ArticlePloS one2016
aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 15 citations in OpenAlex.
- Applications of Synthetic Pentatricopeptide Repeat Proteins.Plant & cell physiology · 2024Review
- Article
- Cofactor-independent RNA editing by a synthetic S-type PPR protein.Synthetic biology (Oxford, England) · 2021Article
- Yeast pentatricopeptide protein Dmr1 (Ccm1) binds a repetitive AU-rich motif in the small subunit mitochondrial ribosomal RNA.RNA (New York, N.Y.) · 2020Article
- Identification of soybean trans-factors associated with plastid RNA editing sites.Genetics and molecular biology · 2020Article
- Unparalleled Variation in RNA Editing amongPlant physiology · 2020Article
- Delineation of pentatricopeptide repeat codes for target RNA prediction.Nucleic acids research · 2019Article
- Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae.BMC evolutionary biology · 2018Article
- Analysis of healthcare service utilization after transport-related injuries by a mixture of hidden Markov models.PloS one · 2018Article
- CRP1 Protein: (dis)similarities betweenFrontiers in plant science · 2017Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pentatricopeptide repeat containing proteins (PPRs) bind to RNA transcripts originating from mitochondria and plastids. There are two classes of PPR proteins. The [Formula: see text] class contains tandem [Formula: see text]-type motif sequences, and the [Formula: see text] class contains alternating [Formula: see text], [Formula: see text] and [Formula: see text] type sequences. In this paper, we describe a novel tool that predicts PPR-RNA interaction; specifically, our method, which we call aPPRove, determines where and how a [Formula: see text]-class PPR protein will bind to RNA when given a PPR and one or more RNA transcripts by using a combinatorial binding code for site specificity proposed by Barkan et al. Our results demonstrate that aPPRove successfully locates how and where a PPR protein belonging to the [Formula: see text] class can bind to RNA. For each binding event it outputs the binding site, the amino-acid-nucleotide interaction, and its statistical significance. Furthermore, we show that our method can be used to predict binding events for [Formula: see text]-class proteins using a known edit site and the statistical significance of aligning the PPR protein to that site. In particular, we use our method to make a conjecture regarding an interaction between CLB19 and the second intronic region of ycf3. The aPPRove web server can be found at www.cs.colostate.edu/~approve.
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