RNAstructure: web servers for RNA secondary structure prediction and analysis

Bellaousov, Stanislav; Reuter, Jessica S.; Seetin, Matthew G.; Mathews, David H.

doi:10.1093/nar/gkt290

Cited by 359 publications

(314 citation statements)

References 41 publications

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“…Figure 1A shows the unconstrained predicted structure, whereas Figure 1B shows the SHAPE-validated MPMV structure. An average of SHAPE reactivities numerical data for each nucleotide that were drawn from two to four experiments were applied as pseudo energy constraints in RNAstructure (Reuter and Mathews 2010;Bellaousov et al 2013). As shown in Figure 1B, the SHAPE data robustly corroborated the freeenergy minimized predicted structure of the MPMV packaging signal RNA presented in Figure 1A.…”

Section: Resultsmentioning

confidence: 58%

SHAPE analysis of the 5′ end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization

Aktar

Jabeen

Ali

et al. 2013

RNA

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Earlier genetic and structural prediction analyses revealed that the packaging determinants of Mason Pfizer monkey virus (MPMV) include two discontinuous core regions at the 5 ′ end of its genomic RNA. RNA secondary structure predictions suggested that these packaging determinants fold into several stem-loops (SLs). To experimentally validate this structural model, we employed selective 2 ′ hydroxyl acylation analyzed by primer extension (SHAPE), which examines the flexibility of the RNA backbone at each nucleotide position. Our SHAPE data validated several predicted structural motifs, including U5/Gag longrange interactions (LRIs), a stretch of single-stranded purine (ssPurine)-rich region, and a distinctive G-C-rich palindromic (pal) SL. Minimum free-energy structure predictions, phylogenetic, and in silico modeling analyses of different MPMV strains revealed that the U5 and gag sequences involved in the LRIs differ minimally within strains and maintain a very high degree of complementarity. Since the pal SL forms a helix loop containing a canonical "GC" dyad, it may act as a RNA dimerization initiation site (DIS), enabling the virus to package two copies of its genome. Analyses of wild-type and pal mutant RNAs revealed that disruption of pal sequence strongly affected RNA dimerization. However, when in vitro transcribed transcomplementary pal mutants were incubated together showed RNA dimerization was restored authenticating that the pal loop (5 ′ -CGGCCG-3 ′ ) functions as DIS.

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Section: Resultsmentioning

confidence: 58%

SHAPE analysis of the 5′ end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization

Aktar

Jabeen

Ali

et al. 2013

RNA

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“…All proteincoding genes have typical initiation and termination codons of ATN and TAA, respectively, except COI and ND4, which terminate with a single T. The single T is an incomplete stop codon, which are frequent in the mitogenomes of insects (Wang et al 2014). All of the tRNAs exhibit a classic cloverleaf secondary structure, which we predicted with tRNAscan-SE v1.21 and/or RNA structure (Lowe & Eddy 1997;Bellaousov et al 2013). The mitogenome of S. chinensis has a high A þ T content of 84.2% (A: 45.1%; T: 39.1%; C: 10.2%; G: 5.6%), which is similar to other aphids (range: 82.8-84.7%; n ¼ 10).…”

mentioning

confidence: 62%

Complete mitochondrial genome of the Rhus gall aphid Schlechtendalia chinensis (Hemiptera: Aphididae: Eriosomatinae)

Ren

Bai

Harris

et al. 2016

Mitochondrial DNA Part B

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We sequenced the first complete mitochondrial genome for the aphid subfamily, Eriosomatinae, from a Rhus gall aphid, Schlechtendalia chinensis . The mitogenome of S. chinensis is 16,047 bp in length with a high A + T content of 84.2% and consists of 13 protein-coding genes, 24 tRNA genes including two extra tRNA Phe , two rRNA genes, a repeat region, and a control region. All protein-coding genes have a typical ATN initiation codon and TAA termination codon except COI and ND4, which terminate with a single T. All 24 tRNAs have the expected clover-leaf secondary structure and range in size from 62 to 73 bp. The lengths of rrnL and rrnS genes are 1274 and 772 bp, respectively. The repeat region is 335 bp and is uncommon among known aphid sequences for starting with a tRNA Phe . The control region is 705 bp in length and is located between rrnS and tRNA Ile . We present a phylogeny of mitogenomes showing that S. chinensis is sister to Aphidinae.

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“…Subsequently, the RNA was folded at 25°C using default slope and intercept parameters. This server uses RNAstructure 40,41 (http:// rna.urmc.rochester.edu/index.html) as the backend.…”

Section: Methodsmentioning

confidence: 99%

Determination of in vivo RNA structure in low-abundance transcripts

et al. 2013

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RNA structure plays important roles in diverse biological processes. However, the structures of all but the few most abundant RNAs are presently unknown in vivo. Here we introduce DMS/SHAPE-LMPCR to query the in vivo structures of low-abundance transcripts. DMS/ SHAPE-LMPCR achieves attomole sensitivity, a 100,000-fold improvement over conventional methods. We probe the structure of low-abundance U12 small nuclear RNA (snRNA) in Arabidopsis thaliana and provide in vivo evidence supporting our derived phylogenetic structure. Interestingly, in contrast to mammalian U12 snRNAs, the loop of the SLIIb in U12 snRNA is variable among plant species, and DMS/SHAPE-LMPCR determines it to be unstructured. We reveal the effects of proteins on 25S rRNA, 5.8S rRNA and U12 snRNA structure, illustrating the critical importance of mapping RNA structure in vivo. Our universally applicable method opens the door to identifying and exploring the specific structure-function relationships of the multitude of low-abundance RNAs that prevail in living cells.

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RNAstructure: web servers for RNA secondary structure prediction and analysis

Cited by 359 publications

References 41 publications

SHAPE analysis of the 5′ end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization

SHAPE analysis of the 5′ end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization

Complete mitochondrial genome of the Rhus gall aphid Schlechtendalia chinensis (Hemiptera: Aphididae: Eriosomatinae)

Determination of in vivo RNA structure in low-abundance transcripts

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