Nanocompore

Nanocompore detects RNA modifications from nanopore direct-RNA sequencing by comparing raw electrical signal profiles between experimental conditions to map post-transcriptional modifications across the transcriptome.

Key Features:

• Modification Detection: Identifies differences in raw sequencing signals from nanopore direct-RNA sequencing that correspond to RNA modifications by comparing two samples under different experimental conditions.
• Comparative Analysis: Compares direct-RNA sequencing datasets from distinct experimental setups (e.g., control versus knockdown or knockout of modification enzymes) to identify changes in PTM patterns.
• Replication and Variability Modeling: Recommends using at least two replicates per condition to account for biological variability and enhance robustness of the analysis.
• No Training Set Required: Does not require a training set, facilitating application across diverse datasets without prior calibration.
• Single-Molecule Resolution: Detects RNA modifications at single-molecule resolution to map PTMs precisely across the transcriptome.
• Validation and Correlation: Results have been validated against orthogonal methods, confirming identification of known sites such as N6-methyladenosine (m6A) and reporting modifications in coding and non-coding RNAs.

Scientific Applications:

• Transcriptomics: Provides detailed maps of RNA modifications to support investigation of how PTMs affect gene expression regulation.
• Epitranscriptomics: Enables study of epigenetic-like modifications on RNA molecules and their functional implications.
• Disease Research: Facilitates analysis of altered RNA modification patterns in disease contexts to explore underlying mechanisms and potential targets.

Methodology:

Compares raw nanopore direct-RNA sequencing signals from a sample of interest and a non-modified control to identify signal variations attributable to RNA modifications; the approach does not require a training set and models biological variability through replicates to ensure detected modifications are statistically significant and biologically relevant.