O-SNAP: A comprehensive pipeline for spatial profiling of chromatin architecture

Area of Science:

• Cellular and Molecular Biology
• Genomics and Epigenetics
• Microscopy and Imaging Techniques

Background:

• Understanding nuclear architecture and chromatin organization is crucial for deciphering cellular functions and disease mechanisms.
• Single-molecule localization microscopy (SMLM) provides high-resolution insights into nanoscale nuclear structures.
• Automated and quantitative analysis of SMLM data is needed to extract meaningful biological information.

Purpose of the Study:

• To introduce O-SNAP (Objective Single-Molecule Nuclear Architecture Profiler), a comprehensive computational pipeline.
• To enable automated extraction, comparison, and classification of nuclear features from SMLM data.
• To provide a robust tool for analyzing nanoscale chromatin organization and histone mark distributions.

Main Methods:

• Development of a pipeline for automated feature extraction from SMLM data.
• Quantification of 144 biologically grounded spatial features related to chromatin organization.
• Implementation of modules for pairwise comparison (volcano plots), feature enrichment analysis, feature selection, cell state classification, and pseudotime trajectory inference.

Main Results:

• O-SNAP successfully quantifies nanoscale chromatin organization and histone mark distributions.
• The pipeline demonstrated its capability in diverse biological contexts, including cell reprogramming and disease models.
• Subtle changes in nanoscale chromatin organization were detected across various biological transitions.

Conclusions:

• O-SNAP offers a powerful and versatile platform for quantitative analysis of nuclear architecture using SMLM.
• The tool facilitates the discovery of novel insights into chromatin dynamics during biological processes.
• O-SNAP is applicable to a wide range of research areas investigating nuclear organization and cell fate.