NucleoATAC

NucleoATAC infers nucleosome positions and quantitative occupancy from ATAC-seq data to map chromatin organization and nucleosome rotational and translational positioning at base-pair resolution.

Key Features:

• High-Resolution Mapping: Utilizes a two-dimensional "fingerprint" derived from ATAC-seq fragment lengths and positions to identify nucleosome rotational and translational positions at up to base-pair resolution in species including Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human cells.
• Quantitative Analysis: Provides quantitative measures of nucleosome occupancy to assess chromatin dynamics and impacts on gene regulation.
• Chromatin Biology Analyses: Enables analysis of sequence features influencing nucleosome positioning; investigation of promoter chromatin architecture across species; detection of transient changes in nucleosome occupancy and positioning during dynamic cellular responses; and integration of nucleosome occupancy analysis with transcription factor binding.

Scientific Applications:

• Nucleosome positioning and gene regulation: Maps nucleosome locations to study how nucleosome positioning affects gene regulation using ATAC-seq data.
• Comparative chromatin architecture: Performs comparative analyses of chromatin architecture across Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human cells.
• Transcription factor interplay: Examines the interplay between nucleosomes and transcription factors by integrating nucleosome occupancy with transcription factor binding data.
• Chromatin dynamics: Detects transient changes in nucleosome occupancy and positioning during dynamic cellular responses.

Methodology:

Analyzes ATAC-seq fragment lengths and genomic positions to extract a two-dimensional "fingerprint" of nucleosome-associated patterns, which is interpreted to infer nucleosome rotational and translational positions and to quantify nucleosome occupancy.