SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• Current chromatin accessibility studies require purified nuclei and enzymatic treatments, limiting in vivo analysis.
• Existing methods face challenges in profiling native chromatin dynamics and heterogeneity.

Purpose of the Study:

• Introduce a novel nanopore sequencing technique, SMAdd-seq, for direct in vivo chromatin accessibility profiling.
• Develop a computational tool (NEMO) to analyze sequencing data and map chromatin structure.
• Assess the method's performance on both purified nuclei and intact cells.

Main Methods:

• Small-molecule adduct sequencing (SMAdd-seq) using angelicin to label accessible DNA in intact cells or nuclei.
• Nanopore sequencing to detect angelicin-modified DNA via distinct current signals.
• Development and application of a neural network model (NEMO) for modification calling and chromatin analysis.

Main Results:

• SMAdd-seq successfully detected angelicin modifications in DNA using nanopore signals.
• NEMO accurately identified nucleosome occupancy patterns at transcription start sites.
• Observed heterogeneity in chromatin structure at single-molecule and bulk levels.

Conclusions:

• SMAdd-seq enables direct in vivo chromatin labeling and profiling of DNA accessibility.
• The method accurately measures chromatin structure, dynamics, and heterogeneity.
• SMAdd-seq offers a promising approach for studying native chromatin organization in various biological contexts.