Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

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Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1093/NAR/GKV1039
P932PMC publication ID4666355
P698PubMed publication ID26476446
P5875ResearchGate publication ID282945158

P50authorJørgen KjemsQ55277197
Ernst Stefan SeemannQ64771840
Jan GorodkinQ41050071
P2093author name stringZsuzsanna Sükösd
Ebbe S Andersen
Mads Krogh Jensen
Mathias Hansen
P2860cites workRole of RNA structure and protein factors in the control of HIV-1 splicing.Q51776461
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A bulge structure in HIV-1 TAR RNA is required for Tat binding and Tat-mediated trans-activationQ68583028
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The biased nucleotide composition of HIV-1 triggers type I interferon response and correlates with subtype D increased pathogenicityQ24498366
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structureQ24562398
Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol geneQ24652354
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignmentsQ24657990
Pfold: RNA secondary structure prediction using stochastic context-free grammarsQ24671753
A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbationQ24801326
HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genomeQ24802185
The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAsQ24802442
Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistenceQ27472977
Circularization of the HIV-1 RNA genomeQ27481058
Bioinformatic and Physical Characterizations of Genome-Scale Ordered RNA Structure in Mammalian RNA VirusesQ27487338
The structure of the HIV-1 RRE high affinity rev binding site at 1.6 A resolutionQ27621195
Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulgeQ27733920
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureQ27860806
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony MethodsQ27860929
In vitro evidence for a long range pseudoknot in the 5'-untranslated and matrix coding regions of HIV-1 genomic RNAQ28211352
RNA interactions in the 5' region of the HIV-1 genomeQ28241918
RNA structures facilitate recombination-mediated gene swapping in HIV-1Q30394295
Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammarsQ33875915
Understanding the errors of SHAPE-directed RNA structure modelingQ34208095
GTfold: enabling parallel RNA secondary structure prediction on multi-core desktopsQ34285050
The leader of the HIV-1 RNA genome forms a compactly folded tertiary structureQ34362436
PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data.Q34373242
The human immunodeficiency virus type 1 packaging signal and major splice donor region have a conserved stable secondary structureQ34434755
HIV-1 RNA dimerization: It takes two to tangoQ34666010
Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifsQ34671913
Quantifying variances in comparative RNA secondary structure predictionQ34698694
UNAFold: software for nucleic acid folding and hybridizationQ34810481
Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant formQ35947721
Evaluating the accuracy of SHAPE-directed RNA secondary structure predictionsQ36684726
Interplay between RNA structure and protein evolution in HIV-1.Q37816762
Computational analysis of conserved RNA secondary structure in transcriptomes and genomesQ38217501
The ability of the HIV-1 AAUAAA signal to bind polyadenylation factors is controlled by local RNA structureQ39726727
The structure of HIV-1 genomic RNA in the gp120 gene determines a recombination hot spot in vivoQ40541616
Circularization of the HIV-1 genome facilitates strand transfer during reverse transcriptionQ40675740
Deficient dimerization of human immunodeficiency virus type 1 RNA caused by mutations of the u5 RNA sequencesQ40683458
Structure and function of the human immunodeficiency virus leader RNA.Q41080184
RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP).Q41847185
On the role of four small hairpins in the HIV-1 RNA genomeQ41851074
The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequencesQ42021152
The HIV-1 Rev response element: an RNA scaffold that directs the cooperative assembly of a homo-oligomeric ribonucleoprotein complexQ42145543
A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codonQ42689207
Role of the trans-activation response element in dimerization of HIV-1 RNA.Q47968773
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue21
P407language of work or nameEnglishQ1860
P304page(s)10168-10179
P577publication date2015-10-17
P1433published inNucleic Acids ResearchQ135122
P1476titleFull-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain
P478volume43

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cites work (P2860)
Q90218662A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance
Q38961905Bridging the gap between in vitro and in vivo RNA folding
Q37296803Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic
Q55343600Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts.
Q37323917HIV-1 Vpr N-terminal tagging affects alternative splicing of the viral genome
Q33589204In vivo mutation rates and the landscape of fitness costs of HIV-1.
Q92718207Integrative modeling of the HIV-1 ribonucleoprotein complex
Q49962951RNA secondary structure profiling in zebrafish reveals unique regulatory features
Q40066032RNA structure inference through chemical mapping after accidental or intentional mutations
Q36518316Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1
Q37093478Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity

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