Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag

Area of Science:

• Epigenetics
• Molecular Biology
• Plant Science

Background:

• Cleavage under targets and tagmentation (CUT&Tag) is an epigenomic analysis technique.
• Previous applications focused on cultured cell lines, yielding high-resolution, low-noise data.
• CUT&Tag is suitable for small plant samples like ovules, anthers, and fibers.

Purpose of the Study:

• To present a step-by-step CUT&Tag protocol optimized for plant cells using isolated nuclei.
• To quantify nuclei input for CUT&Tag reactions in plants.
• To compare the efficiency of CUT&Tag with ChIP-seq in cotton leaves.

Main Methods:

• Development of a CUT&Tag protocol utilizing intact, isolated plant nuclei.
• Quantification of nuclei for CUT&Tag reactions.
• Bioinformatic analysis workflow for CUT&Tag data.
• Comparative analysis with chromatin immunoprecipitation with sequencing (ChIP-seq) in cotton.

Main Results:

• The CUT&Tag protocol was successfully adapted for plant cells.
• Quantification of nuclei input was established for the protocol.
• CUT&Tag demonstrated faster performance than ChIP-seq.
• CUT&Tag yielded higher resolution and lower background signals compared to ChIP-seq.

Conclusions:

• A refined CUT&Tag protocol is now available for plant epigenomic studies.
• The protocol is effective using isolated intact plant nuclei.
• CUT&Tag provides an advantageous alternative to ChIP-seq for plant epigenomic profiling.