ISDH-seq: a robust methodology for profiling and characterization of open chromatin

Area of Science:

• Genomics
• Epigenetics
• Plant Biology

Background:

• Profiling open chromatin sites (OCSs) is crucial for understanding DNA regulation.
• Existing methods for OCS detection show variability, necessitating orthogonal approaches, especially in plants.

Purpose of the Study:

• To develop and validate an in situ DNase I hypersensitivity sequencing (ISDH-seq) method for efficient open chromatin characterization.
• To compare ISDH-seq with existing DNase-seq and ATAC-seq methods in rice.

Main Methods:

• Development of in situ DNase I hypersensitivity sequencing (ISDH-seq).
• Application of ISDH-seq to rice tissues, processing 50-200K nuclei.
• Comparative analysis with DNase-seq and ATAC-seq data from the same tissue batch.

Main Results:

• ISDH-seq identified 72% and 120% more OCSs than DNase-seq and ATAC-seq, respectively.
• ISDH-specific OCSs showed distinct epigenetic features: hypomethylation, association with H3K27me3, and spatial chromatin interactions.
• Genes linked to H3K27me3-enriched ISDH-specific OCSs displayed stress- and tissue-dependent expression and evolutionary conservation.

Conclusions:

• ISDH-seq effectively expands the identification of regulatory landscapes in plant genomes.
• The method complements existing techniques and offers insights into gene regulation, evolutionary conservation, and agronomic traits.
• ISDH-seq is adaptable for non-plant systems.