Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue

Area of Science:

• Epigenetics
• Genomics
• Molecular Biology

Background:

• Spatial epigenetic mapping is crucial for understanding gene regulation within local tissue environments.
• Existing methods may require prior knowledge of specific markers, limiting unbiased exploration.
• High-resolution spatial profiling is needed to capture cellular functions dependent on tissue context.

Purpose of the Study:

• To provide a comprehensive protocol for two novel spatial epigenomic profiling methods: spatial-CUT&Tag and spatial-ATAC-sequencing.
• To enable genome-wide, unbiased epigenetic profiling at a pixel-by-pixel level with single-base resolution.
• To facilitate the adaptation of these techniques for diverse species and tissues.

Main Methods:

• Development of in-tissue Tn5 transposition for genomic locus recognition.
• Integration of microfluidic deterministic barcoding for spatial address coding.
• Established protocols for sample preparation, library construction, sequencing, and data analysis.

Main Results:

• Demonstrated feasibility of spatial-CUT&Tag for histone modification profiling.
• Showcased spatial-ATAC-sequencing for chromatin accessibility mapping.
• Achieved 10 μm pixel size resolution and single-base resolution for epigenetic landscapes.
• Provided custom analysis pipelines for data interpretation.

Conclusions:

• Spatial epigenomic profiling methods like spatial-CUT&Tag and spatial-ATAC-sequencing offer powerful tools for studying tissue-specific epigenetic regulation.
• These methods are adaptable across species and do not require prior marker knowledge.
• The protocol is efficient, completable in 2-3 days for four samples, and accessible via GitHub.