ConStruct: Improved construction of RNA consensus structures

Wilm, Andreas; Linnenbrink, Kornelia; Steger, Gerhard

doi:10.1186/1471-2105-9-219

Cited by 36 publications

(24 citation statements)

References 63 publications

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“…In lines labeled ''Logo,'' the size of nucleotide characters is proportional to the frequency of occurrence of this nucleotide at this position; the height of the character stack signifies the information content (in bits) of the sequences at that position (Beitz 2000). The last line of the alignments shows the predicted consensus structure in bracket-dot notation (Wilm et al 2008). In the structure model of 5S rRNA, binding sites of TFIIIA and ribosomal protein L5 are shaded in gray.…”

Section: Discussionmentioning

confidence: 99%

“…2B and Supplemental Fig. 2B) were generated with mafft (ginsi version 6.240) (Katoh et al 2005) and hand-optimized with respect to a consensus secondary structure using ConStruct (Wilm et al 2008). We created a common alignment by inserting gap-only columns into the individual alignments (shown in Supplemental Fig.…”

Section: Collection and Gene Structure Prediction Of Tfiiia Orthologsmentioning

confidence: 99%

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Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA

Fu¹,

Bannach²,

Chen³

et al. 2009

Genome Res.

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Identifying conserved alternative splicing (AS) events among evolutionarily distant species can prioritize AS events for functional characterization and help uncover relevant cis-and trans-regulatory factors. A genome-wide search for conserved cassette exon AS events in higher plants revealed the exonization of 5S ribosomal RNA (5S rRNA) within the gene of its own transcription regulator, TFIIIA (transcription factor for polymerase III A). The 5S rRNA-derived exon in TFIIIA gene exists in all representative land plant species but not in green algae and nonplant species, suggesting it is specific to land plants. TFIIIA is essential for RNA polymerase III-based transcription of 5S rRNA in eukaryotes. Integrating comparative genomics and molecular biology revealed that the conserved cassette exon derived from 5S rRNA is coupled with nonsense-mediated mRNA decay. Utilizing multiple independent Arabidopsis overexpressing TFIIIA transgenic lines under osmotic and salt stress, strong accordance between phenotypic and molecular evidence reveals the biological relevance of AS of the exonized 5S rRNA in quantitative autoregulation of TFIIIA homeostasis. Most significantly, this study provides the first evidence of ancient exaptation of 5S rRNA in plants, suggesting a novel gene regulation model mediated by the AS of an anciently exonized noncoding element.

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Section: Discussionmentioning

confidence: 99%

Section: Collection and Gene Structure Prediction Of Tfiiia Orthologsmentioning

confidence: 99%

Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA

Fu¹,

Bannach²,

Chen³

et al. 2009

Genome Res.

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“…Degradome mapping was performed using Visual Cloning 2000 (Redasoft). The PSTVd consensus structure was based on a sequence alignment by mafft/Q-INS-i (Katoh and Toh, 2008) and ConStruct (Wilm et al, 2008); the structure was drawn by R2R (Weinberg and Breaker, 2011). PSTVd sequences were taken from GenBank.…”

Section: Bioinformatic Methodsmentioning

confidence: 99%

“…These variants differ from (Katoh and Toh, 2008) and ConStruct (Wilm et al, 2008) of 234 different PSTVd variants; the structure is drawn by R2R (Weinberg and Breaker, 2011). The domain boundaries of Pospiviroids are marked and named according to Keese and Symons (1985) in gray color.…”

Section: Characterization Of Selected Pstvd Variants That Produce Difmentioning

confidence: 99%

Expression of SANT/HTH Myb mRNA, a plant morphogenesis-regulating transcription factor, changes due to viroid infection

Matoušek

Piernikarczyk

Týcová

et al. 2015

Journal of Plant Physiology

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“…The program ConStruct simultaneously aligns multiple RNA sequences and finds a consensus RNA structure, thus combining information on thermodynamic stability and phylogeny (103). Because sequence alignment often requires manual editing, ConStruct offers an interactive user interface that allows manual editing of the alignment.…”

Section: Programs For Predicting Secondary Structures With Pseudoknotsmentioning

confidence: 99%

Advances in RNA Structure Prediction from Sequence: New Tools for Generating Hypotheses about Viral RNA Structure-Function Relationships

Schroeder

2009

J Virol

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Advances in sequencing technology have made abundant RNA sequence information available, but the challenge of how to interpret these data remains. The RNA sequence contains many layers of information. RNA sequences code for proteins and small RNAs, such as microRNAs or transacting small interfering RNAs (siRNAs). RNA encodes information about both structure and function. Viral RNA structures, such as riboswitches, internal ribosome entry sites (75), and panhandles (71), regulate the stages of the viral life cycle, including replication (100), transcription (99), splicing (40, 48), aminoacylation (31, 55), translation (12,75,98), and encapsidation (27,60,71,84). Because viral RNAs are structurally dynamic, current prediction methods focusing on a single minimum freeenergy structure may not always identify functionally relevant structures without additional experimental restraints. Because RNA structure determination is often experimentally difficult despite tremendous advances in RNA crystallography, nuclear magnetic resonance spectroscopy, and chemical modification, RNA structure prediction is an important tool for generating hypotheses about structure-function relationships in RNA. RNA structure prediction can be useful for interpreting or designing mutagenesis experiments, identifying conserved structural features, and designing siRNA strategies. This review will briefly outline the basic ideas and assumptions underlying RNA structure prediction, compare different approaches to RNA structure prediction from a user's perspective, and discuss some applications of RNA structure prediction to viral RNA interference (RNAi) research.The RNA sequence, or primary structure, determines the secondary structure, or pattern of canonical Watson-Crick pairs forming duplexes and irregular regions, such as loops and single-stranded regions. The secondary structure then determines the tertiary structure or overall three-dimensional shape of the molecule. The tertiary structure contains the interaction sites for proteins, other RNA molecules, carbohydrates, or other small molecules and thus determines the quaternary or higher-order structure. The greater thermodynamic stability of RNA helices than that of tertiary interactions makes the RNA folding process hierarchical (35). For example, the favorable free energy involved in forming two stacked base pairs (0.4 to 0.9 kcal/mol per nucleotide) (105) is larger than the favorable free energy to form tertiary interactions, such as ribose zippers or tetraloop-receptor interactions (0.1 to 0.5 kcal/mol per nucleotide) (25, 97). Note that 1.4 kcal/mol is equivalent to 1 order of magnitude in a binding constant at 37°C. The hierarchical nature of RNA folding makes RNA structure prediction a tractable challenge (92). WHAT IS RNA STRUCTURE PREDICTION?Phylogenetic analysis of RNA sequences remains the gold standard of RNA structure prediction. Phylogenetic analysis involves generating an alignment of many RNA sequences and looking for patterns of covariation between two nucleotides. Two nu...

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ConStruct: Improved construction of RNA consensus structures

Cited by 36 publications

References 63 publications

Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA

Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA

Expression of SANT/HTH Myb mRNA, a plant morphogenesis-regulating transcription factor, changes due to viroid infection

Advances in RNA Structure Prediction from Sequence: New Tools for Generating Hypotheses about Viral RNA Structure-Function Relationships

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