scNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling...

Area of Science:

• Epigenetics and Genomics
• Single-cell analysis
• Molecular biology

Background:

• Chromatin modifications are crucial epigenetic marks regulating genome function.
• Profiling chromatin modifications in repetitive and complex genomic regions at single-cell resolution remains challenging.
• Existing methods lack efficiency and accuracy for these difficult genomic areas.

Purpose of the Study:

• To develop a streamlined, single-cell method for genome-wide chromatin modification profiling.
• To adapt Cleavage Under Targets and Tagmentation (CUT&Tag) for nanopore sequencing.
• To enable accurate profiling of histone marks and transcription factor occupancy in complex and repetitive genomic regions.

Main Methods:

• Adaptation of CUT&Tag chemistry for nanopore sequencing.
• Development of scNanoSeq-CUT&Tag for single-cell resolution.
• Application to human and mouse genomes for profiling repetitive elements.

Main Results:

• scNanoSeq-CUT&Tag accurately profiles histone marks and transcription factor occupancy at single-cell resolution.
• The method distinguishes between different cell types.
• Allele-specific chromatin modifications and co-occupancy patterns are efficiently mapped.
• Accurate detection of chromatin modifications in individual copies of repetitive elements is achieved.

Conclusions:

• scNanoSeq-CUT&Tag is a valuable single-cell tool for chromatin modification profiling.
• The method excels in analyzing complex genomic regions and repetitive elements.
• Enables efficient profiling of histone marks and transcription factor occupancies in previously challenging areas.