Episo

Episo: Isoform-level quantification of RNA 5-methylcytosine (m5C) from RNA-BisSeq data

Episo quantifies RNA 5-methylcytosine (m5C) modifications at single-nucleotide resolution and transcript isoform level using high-throughput sequencing of bisulfite-treated RNA (RNA-BisSeq) data.

Key Features:

• Isoform-Level Quantification: Estimates m5C levels for individual transcript isoforms to characterize differential m5C distribution and splicing-associated regulation.
• Probabilistic Modeling: Applies a probabilistic model to estimate isoform-specific m5C levels from RNA-BisSeq reads.
• Mapper Module: Aligns RNA-BisSeq reads to reference transcriptomes.
• Quant Module: Computes isoform-level m5C modification levels.
• Bisulfitefq Module: Simulates RNA-BisSeq datasets for validation and benchmarking.
• Tool Integration: Integrates with Bowtie, Tophat, Cufflinks, and Kallisto for alignment and transcript quantification workflows.
• Input Support: Accepts reference transcriptome sequences in FastA format (.fa, .fasta).

Scientific Applications:

• Epitranscriptome Analysis: Characterizes non-uniform RNA m5C distribution across human and mouse transcript isoforms to investigate gene expression regulation and disease-associated mechanisms.

Methodology:

Episo processes RNA-BisSeq data by mapping reads to reference transcriptomes derived from Ensembl or NCBI annotations, estimating isoform-specific m5C levels using a probabilistic framework, and validating performance through simulated datasets and m5C-specific methylated RNA immunoprecipitation (meRIP) experiments.