NRL

NRL calculates nucleosome repeat length (NRL) across genomic regions using phasograms from NucTools to analyze nucleosome positioning and chromatin boundaries influenced by the CCCTC-binding factor (CTCF).

Key Features:

• Integration with NucTools: Uses phasograms computed by NucTools as the input basis for NRL calculation and nucleosome positioning analysis.
• Phasogram-based NRL calculation: Performs bulk NRL calculations across multiple genomic loci using phasogram data.
• Asymmetric NDR analysis: Analyzes nucleosome-depleted regions (NDRs) positioned asymmetrically around CTCF motifs, typically more than 40 nucleotides upstream.
• CTCF and cohesin correlation analysis: Quantifies correlations between CTCF and cohesin binding strength and changes in NRL and nucleosome array symmetry.
• Chromatin remodeler assessment: Evaluates contributions of chromatin remodelers such as Snf2h and Chd4 to NRL changes and nucleosome arrangement.
• Differentiation tracking: Tracks preserved and lost CTCF sites and associated nucleosome rearrangements during cellular differentiation.
• TAD and motif configuration analysis: Analyzes CTCF-associated chromatin boundaries and topologically associated domains (TADs), including inward-oriented CTCF motif configurations.

Scientific Applications:

• CTCF-mediated chromatin organization: Investigating CTCF roles in three-dimensional DNA looping and one-dimensional boundary setting.
• NRL variation near CTCF sites: Studying regions with decreased NRL near CTCF sites to understand chromatin state transitions.
• Chromatin remodeler function studies: Assessing how remodelers like Snf2h and Chd4 modify nucleosome arrays and NRL.
• Developmental chromatin dynamics: Analyzing genome organization and CTCF-associated boundary effects in mouse embryonic stem cells, affecting up to 10% of the genome.
• TAD boundary characterization: Characterizing topologically associated chromatin domains (TADs) with inward-oriented CTCF motifs that influence boundary formation.

Methodology:

Uses phasograms generated by NucTools; analyzes asymmetric NDRs around CTCF motifs (typically >40 nt upstream); quantifies correlations between CTCF/cohesin binding strength and NRL and nucleosome array symmetry; assesses contributions of Snf2h and Chd4; tracks preserved versus lost CTCF sites and associated nucleosome rearrangements during differentiation.