nucleosome_prediction

nucleosome_prediction predicts genome-wide nucleosome positions from DNA sequence and in vitro occupancy data to elucidate intrinsic DNA sequence preferences that shape chromatin structure and gene regulation.

Key Features:

• Genome-wide nucleosome prediction: Predicts nucleosome positions across the genome based on intrinsic DNA sequence preferences.
• In vitro occupancy data: Uses genome-wide nucleosome occupancy measurements on purified yeast genomic DNA to isolate sequence-encoded positioning signals.
• Affinity measurements: Incorporates a micrococcal nuclease-independent experiment measuring nucleosome affinity for approximately 40,000 double-stranded 150-base-pair oligonucleotides.
• Nucleosome depletion detection: Identifies depletion at transcription factor binding sites and around gene start and end sites, indicating sequence-encoded depletions.
• Model validation: Employs a computational model that shows significant correlation with in vivo nucleosome occupancy in Caenorhabditis elegans.
• Recapitulation of in vivo patterns: Recovers patterns similar to those observed under different in vivo growth conditions, highlighting the role of intrinsic sequence preferences.

Scientific Applications:

• Chromatin structure analysis: Analyze chromatin organization and its impact on gene regulation using sequence-derived nucleosome maps.
• Transcription factor interplay: Investigate the interplay between nucleosome positioning and transcription factor binding sites.
• Comparative and evolutionary studies: Explore evolutionary conservation of nucleosome positions across species using predicted and experimental occupancy data.

Methodology:

Developed a computational model using in vitro nucleosome occupancy data and sequence-derived affinity measurements to predict nucleosome positions from DNA sequence, validated by correlation with in vivo occupancy in Caenorhabditis elegans.