# Functional Characterization of Accessible Chromatin in Common Wheat

## TL;DR

This study explores how chromatin accessibility and DNA methylation influence gene expression in wheat, revealing key regulatory elements involved in tissue development and agronomic traits.

## Contribution

The study identifies chromatin openness and CHH methylation as regulators of gene expression and homoeolog bias in wheat.

## Key findings

- Differential chromatin openness between seedling and spikelet stages regulates gene expression and tissue development.
- CHH methylation affects transcription factor binding and target gene expression.
- Sequence variations in MNase hypersensitive sites influence key agronomic traits in wheat.

## Abstract

Eukaryotic gene transcription is fine-tuned by precise spatiotemporal interactions between cis-regulatory elements (CREs) and trans-acting factors. However, how CREs individually or coordinated with epigenetic marks function in regulating homoeolog bias expression is still largely unknown in wheat. In this study, through comprehensively characterizing open chromatin coupled with DNA methylation in the seedling and spikelet of common wheat, we observed that differential chromatin openness occurred between the seedling and spikelet, which plays important roles in tissue development through regulating the expression of related genes or through the transcription factor (TF)-centered regulatory network. Moreover, we found that CHH methylation may act as a key determinant affecting the differential binding of TFs, thereby resulting in differential expression of target genes. In addition, we found that sequence variations in MNase hypersensitive sites (MHSs) result in the differential expression of key genes responsible for important agronomic traits. Thus, our study provides new insights into the roles of CREs in regulating tissue or homoeolog bias expression, and controlling important agronomic traits in common wheat. It also provides potential CREs for genetic and epigenetic manipulation toward improving desirable traits for wheat molecule breeding.