Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues.

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• Accessible chromatin is crucial for gene expression and chromatin structure.
• Existing methods for profiling accessible chromatin are complex, requiring optimization and extra steps.
• There is a need for a streamlined and versatile method for accessible chromatin analysis.

Purpose of the Study:

• To develop an improved accessible chromatin profiling method that eliminates optimization.
• To enhance the signal-to-noise ratio and robustness of accessible chromatin assays.
• To enable direct library preparation from various sample types, including challenging FFPE tissues.

Main Methods:

• Developed Universal NicE-seq (UniNicE-seq) incorporating 5-methyldeoxycytidine triphosphate labeling and on-bead library preparation.
• Applied UniNicE-seq to diverse samples: cell lines, mouse T cells, mouse kidney, and human frozen tissue sections.
• Demonstrated a one-tube UniNicE-seq protocol for FFPE tissue sections, bypassing sonication and DNA purification.

Main Results:

• UniNicE-seq significantly improved the signal-to-noise ratio compared to standard methods.
• The method demonstrated effectiveness across various mammalian cell and tissue types.
• Direct NGS library preparation from FFPE tissues was achieved without prior DNA purification or sonication.

Conclusions:

• UniNicE-seq offers a robust, optimized, and versatile approach for accessible chromatin profiling.
• This method facilitates high-resolution genomic studies across a wide range of sample types.
• UniNicE-seq simplifies workflows, saving time and resources in chromatin accessibility analysis.