NXSensor

NXSensor predicts nucleosome-free regions in DNA by identifying nucleosome exclusion sequences and quantifying chromatin accessibility to inform analyses of chromatin structure and gene regulation.

Key Features:

• Nucleosome Exclusion Sequence Identification: Identifies DNA sequences empirically or theoretically associated with exclusion of nucleosomes, incorporating DNA bending and flexibility factors.
• Evaluation of Length and Spacing: Assesses the length and spacing of exclusion sequences to evaluate their potential impact on chromatin accessibility.
• Accessibility Score Calculation: Computes an accessibility score that quantifies the proportion of base pairs likely to be nucleosome-free within specified genomic regions.

Scientific Applications:

• Chromatin accessibility near TSSs: Assesses chromatin openness near transcription start sites (TSSs) and promoters to inform studies of transcriptional regulation.
• Comparative promoter analysis (HK vs TS genes): Enables comparison of promoter regions, revealing that housekeeping (HK) genes exhibit higher openness near TSSs than tissue-specific (TS) genes.
• Epigenetics and chromatin remodeling studies: Supports investigations of gene regulation, epigenetics, and chromatin remodeling by predicting nucleosome exclusion sequences and quantifying accessibility.

Methodology:

Analyzes DNA sequences using empirical and theoretical data on DNA bending and flexibility to evaluate factors affecting nucleosome positioning and stability.