Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Computational approaches to insertional RNA editing.

Ralf Bundschuh1

  • 1Department of Physics, The Ohio State University, Columbus, Ohio, USA.

Methods in Enzymology
|July 31, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Role of the anti-Shine-Dalgarno sequence of 16S rRNA in Flavobacterium johnsoniae.

Nucleic acids research·2026
Same author

Addition of Ianalumab (VAY736) to Ibrutinib in Patients with Chronic Lymphocytic Leukemia on Ibrutinib Therapy: Results from a Phase Ib Study.

Clinical cancer research : an official journal of the American Association for Cancer Research·2025
Same author

The structural effects of indel polymorphisms outside the binding site on RNA-protein interactions are shaped by selection.

PLoS computational biology·2025
Same author

Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.

bioRxiv : the preprint server for biology·2025
Same author

PYM1 limits non-canonical Exon Junction Complex occupancy in a gene architecture dependent manner to tune mRNA expression.

Nature communications·2025
Same author

PYM1 limits non-canonical Exon Junction Complex occupancy in a gene architecture dependent manner to tune mRNA expression.

bioRxiv : the preprint server for biology·2025
Same journal

1,2-Aminothiol-specific conjugation for dual-color fluorescent labeling via ultrafast TAMM conjugates.

Methods in enzymology·2026
Same journal

Nitrone dipoles in bioorthogonal chemistry applications.

Methods in enzymology·2026
Same journal

Bioorthogonal labeling of sialic acid isomers for detection of glycoconjugates by mass spectrometry imaging and microscopy.

Methods in enzymology·2026
Same journal

Bioorthogonal photocatalytic proximity labeling for quantitative mapping of cell-cell interactions.

Methods in enzymology·2026
Same journal

inCu-click: Enabling copper-catalyzed click chemistry inside living cells.

Methods in enzymology·2026
Same journal

Site-specific antibody labeling via endo-S2 mediated Fc glycan remodeling.

Methods in enzymology·2026
See all related articles

Computational tools simplify locating RNA editing sites in genes. Our Predictor of Insertional Editing (PIE) software aids in identifying these sites, facilitating experimental validation.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Insertional RNA editing presents challenges in identifying specific edited genes and their editing sites.
  • Computational methods offer a promising approach to predict gene and editing site locations, aiding experimental verification.

Purpose of the Study:

  • To describe a step-by-step methodology for utilizing the Predictor of Insertional Editing (PIE) tool.
  • To demonstrate the application of PIE for locating genes and predicting editing sites.
  • To use the nad4L genes from *Physarum polycephalum*'s mitochondrial genome as a case study.

Main Methods:

  • Development and application of the Predictor of Insertional Editing (PIE) computational tool.
  • Detailed sequence analysis tailored to the specific gene of interest, acknowledging that full automation is limited.

Related Experiment Videos

  • Case study using mitochondrial nad4L genes from *Physarum polycephalum*.

    • Main Results:

    • The PIE tool provides predictions for gene locations and specific editing sites.
    • These predictions are suitable for designing primers for experimental validation.
    • The methodology is demonstrated effectively using the chosen example genes.

    Conclusions:

    • Computational approaches, exemplified by PIE, are valuable for overcoming challenges in studying insertional RNA editing.
    • PIE facilitates the identification of RNA editing sites, streamlining experimental validation processes.
    • The tool's application on *Physarum polycephalum* mitochondrial nad4L genes showcases its practical utility.