Single-molecule views of chromatin accessibility and structure during photomorphogenesis

Abstract

The dynamic organization of chromatin governs gene expression by regulating DNA accessibility. In plants, light not only initiates photomorphogenesis but also reshapes higher-order chromatin architecture. However, the limited resolution of current techniques impedes investigation of chromatin dynamics at the single-molecule level. Here, we applied Fiber-seq, a long-read, single-molecule chromatin profiling method, to construct near-nucleotide resolution maps of chromatin accessibility, nucleosome positioning, and cytosine methylation in Arabidopsis thaliana and maize. We observed that light exposure during photomorphogenesis led to significant, locus-specific changes in chromatin accessibility—both increases and decreases—especially in genes related to photosynthesis, hormone signaling, and development. Analysis of chromatin accessibility changes in cop1-6 , pifq , and hy5 hyh mutants revealed that classical light signaling pathways regulate chromatin accessibility. Additionally, using high-fidelity long-read sequencing, we profiled DNA methylation in previously inaccessible repetitive regions such as 5S rRNA gene clusters and CEN180 satellite repeats. These heterochromatic loci exhibited distinct light-dependent changes in chromatin accessibility that were undetectable using prior methods. In maize, we demonstrated that Fiber-seq identifies a broader range of biologically relevant open chromatin regions, enabling both high-accuracy de novo genome assembly and the detection of fine-scale structural variants. Collectively, Fiber-seq offers an integrated view of chromatin states across regulatory and repetitive elements, providing critical insights into how environmental signals reshape plant epigenomes.