PeakFinder

PeakFinder identifies and annotates cohesin binding sites from chromatin immunoprecipitation microarray (ChIP-chip) data to enable genome-wide analysis of cohesin distribution in Saccharomyces cerevisiae during meiosis and mitosis.

Key Features:

• Automated Peak Identification: Detects peaks in ChIP-chip signal using computational algorithms to identify potential cohesin binding sites.
• Genome-wide ChIP-chip Data Processing: Processes genome-wide ChIP-chip datasets to map cohesin binding across the yeast genome.
• Plotting Measurements vs Genome Coordinates: Generates plots of measurements against genome coordinates to examine binding-site positions.
• Annotation Based on Local Curve Properties: Annotates peaks by analyzing local curve properties to characterize cohesin-binding signal features.

Scientific Applications:

• Genome-Wide Cohesin Binding Analysis: Maps cohesin distribution across the genome to study cohesin roles in chromosome structure and function during meiosis and mitosis.
• Conservation and Spacing of Cohesin Sites: Detects semiperiodic spacing (~11 kb) of cohesin sites that is conserved between meiotic and mitotic chromosomes and correlates with AT content.
• Correlation with Convergent Transcription Units: Identifies enrichment of cohesin binding in regions located between convergent transcription units.
• Cohesin-Transcription Dynamics: Reveals an incompatibility between transcription elongation and cohesin presence, indicating transcript elongation can displace cohesins from binding sites.
• Implications for Meiotic Recombination: Shows a negative correlation between cohesin sites and meiotic recombination locations, suggesting cohesin-based chromosome structure influences meiotic exchange.

Methodology:

Processes ChIP-chip data, employs algorithms to detect peaks representing potential binding sites, and annotates peaks by analyzing local curve properties.