DTA

DTA quantifies genome-wide RNA synthesis and decay rates to measure RNA turnover and transcriptome dynamics using metabolic RNA labeling combined with transcriptomic measurements.

Key Features:

• Genome-wide quantification: Measures RNA synthesis and decay rates across the genome.
• Metabolic RNA labeling integration: Combines metabolic RNA labeling with microarray or RNAseq-based transcriptomics.
• Kinetic modeling: Applies kinetic modeling to derive synthesis and decay rates from individual microarray or RNAseq measurements.
• Absolute quantification and comparison: Enables absolute quantification and comparison of RNA turnover across conditions or time points.
• Temporal resolution and sensitivity: Facilitates monitoring of cellular responses to perturbations with improved temporal resolution and sensitivity.
• Implementation platform: Implemented within the R/Bioconductor framework.

Scientific Applications:

• Gene regulation studies: Dissects transcriptional control by separating synthesis and decay contributions to RNA levels.
• Cellular response to perturbations: Tracks dynamic RNA turnover during responses to environmental changes or experimental perturbations.
• Temporal transcriptomics: Resolves temporal aspects of transcriptomic alterations by measuring turnover rates over time-series.
• Systems biology and disease research: Integrates RNA dynamics into studies of molecular biology, genetics, and systems-level mechanisms underlying diseases.

Methodology:

Combines metabolic RNA labeling with microarray or RNAseq transcriptomic measurements and uses kinetic modeling to obtain absolute synthesis and decay rates and to compare RNA turnover across conditions or time points; implemented within the R/Bioconductor framework.