SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial...

Area of Science:

• Genomics
• Molecular Biology
• Cell Biology

Background:

• Cell-type-specific gene expression is crucial for cellular function.
• Understanding DNA packaging's role in gene regulation requires advanced interaction mapping techniques.

Purpose of the Study:

• To present a detailed protocol for the Split-Pool Recognition of Interactions by Tag Extension (SPRITE) method.
• To enable researchers to map higher-order DNA interactions within the nucleus and study their influence on gene regulation.

Main Methods:

• SPRITE involves cross-linking interacting DNA, RNA, and protein molecules.
• Iterative split-and-pool barcoding is used to tag spatially proximal DNA molecules.
• Sequencing and computational analysis of barcoded DNA fragments reconstructs interaction networks.

Main Results:

• SPRITE accurately maps pairwise DNA interactions and higher-order spatial contacts.
• The method can capture interactions among thousands of simultaneously interacting molecules.
• A detailed experimental protocol and an automated computational pipeline are provided.

Conclusions:

• SPRITE is a powerful tool for investigating the relationship between nuclear architecture and gene regulation.
• The provided protocol and pipeline facilitate the application of SPRITE in diverse research settings.
• This method advances our understanding of how DNA packaging influences cell-specific gene expression.