KAS-Analyzer

KAS-Analyzer analyzes Kethoxal-assisted ssDNA sequencing (KAS-seq) and strand-specific spKAS-seq data to profile genome-wide single-stranded DNA (ssDNA) and characterize transcriptionally engaged RNA polymerases and R-loop structures.

Key Features:

• Genome-wide ssDNA profiling: Profiles single-stranded DNA (ssDNA) across the genome using KAS-seq and spKAS-seq data.
• Transcription-related metrics: Calculates transcription-related metrics to quantify transcriptional engagement of RNA polymerases.
• SST enhancer identification: Identifies single-stranded transcribing (SST) enhancers from KAS-seq signals.
• R-loop mapping: Maps R-loop structures by detecting ssDNA imbalances across strands using strand-specific spKAS-seq.
• Differential RNA polymerase activity analysis: Performs differential analyses to detect changes in RNA polymerase activity across conditions.
• Time-course dynamic analysis: Analyzes time-course KAS-seq datasets to investigate dynamic transcriptional regulatory programs, including responses to UVB radiation.

Scientific Applications:

• Transcription dynamics: Enables quantification and comparison of RNA polymerase engagement and transcriptional changes across conditions or time points.
• R-loop and genome regulation studies: Provides high-resolution mapping of R-loop structures to study their role in genome regulation.
• Enhancer biology: Facilitates identification and characterization of SST enhancers to investigate enhancer-mediated transcriptional modulation.
• Response to external stimuli: Supports analysis of transcriptional regulatory programs in response to external stimuli such as UVB radiation.

Methodology:

KAS-Analyzer applies computational algorithms and both standard and novel analytical techniques to KAS-seq and spKAS-seq data to profile genome-wide ssDNA landscapes and to compute transcription-related metrics, detect SST enhancers, map R-loops, and perform differential RNA polymerase activity analysis.