scholarly journals An RNA Mapping DataBase for curating RNA structure mapping experiments

2012 ◽  
Vol 28 (22) ◽  
pp. 3006-3008 ◽  
Author(s):  
Pablo Cordero ◽  
Julius B. Lucks ◽  
Rhiju Das
Keyword(s):  
Rna Structure ◽  
Structure Mapping ◽  
Rna Mapping ◽  
Rna Structure Mapping

scholarly journals Evaluation of the information content of RNA structure mapping data for secondary structure prediction

RNA ◽  
2010 ◽  
Vol 16 (6) ◽  
pp. 1108-1117 ◽  
Author(s):  
S. Quarrier ◽  
J. S. Martin ◽  
L. Davis-Neulander ◽  
A. Beauregard ◽  
A. Laederach
Keyword(s):  
Secondary Structure ◽  
Information Content ◽  
Rna Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Structure Mapping ◽  
Mapping Data ◽  
Rna Structure Mapping

scholarly journals Rational experiment design for sequencing-based RNA structure mapping

RNA ◽  
2014 ◽  
Vol 20 (12) ◽  
pp. 1864-1877 ◽  
Author(s):  
Sharon Aviran ◽  
Lior Pachter
Keyword(s):  
Rna Structure ◽  
Experiment Design ◽  
Structure Mapping ◽  
Rna Structure Mapping

scholarly journals Keth-seq for transcriptome-wide RNA structure mapping

2020 ◽  
Vol 16 (5) ◽  
pp. 489-492 ◽  
Author(s):  
Xiaocheng Weng ◽  
Jing Gong ◽  
Yi Chen ◽  
Tong Wu ◽  
Fang Wang ◽  
...  
Keyword(s):  
Rna Structure ◽  
Structure Mapping ◽  
Rna Structure Mapping

scholarly journals Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction

2018 ◽  
Author(s):  
Hengyi Xu ◽  
Jun Yao ◽  
Douglas C. Wu ◽  
Alan M. Lambowitz
Keyword(s):  
Rna Structure ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Structure Mapping ◽  
Dimer Formation ◽  
Biochemical Basis ◽  
Reverse Transcriptases ◽  
Small Ncrnas ◽  
Rna Structure Mapping ◽  
Insight Into

ABSTRACTThermostable group II intron reverse transcriptases (TGIRTs) with high fidelity and processivity have been used for a variety of RNA sequencing (RNA-seq) applications, including comprehensive profiling of whole-cell, exosomal, and human plasma RNAs; quantitative tRNA-seq based on the ability of TGIRT enzymes to give full-length reads of tRNAs and other structured small ncRNAs; high-throughput mapping of post-transcriptional modifications; and RNA structure mapping. Here, we improved TGIRT-seq methods for comprehensive transcriptome profiling by (i) rationally designing RNA-seq adapters that minimize adapter dimer formation, and (ii) developing biochemical and computational methods that remediate 5’- and 3’-end biases. These improvements, some of which may be applicable to other RNA-seq methods, increase the efficiency of TGIRT-seq library construction and improve coverage of very small RNAs, such as miRNAs. Our findings provide insight into the biochemical basis of 5’- and 3’-end biases in RNA-seq and suggest general approaches for remediating biases and decreasing adapter dimer formation.

scholarly journals Direct RNA sequencing reveals structural differences between transcript isoforms

2020 ◽  
Author(s):  
Jong Ghut Ashley Aw ◽  
Shaun W. Lim ◽  
Jia Xu Wang ◽  
Yang Shen ◽  
Pornchai Kaewsapsak ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Rna Structure ◽  
Embryonic Stem ◽  
Structural Features ◽  
Support Vector ◽  
Specific Gene ◽  
Structure Mapping ◽  
Individual Gene ◽  
Structure Information ◽  
Structural Differences

AbstractThe ability to correctly assign structure information to an individual transcript in a continuous and phased manner is critical to understanding RNA function. RNA structure play important roles in every step of an RNA’s lifecycle, however current short-read high throughput RNA structure mapping strategies are long, complex and cannot assign unique structures to individual gene-linked isoforms in shared sequences. To address these limitations, we present an approach that combines structure probing with SHAPE-like compound NAI-N3, nanopore direct RNA sequencing, and one-class support vector machines to detect secondary structures on near full-length RNAs (PORE-cupine). PORE-cupine provides rapid, direct, accurate and robust structure information along known RNAs and recapitulates global structural features in human embryonic stem cells. The majority of gene-linked isoforms showed structural differences in shared sequences both local and distal to the alternative splice site, highlighting the importance of long-read sequencing for phasing of structures. Structural differences between gene-linked isoforms are associated with differential translation efficiencies globally, highlighting the role of structure as a pervasive mechanism for regulating isoform-specific gene expression inside cells.

scholarly journals trp RNA-Binding Attenuation Protein-5′ Stem-Loop RNA Interaction Is Required for Proper Transcription Attenuation Control of the Bacillus subtilis trpEDCFBAOperon

2000 ◽  
Vol 182 (7) ◽  
pp. 1819-1827 ◽  
Author(s):  
Hansen Du ◽  
Alexander V. Yakhnin ◽  
Subramanian Dharmaraj ◽  
Paul Babitzke
Keyword(s):  
Bacillus Subtilis ◽  
Rna Structure ◽  
Rna Binding ◽  
Structure Mapping ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
Expression Studies ◽  
Attenuation Mechanism ◽  
Transcription Attenuation ◽  
Rna Interaction

ABSTRACT The trp RNA-binding attenuation protein (TRAP) regulates expression of the Bacillus subtilis trpEDCFBAoperon by a novel transcription attenuation mechanism. Tryptophan-activated TRAP binds to the nascent trp leader transcript by interacting with 11 (G/U)AG repeats, 6 of which are present in an antiterminator structure. TRAP binding to these repeats prevents formation of the antiterminator, thereby promoting formation of an overlapping intrinsic terminator. A third stem-loop structure that forms at the extreme 5′ end of the trp leader transcript also plays a role in the transcription attenuation mechanism. The 5′ stem-loop increases the affinity of TRAP fortrp leader RNA. Results from RNA structure mapping experiments demonstrate that the 5′ stem-loop consists of a 3-bp lower stem, a 5-by-2 asymmetric internal loop, a 6-bp upper stem, and a hexaloop at the apex of the structure. Footprinting results indicate that TRAP interacts with the 5′ stem-loop and that this interaction differs depending on the number of downstream (G/U)AG repeats present in the transcript. Expression studies with trpE′-′lacZtranslational fusions demonstrate that TRAP-5′ stem-loop interaction is required for proper regulation of the trp operon. 3′ RNA boundary experiments indicate that the 5′ structure reduces the number of (G/U)AG repeats required for stable TRAP-trp leader RNA association. Thus, TRAP-5′ stem-loop interaction may increase the likelihood that TRAP will bind to the (G/U)AG repeats in time to block antiterminator formation.

scholarly journals An InternalRibosome Entry Site Directs Translation of the Murine Gammaherpesvirus68 MK3 Open ReadingFrame

2003 ◽  
Vol 77 (24) ◽  
pp. 13093-13105 ◽  
Author(s):  
Heather M. Coleman ◽  
Ian Brierley ◽  
Philip G. Stevenson
Keyword(s):  
Rna Structure ◽  
Molecular Mechanisms ◽  
Structure Mapping ◽  
Proliferating Cells ◽  
Entry Site ◽  
Stem Loop ◽  
Internal Ribosome Entry ◽  
Reading Frame ◽  
Murine Gammaherpesvirus

ABSTRACT The gammaherpesviruses characteristically drive the proliferation of latently infected lymphocytes. The murine gammaherpesvirus 68 (MHV-68) MK3 protein contributes to this process in vivo by evading CD8+-T-cell recognition during latency, as well as during lytic infection. We analyzed some of the molecular mechanisms that control MK3 expression. No dedicated MK3 mRNA was detected. Instead, the MK3 open reading frame (ORF) was transcribed as part of a bicistronic mRNA, downstream of a previously unidentified ORF, 13M. The 13M/MK3 promoter appeared to extend approximately 1 kb 5′ of the transcription start site and included elements both dependent on and independent of the ORF50 lytic transactivator. MK3 was translated from the bicistronic transcript by virtue of an internal ribosome entry site (IRES) element. RNA structure mapping identified two stem-loops between 13M and MK3 that were sufficient for IRES activity in a bicistronic reporter plasmid and a third stem-loop just within the MK3 coding sequence, with a subtler, perhaps regulatory role. Overall, translation of the MHV-68 MK3 bore a striking resemblance to that of the Kaposi's sarcoma-associated herpesvirus vFLIP, suggesting that IRES elements are a common theme of latent gammaherpesvirus immune evasion in proliferating cells.

scholarly journals Anomalous reverse transcription through chemical modifications in polyadenosine stretches

2020 ◽  
Author(s):  
Wipapat Kladwang ◽  
Ved V. Topkar ◽  
Bei Liu ◽  
Tracy L. Hodges ◽  
Sarah C. Keane ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Reverse Transcription ◽  
Rna Structure ◽  
Dimethyl Sulfate ◽  
Resonance Spectroscopy ◽  
Structure Mapping ◽  
Chemical Modifications ◽  
Unusual Structure ◽  
Reverse Transcriptases ◽  
Chemically Modified

AbstractThermostable reverse transcriptases are workhorse enzymes underlying nearly all modern techniques for RNA structure mapping and for transcriptome-wide discovery of RNA chemical modifications. Despite their wide use, these enzymes’ behaviors at chemical modified nucleotides remain poorly understood. Wellington-Oguri et al. recently reported an apparent loss of chemical modification within putatively unstructured polyadenosine stretches modified by dimethyl sulfate or 2’ hydroxyl acylation, as probed by reverse transcription. Here, re-analysis of these and other publicly available data, capillary electrophoresis experiments on chemically modified RNAs, and nuclear magnetic resonance spectroscopy on A12 and variants show that this effect is unlikely to arise from an unusual structure of polyadenosine. Instead, tests of different reverse transcriptases on chemically modified RNAs and molecules synthesized with single 1-methyladenosines implicate a previously uncharacterized reverse transcriptase behavior: near-quantitative bypass through chemical modifications within polyadenosine stretches. All tested natural and engineered reverse transcriptases (MMLV; SuperScript II, III, and IV; TGIRT-III; and MarathonRT) exhibit this anomalous bypass behavior. Accurate DMS-guided structure modeling of the polyadenylated HIV-1 3’ untranslated region RNA requires taking into account this anomaly. Our results suggest that poly(rA-dT) hybrid duplexes can trigger unexpectedly effective reverse transcriptase bypass and that chemical modifications in poly(A) mRNA tails may be generally undercounted.

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