NDLI: Analysis of the nucleotide context of Arabidopsis thaliana mitochondrial mRNA editing sites

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Analysis of the nucleotide context of Arabidopsis thaliana mitochondrial mRNA editing sites

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Biophysics : Volume 51, Issue 1, January 2006

Analysis of the nucleotide context of Arabidopsis thaliana mitochondrial mRNA editing sites

Content Provider	Springer Nature Link
Author	Vishnevsky, O. V. Titov, I. I. Konstantiv, Yu. M.
Copyright Year	2006
Abstract	C → T deamination is among the most widespread types of mitochondrial mRNA editing in higher plants. In the majority of cases, the first and second codon positions are edited, which leads to “correction” of the codon, substitution in amino acid sequence, and synthesis of a fully functional protein. Numerous experimental works have demonstrated that the 5′-and 3′-flanks of the editing site are important for precise and efficient editing. However, no significant motifs have been detected in the flanking regions, and the editing mechanism is still unknown. We analyzed the editing sites of Arabidopsis thaliana mitochondrial mRNA using region-specific degenerate oligonucleotide motifs and trinucleotide weight matrices. In addition, we compared the mRNA folding energies in the regions of editing sites. Significant oligonucleotide patterns were discovered in the region [−50; 50] relative to the editing site. Jackknife assessment suggested that such signals could play an important role in the functioning of editing sites. However, the detected characteristics alone were insufficient for efficient recognition of editing sites in A. thaliana mitochondrial mRNA.
Starting Page	1
Ending Page	6
Page Count	6
File Format	PDF
ISSN	00063509
Journal	Biophysics
Volume Number	51
Issue Number	1
e-ISSN	15556654
Language	English
Publisher	SP MAIK Nauka/Interperiodica
Publisher Date	2008-06-05
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	plant mRNA editing degenerate motifs nucleotide weight matrix site recognition Biophysics/Biomedical Physics
Content Type	Text
Resource Type	Article
Subject	Biophysics

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Running Title: Computational Analysis of RNA Editing Sites (2007)

Computational structural and functional genomics and transcriptomics 193 Chapter # ANALYSIS OF THE NUCLEOTIDE CONTEXT OF HIGHER PLANT MITOCHONDRIAL mRNA EDITING SITES

A systems approach to morphogenesis in Arabidopsis thaliana: I. AGNS database

Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources

Recognition of transcription factor binding sites by the SiteGA method

Mitochondrial transcript length polymorphisms are a widespread phenomenon in Arabidopsis thaliana

Targeted base editing in the mitochondrial genome of Arabidopsis thaliana.

Solid-state NMR characterization of the putative membrane anchor of TWD1 from Arabidopsis thaliana

Dysfunctional chloroplasts up-regulate the expression of mitochondrial genes in Arabidopsis seedlings

Analysis of the nucleotide context of Arabidopsis thaliana mitochondrial mRNA editing sites

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Running Title: Computational Analysis of RNA Editing Sites (2007)

Computational structural and functional genomics and transcriptomics 193 Chapter # ANALYSIS OF THE NUCLEOTIDE CONTEXT OF HIGHER PLANT MITOCHONDRIAL mRNA EDITING SITES

A systems approach to morphogenesis in Arabidopsis thaliana: I. AGNS database

Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources

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Mitochondrial transcript length polymorphisms are a widespread phenomenon in Arabidopsis thaliana

Targeted base editing in the mitochondrial genome of Arabidopsis thaliana.

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