PAQR

PAQR quantifies transcript 3' ends and polyadenylation (poly(A)) site usage from RNA sequencing (RNA-seq) data to analyze regulation of 3' untranslated regions (3' UTRs) in biological and disease contexts.

Key Features:

• Quantification of Poly(A) Site Use: Precisely quantifies poly(A) site usage from RNA-seq data to measure transcript 3' end choice.
• Integration with KAPAC: Integrates with KAPAC (K-mer Analysis for Polyadenylation Control) to infer activities of oligomeric sequence motifs that influence poly(A) site selection.
• Application to Normal and Tumor Samples: Applied to RNA-seq data from normal and tumor tissue samples to reveal disease-specific changes in polyadenylation patterns and associated sequence motifs.
• Identification of Key Regulators: Facilitates identification of regulatory proteins involved in poly(A) site choice, including implicating polypyrimidine tract binding protein 1 in glioblastoma.

Scientific Applications:

• Post-transcriptional regulation: Elucidates how poly(A) site selection and 3' UTR variation contribute to gene expression regulation.
• Comparative transcriptome analysis: Detects dynamic changes in polyadenylation across cellular states and experimental conditions using RNA-seq.
• Cancer research: Identifies aberrant polyadenylation patterns and sequence motifs that may underlie cleavage and polyadenylation alterations in cancers.

Methodology:

Processes RNA-seq data to quantify poly(A) site usage and integrates KAPAC motif analysis to infer activities of oligomeric sequence motifs affecting poly(A) site selection.