ARTDeco

ARTDeco quantifies transcriptional readthrough from RNA sequencing data to identify readthrough genes, read-in genes, and downstream-of-gene (DoG) transcripts and to correct gene expression for upstream readthrough contributions.

Key Features:

• Quantification of Readthrough Events: Quantifies transcriptional readthrough using metrics including read-in levels, readthrough levels, and detection of downstream-of-gene (DoG) transcripts.
• Gene Expression Correction: Uses read-in levels to deconvolute native gene expression from contributions arising from upstream readthrough transcription.
• Versatile Data Compatibility: Supports single-end and paired-end reads, stranded and unstranded data, and forward and reverse strand orientations.
• Robust Detection and Analysis: Identifies genes that fail to terminate (readthrough genes), read-in genes, and novel DoG transcripts, validated across experimental systems with termination defects.
• Application in Disease Contexts: Applied to analyze readthrough transcription during influenza A virus (IAV) infection, including comparisons with a mutant virus that fails to block transcription termination.
• Enhanced Interpretation of eQTLs: Enables detection of how read-in gene-associated expression quantitative trait loci (eQTLs) regulate genes upstream of read-in genes.

Scientific Applications:

• Viral infection studies: Analyze transcriptional readthrough during influenza A virus (IAV) infection and assess effects of viral mutants on termination.
• eQTL interpretation: Disentangle eQTL effects attributable to upstream readthrough versus native gene regulation in datasets with disrupted termination.
• Transcription termination research: Characterize the impact of termination failures on gene expression and identify DoG transcripts across experimental conditions and disease contexts.

Methodology:

Quantifies readthrough using read-in and readthrough level metrics and DoG detection, deconvolutes gene expression using read-in levels, identifies readthrough genes, read-in genes and DoG transcripts, and accepts single-end/paired-end and stranded/unstranded RNA-seq orientations.