SymCurv

SymCurv predicts nucleosome positioning from DNA sequence by modeling symmetric DNA curvature around local curvature minima and related structural properties to identify likely nucleosome locations for studies of chromatin architecture.

Key Features:

• Ab initio prediction: Uses an ab initio computational approach that does not rely on pre-existing positioning maps to infer nucleosome locations from sequence-derived properties.
• DNA curvature symmetry: Leverages the symmetry of DNA curvature and local curvature minima as primary structural signals for nucleosome-forming sequences.
• Identification of positioned nucleosomes and NFRs: Detects consistently positioned nucleosomes and adjacent nucleosome-free regions (NFRs) from sequence and comparative data.
• Genome-scale analysis: Scales to genome-wide studies to define nucleosomal landscapes and sequence constraints across genomes.
• Integration with high-throughput data: Aligns predictions with high-throughput nucleosome-positioning datasets to refine analyses of chromatin architecture.

Scientific Applications:

• Understanding chromatin architecture: Predicts nucleosome positions to study how chromatin structure influences transcription and RNA processing, including exon definition and splicing mechanisms.
• Gene expression regulation: Identifies promoter and gene architectures influenced by nucleosome positioning to investigate roles of topoisomerase II and chromatin-remodeling complexes.
• Evolutionary insights: Provides a framework to examine how sequence constraints have evolved to shape nucleosome-forming sequences and chromatin structure.

Methodology:

Ab initio computational modeling based on DNA curvature symmetry around local minima, coupled with comparative analyses of nucleosome-positioning datasets to identify consistently positioned nucleosomes and adjacent nucleosome-free regions while considering statistical positioning and secondary constraints.