MINES

MINES identifies N6-methyladenosine (m6A) modifications in RNA transcripts from Oxford Nanopore direct RNA sequencing to map modification sites at single-nucleotide and isoform resolution.

Key Features:

• Single-Coordinate Resolution: Provides precise identification of m6A modifications at individual nucleotide positions within RNA transcripts.
• De Novo Identification: Detects previously unannotated m6A sites from direct RNA sequencing data.
• Isoform-Level Resolution: Resolves m6A sites at the transcript isoform level to enable transcript-specific methylation mapping.
• Sensitivity to Enzymatic Regulation: Detects changes in m6A modification patterns sensitive to the m6A writer METTL3 and eraser ALKBH5.

Scientific Applications:

• Epigenetic Research: Mapping m6A at high precision to study epigenetic regulation of gene expression and cellular differentiation.
• Transcriptomics: Enabling analysis of alternative splicing and transcript-specific methylation through isoform-resolved m6A mapping.
• Disease Mechanisms: Investigating roles of m6A dysregulation in diseases, including cancer, where altered methylation patterns may affect progression.

Methodology:

MINES applies a random forest classifier trained on experimentally validated N6-methyladenosine (m6A) sites within DRACH motifs to predict m6A status from Oxford Nanopore direct RNA sequencing data.