drought Tolerance

2019 ◽  
Vol 20 (6) ◽  
pp. 1303 ◽  
Author(s):  
Rui Yang ◽  
Ming Chen ◽  
Jian-Chang Sun ◽  
Yue Yu ◽  
Dong-Hong Min ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Tolerance ◽  
Transgenic Rice ◽  
Metabolic Regulation ◽  
Cell Damage ◽  
Regulation Of Gene Expression ◽  
Foxtail Millet ◽  
Gene Promoters ◽  
Cis Acting ◽  
Lim Proteins

LIM proteins have been found to play important roles in many life activities, including the regulation of gene expression, construction of the cytoskeleton, signal transduction and metabolic regulation. Because of their important roles in many aspects of plant development, LIM genes have been studied in many plant species. However, the LIM gene family has not yet been characterized in foxtail millet. In this study, we analyzed the whole genome of foxtail millet and identified 10 LIM genes. All LIM gene promoters contain MYB and MYC cis-acting elements that are related to drought stress. Based on the presence of multiple abiotic stress-related cis-elements in the promoter of SiWLIM2b, we chose this gene for further study. We analyzed SiWLIM2b expression under abiotic stress and hormone treatments using qRT-PCR. We found that SiWLIM2b was induced by various abiotic stresses and hormones. Under drought conditions, transgenic rice of SiWLIM2b-overexpression had a higher survival rate, higher relative water content and less cell damage than wild type (WT) rice. These results indicate that overexpression of the foxtail millet SiWLIM2b gene enhances drought tolerance in transgenic rice, and the SiWLIM2b gene can potentially be used for molecular breeding of crops with increased resistance to abiotic stress.

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