nASAP

nASAP analyzes nascent RNA profiling data to evaluate data quality and perform quantification, pausing, and regulatory network analyses for studies of transcriptional regulation, complementing workflows developed for RNA-seq.

Key Features:

• Quality Assessment: Computes sequencing statistics and mapping ratios and evaluates RNA integrity and mRNA contamination for nascent RNA datasets.
• Quantification Analysis: Quantifies expression of messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), and enhancer RNAs (eRNAs).
• Pausing Analysis: Performs genome-wide pausing analysis based on sequencing reads distribution to analyze RNA polymerase II pausing during transcription initiation and elongation.
• Network Analysis: Identifies annotated enhancer-promoter interactomes to elucidate gene regulatory mechanisms.

Scientific Applications:

• Transcriptional regulation: Supports analysis of RNA polymerase II dynamics, promoter-proximal pausing, and regulatory element activity in transcriptional control.
• Genomics: Enables genome-wide assessment of nascent transcription signals and enhancer activity.
• Molecular biology: Facilitates investigation of RNA species (mRNAs, lncRNAs, eRNAs) and their roles in cellular processes.
• Systems biology: Provides inputs for reconstructing regulatory networks via enhancer-promoter interactome analysis.

Methodology:

Compute sequencing statistics and mapping ratios; evaluate RNA integrity and mRNA contamination; quantify mRNAs, lncRNAs, and eRNAs; perform genome-wide pausing analysis using sequencing read distributions; identify annotated enhancer-promoter interactomes for network analysis.